[med-svn] [cytoscape] 05/07: Update upstream source from tag 'upstream/3.1.0'
Andreas Tille
tille at debian.org
Sun Dec 3 18:14:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cytoscape.
commit ac2a26fbb9fb3e19638259292fef03d570a252c0
Merge: 906c42b 83cb326
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 19:09:26 2017 +0100
Update upstream source from tag 'upstream/3.1.0'
Update to upstream version '3.1.0'
with Debian dir d531401dd3359d998ee782f22c091d4c82b122b8
README.txt | 128 +
acceptance-testing/README | 4 +
acceptance-testing/pom.xml | 33 +
.../java/cytoscape/acceptance/FirstGUITest.java | 67 +
application/pom.xml | 465 +
application/src/main/java/cytoscape/CyEdge.java | 166 +
application/src/main/java/cytoscape/CyMain.java | 489 +
application/src/main/java/cytoscape/CyNetwork.java | 312 +
.../src/main/java/cytoscape/CyNetworkAdapter.java | 59 +
.../src/main/java/cytoscape/CyNetworkData.java | 45 +
.../src/main/java/cytoscape/CyNetworkEvent.java | 108 +
.../src/main/java/cytoscape/CyNetworkListener.java | 57 +
.../main/java/cytoscape/CyNetworkTitleChange.java | 32 +
application/src/main/java/cytoscape/CyNode.java | 305 +
.../src/main/java/cytoscape/CyStartupListener.java | 62 +
application/src/main/java/cytoscape/Cytoscape.java | 2023 +
.../src/main/java/cytoscape/CytoscapeInit.java | 680 +
.../cytoscape/CytoscapeModifiedNetworkManager.java | 138 +
.../src/main/java/cytoscape/CytoscapeVersion.java | 100 +
.../src/main/java/cytoscape/JavaVersion.java | 121 +
.../cytoscape/actions/AlignHorizontalAction.java | 98 +
.../cytoscape/actions/AlignVerticalAction.java | 99 +
.../actions/AlphabeticalSelectionAction.java | 143 +
.../cytoscape/actions/AnimatedLayoutAction.java | 169 +
.../java/cytoscape/actions/ApplyLayoutAction.java | 91 +
.../cytoscape/actions/ApplyVisualStyleAction.java | 71 +
.../main/java/cytoscape/actions/ArrangeAction.java | 127 +
.../cytoscape/actions/BackgroundColorAction.java | 119 +
.../cytoscape/actions/BendSelectedEdgesAction.java | 95 +
.../java/cytoscape/actions/BirdsEyeViewAction.java | 119 +
.../java/cytoscape/actions/BookmarkAction.java | 92 +
.../cytoscape/actions/CheckBoxFileChooser.java | 102 +
.../actions/CloneGraphInNewWindowAction.java | 139 +
.../cytoscape/actions/CreateNetworkViewAction.java | 196 +
.../java/cytoscape/actions/CytoPanelAction.java | 122 +
.../cytoscape/actions/DeSelectAllEdgesAction.java | 86 +
.../cytoscape/actions/DeSelectAllNodesAction.java | 86 +
.../main/java/cytoscape/actions/DeleteAction.java | 191 +
.../main/java/cytoscape/actions/DeleteEdit.java | 93 +
.../java/cytoscape/actions/DeselectAllAction.java | 85 +
.../cytoscape/actions/DestroyNetworkAction.java | 98 +
.../actions/DestroyNetworkViewAction.java | 101 +
.../cytoscape/actions/EdgeManipulationAction.java | 122 +
.../main/java/cytoscape/actions/ExitAction.java | 73 +
.../java/cytoscape/actions/ExpFileChooser.java | 113 +
.../main/java/cytoscape/actions/ExportAction.java | 100 +
.../java/cytoscape/actions/ExportAsGMLAction.java | 266 +
.../cytoscape/actions/ExportAsGraphicsAction.java | 277 +
.../actions/ExportAsInteractionsAction.java | 227 +
.../cytoscape/actions/ExportAsXGMMLAction.java | 286 +
.../actions/ExportEdgeAttributesAction.java | 68 +
.../actions/ExportNetworksAsNNFAction.java | 283 +
.../actions/ExportNodeAttributesAction.java | 68 +
.../java/cytoscape/actions/ExportVizmapAction.java | 156 +
.../java/cytoscape/actions/FitContentAction.java | 83 +
.../src/main/java/cytoscape/actions/GinyUtils.java | 383 +
.../actions/GraphObjectSelectionAction.java | 74 +
.../java/cytoscape/actions/HelpAboutAction.java | 113 +
.../actions/HelpContactHelpDeskAction.java | 69 +
.../java/cytoscape/actions/HelpContentsAction.java | 72 +
.../java/cytoscape/actions/HideSelectedAction.java | 104 +
.../cytoscape/actions/HideSelectedEdgesAction.java | 71 +
.../cytoscape/actions/HideSelectedNodesAction.java | 82 +
.../cytoscape/actions/HideSelectedNodesEdit.java | 91 +
.../actions/ImportEdgeAttributesAction.java | 105 +
.../actions/ImportExpressionMatrixAction.java | 194 +
.../cytoscape/actions/ImportGraphFileAction.java | 176 +
.../actions/ImportNodeAttributesAction.java | 197 +
.../java/cytoscape/actions/ImportVizmapAction.java | 149 +
.../actions/InvertSelectedEdgesAction.java | 90 +
.../actions/InvertSelectedNodesAction.java | 91 +
.../actions/ListFromFileSelectionAction.java | 147 +
.../java/cytoscape/actions/LoadNetworkTask.java | 366 +
.../main/java/cytoscape/actions/LoggerAction.java | 23 +
.../java/cytoscape/actions/MemoryUsageAction.java | 70 +
.../java/cytoscape/actions/NewNetworkAction.java | 43 +
.../java/cytoscape/actions/NewSessionAction.java | 88 +
.../actions/NewWindowSelectedNodesEdgesAction.java | 144 +
.../actions/NewWindowSelectedNodesOnlyAction.java | 153 +
.../java/cytoscape/actions/OpenSessionAction.java | 269 +
.../cytoscape/actions/PluginInstallAction.java | 93 +
.../cytoscape/actions/PluginManagerAction.java | 194 +
.../java/cytoscape/actions/PluginUpdateAction.java | 85 +
.../java/cytoscape/actions/PreferenceAction.java | 87 +
.../main/java/cytoscape/actions/PrintAction.java | 125 +
.../java/cytoscape/actions/ProxyServerAction.java | 86 +
.../actions/RotateSelectedNodesAction.java | 82 +
.../java/cytoscape/actions/SaveSessionAction.java | 217 +
.../cytoscape/actions/SaveSessionAsAction.java | 123 +
.../actions/SelectAdjacentEdgesAction.java | 111 +
.../java/cytoscape/actions/SelectAllAction.java | 90 +
.../cytoscape/actions/SelectAllEdgesAction.java | 85 +
.../cytoscape/actions/SelectAllNodesAction.java | 84 +
.../actions/SelectConnectedNodesAction.java | 92 +
.../actions/SelectFirstNeighborsAction.java | 98 +
.../cytoscape/actions/SelectionModeAction.java | 141 +
.../actions/SetVisualPropertiesAction.java | 114 +
.../main/java/cytoscape/actions/ShowAllAction.java | 77 +
.../actions/ShowCustomGraphicsManagerAction.java | 74 +
.../actions/ShowGraphicsDetailsAction.java | 119 +
.../actions/StraightenSelectedEdgesAction.java | 95 +
.../actions/ToggleVisualMapperAction.java | 97 +
.../cytoscape/actions/UnHideSelectedAction.java | 81 +
.../actions/UnHideSelectedEdgesAction.java | 84 +
.../actions/UnHideSelectedNodesAction.java | 85 +
.../actions/WebServiceNetworkImportAction.java | 25 +
.../main/java/cytoscape/actions/ZoomAction.java | 88 +
.../java/cytoscape/actions/ZoomSelectedAction.java | 88 +
.../src/main/java/cytoscape/actions/package.html | 14 +
.../cytoscape/command/AbstractCommandHandler.java | 382 +
.../java/cytoscape/command/CyCommandException.java | 106 +
.../java/cytoscape/command/CyCommandHandler.java | 199 +
.../java/cytoscape/command/CyCommandManager.java | 281 +
.../java/cytoscape/command/CyCommandNamespace.java | 63 +
.../java/cytoscape/command/CyCommandResult.java | 226 +
.../java/cytoscape/data/AttribTopoGraphNode.java | 68 +
.../main/java/cytoscape/data/AttributeFilter.java | 63 +
.../java/cytoscape/data/AttributeSaverDialog.java | 481 +
.../java/cytoscape/data/AttributeValueVisitor.java | 64 +
.../src/main/java/cytoscape/data/CyAttributes.java | 797 +
.../main/java/cytoscape/data/CyAttributesImpl.java | 1362 +
.../java/cytoscape/data/CyAttributesUtils.java | 880 +
.../java/cytoscape/data/CyNetworkUtilities.java | 245 +
.../main/java/cytoscape/data/ExpressionData.java | 1102 +
.../main/java/cytoscape/data/ImportHandler.java | 531 +
.../src/main/java/cytoscape/data/Interaction.java | 155 +
.../src/main/java/cytoscape/data/NetworkData.java | 834 +
.../src/main/java/cytoscape/data/SelectEvent.java | 211 +
.../java/cytoscape/data/SelectEventListener.java | 52 +
.../src/main/java/cytoscape/data/SelectFilter.java | 489 +
.../src/main/java/cytoscape/data/Semantics.java | 513 +
.../java/cytoscape/data/annotation/Annotation.java | 365 +
.../data/annotation/AnnotationDescription.java | 146 +
.../data/annotation/FlattenIntVectors.java | 95 +
.../java/cytoscape/data/annotation/Ontology.java | 296 +
.../data/annotation/OntologyDescription.java | 101 +
.../cytoscape/data/annotation/OntologyTerm.java | 377 +
.../java/cytoscape/data/annotation/package.html | 12 +
.../readers/AnnotationFlatFileReader.java | 270 +
.../annotation/readers/AnnotationXmlReader.java | 142 +
.../annotation/readers/OntologyFlatFileReader.java | 242 +
.../data/annotation/readers/OntologyXmlReader.java | 143 +
.../cytoscape/data/annotation/readers/package.html | 12 +
.../java/cytoscape/data/attr/CountedIterator.java | 51 +
.../java/cytoscape/data/attr/MultiHashMap.java | 226 +
.../data/attr/MultiHashMapDefinition.java | 172 +
.../data/attr/MultiHashMapDefinitionListener.java | 58 +
.../cytoscape/data/attr/MultiHashMapListener.java | 76 +
.../attr/util/ExtensibleMultiHashMapModel.java | 49 +
.../data/attr/util/MultiHashMapFactory.java | 59 +
.../data/attr/util/MultiHashMapHelpers.java | 333 +
.../data/attr/util/MultiHashMapModel.java | 1029 +
.../main/java/cytoscape/data/mRNAMeasurement.java | 122 +
.../cytoscape/data/ontology/DBCrossReferences.java | 113 +
.../java/cytoscape/data/ontology/DBReference.java | 158 +
.../main/java/cytoscape/data/ontology/GOTerm.java | 120 +
.../java/cytoscape/data/ontology/GeneOntology.java | 139 +
.../java/cytoscape/data/ontology/Ontology.java | 434 +
.../cytoscape/data/ontology/OntologyFactory.java | 113 +
.../java/cytoscape/data/ontology/OntologyTerm.java | 206 +
.../main/java/cytoscape/data/ontology/Triple.java | 196 +
.../ontology/readers/DBCrossReferenceReader.java | 183 +
.../data/ontology/readers/DBXrefKeywords.java | 61 +
.../data/ontology/readers/OBOFlatFileReader.java | 475 +
.../data/ontology/readers/OBOHeaderTags.java | 58 +
.../cytoscape/data/ontology/readers/OBOTags.java | 151 +
.../data/ontology/readers/OntologyReader.java | 75 +
.../src/main/java/cytoscape/data/package.html | 13 +
.../data/readers/AbstractGraphReader.java | 147 +
.../cytoscape/data/readers/BookmarkReader.java | 112 +
.../cytoscape/data/readers/CyAttributesReader.java | 404 +
.../data/readers/CytoscapeSessionReader.java | 1256 +
.../cytoscape/data/readers/EqnAttrTracker.java | 198 +
.../java/cytoscape/data/readers/GMLException.java | 54 +
.../main/java/cytoscape/data/readers/GMLNode.java | 225 +
.../java/cytoscape/data/readers/GMLParser.java | 323 +
.../java/cytoscape/data/readers/GMLReader.java | 1244 +
.../main/java/cytoscape/data/readers/GMLTag.java | 91 +
.../main/java/cytoscape/data/readers/GMLTree.java | 543 +
.../java/cytoscape/data/readers/GMLWriter.java | 615 +
.../java/cytoscape/data/readers/GraphReader.java | 91 +
.../cytoscape/data/readers/InteractionsReader.java | 362 +
.../main/java/cytoscape/data/readers/KeyValue.java | 60 +
.../cytoscape/data/readers/MetadataEntries.java | 69 +
.../cytoscape/data/readers/MetadataParser.java | 212 +
.../java/cytoscape/data/readers/NNFParser.java | 150 +
.../java/cytoscape/data/readers/NNFReader.java | 149 +
.../data/readers/NestedNetworkReader.java | 51 +
.../cytoscape/data/readers/TextFileReader.java | 135 +
.../cytoscape/data/readers/TextHttpReader.java | 173 +
.../java/cytoscape/data/readers/TextJarReader.java | 144 +
.../cytoscape/data/readers/VisualStyleBuilder.java | 314 +
.../cytoscape/data/readers/XGMMLException.java | 52 +
.../java/cytoscape/data/readers/XGMMLParser.java | 1755 +
.../java/cytoscape/data/readers/XGMMLReader.java | 879 +
.../main/java/cytoscape/data/readers/package.html | 12 +
.../java/cytoscape/data/servers/BioDataServer.java | 883 +
.../data/servers/BioDataServerInterface.java | 219 +
.../cytoscape/data/servers/BioDataServerRmi.java | 366 +
.../cytoscape/data/servers/OntologyServer.java | 221 +
.../main/java/cytoscape/data/servers/clear.java | 88 +
.../cytoscape/data/servers/getCanonicalName.java | 87 +
.../java/cytoscape/data/servers/getCommonName.java | 87 +
.../cytoscape/data/servers/loadAnnotation.java | 104 +
.../data/servers/loadAnnotationFromFlatFiles.java | 127 +
.../java/cytoscape/data/servers/loadThesaurus.java | 99 +
.../main/java/cytoscape/data/servers/package.html | 13 +
.../main/java/cytoscape/data/servers/status.java | 86 +
.../java/cytoscape/data/synonyms/AliasType.java | 50 +
.../main/java/cytoscape/data/synonyms/Aliases.java | 277 +
.../java/cytoscape/data/synonyms/Thesaurus.java | 306 +
.../main/java/cytoscape/data/synonyms/package.html | 13 +
.../synonyms/readers/ThesaurusFlatFileReader.java | 222 +
.../cytoscape/data/synonyms/readers/package.html | 12 +
.../data/webservice/AttributeImportQuery.java | 28 +
.../data/webservice/CyWebServiceEvent.java | 91 +
.../data/webservice/CyWebServiceEventListener.java | 54 +
.../data/webservice/CyWebServiceEventSupport.java | 84 +
.../data/webservice/CyWebServiceException.java | 69 +
.../data/webservice/DatabaseSearchResult.java | 27 +
.../webservice/NetworkImportWebServiceClient.java | 51 +
.../data/webservice/WebServiceClient.java | 155 +
.../data/webservice/WebServiceClientImpl.java | 270 +
.../webservice/WebServiceClientImplWithGUI.java | 125 +
.../data/webservice/WebServiceClientManager.java | 148 +
.../webservice/ui/UnifiedNetworkImportDialog.java | 776 +
.../data/webservice/ui/WSImportResultDialog.java | 171 +
.../data/webservice/ui/WebServiceClientGUI.java | 106 +
.../data/webservice/ui/WebServiceContextMenu.java | 138 +
.../ui/WebServiceContextMenuListener.java | 67 +
.../data/webservice/util/NetworkExpansionMenu.java | 200 +
.../webservice/util/WebServiceThemeInstall.java | 174 +
.../cytoscape/data/writers/CyAttributesWriter.java | 241 +
.../data/writers/CytoscapeSessionWriter.java | 1056 +
.../cytoscape/data/writers/InteractionWriter.java | 160 +
.../java/cytoscape/data/writers/XGMMLWriter.java | 1373 +
.../java/cytoscape/dialogs/ColorScaleTable.java | 170 +
.../dialogs/EdgeAttributesPopupDetails.java | 138 +
.../cytoscape/dialogs/EditNetworkTitleDialog.java | 167 +
.../dialogs/ExportAsGraphicsFileChooser.java | 410 +
.../dialogs/ExportBitmapOptionsDialog.java | 391 +
.../dialogs/ExpressionDataPopupTable.java | 366 +
.../cytoscape/dialogs/GinyEdgeControlDialog.java | 493 +
.../cytoscape/dialogs/GraphObjectSelection.java | 459 +
.../main/java/cytoscape/dialogs/GridBagGroup.java | 116 +
.../java/cytoscape/dialogs/IconPopupButton.java | 328 +
.../dialogs/ImportAttributeMatrixDialog.java | 255 +
.../cytoscape/dialogs/ImportNetworkDialog.java | 657 +
.../java/cytoscape/dialogs/IntegerEntryField.java | 200 +
.../java/cytoscape/dialogs/JointIntegerEntry.java | 255 +
.../java/cytoscape/dialogs/LabelTextPanel.java | 120 +
.../src/main/java/cytoscape/dialogs/MiscGB.java | 247 +
.../cytoscape/dialogs/NetworkMetaDataDialog.java | 267 +
.../dialogs/NetworkMetaDataTableModel.java | 182 +
.../src/main/java/cytoscape/dialogs/NewSlider.java | 308 +
.../cytoscape/dialogs/NewStringPopupDialog.java | 137 +
.../java/cytoscape/dialogs/PhoebeNodeControl.java | 611 +
.../main/java/cytoscape/dialogs/PopupTextArea.java | 138 +
.../cytoscape/dialogs/SetNestedNetworkDialog.java | 222 +
.../java/cytoscape/dialogs/ShrinkExpandGraph.java | 125 +
.../cytoscape/dialogs/ShrinkExpandGraphUI.java | 63 +
.../java/cytoscape/dialogs/VizChooser.java.old | 1014 +
.../cytoscape/dialogs/logger/LoggerDialog.java | 332 +
.../src/main/java/cytoscape/dialogs/package.html | 14 +
.../cytoscape/dialogs/plugins/LicenseDialog.java | 316 +
.../cytoscape/dialogs/plugins/ManagerModel.java | 301 +
.../cytoscape/dialogs/plugins/PluginIndex.java | 128 +
.../dialogs/plugins/PluginManageDialog.java | 1492 +
.../dialogs/plugins/PluginUpdateDialog.java | 447 +
.../cytoscape/dialogs/plugins/PluginUrlDialog.java | 414 +
.../dialogs/plugins/TreeCellRenderer.java | 57 +
.../java/cytoscape/dialogs/plugins/TreeNode.java | 347 +
.../dialogs/preferences/BookmarkDialog.java | 412 +
.../dialogs/preferences/EditBookmarkDialog.java | 267 +
.../dialogs/preferences/PluginsTableModel.java | 420 +
.../dialogs/preferences/PreferenceTableModel.java | 279 +
.../dialogs/preferences/PreferenceValueDialog.java | 219 +
.../dialogs/preferences/PreferencesDialog.java | 568 +
.../dialogs/preferences/ProxyServerDialog.java | 447 +
.../main/java/cytoscape/ding/CyGraphAllLOD.java | 66 +
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.../main/java/cytoscape/ding/DingNetworkView.java | 585 +
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.../cytoscape/giny/CytoscapeFingRootGraph.java | 204 +
.../java/cytoscape/giny/CytoscapeRootGraph.java | 108 +
.../main/java/cytoscape/giny/FingCyNetwork.java | 713 +
.../src/main/java/cytoscape/groups/CyGroup.java | 225 +
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.../main/java/cytoscape/groups/CyGroupImpl.java | 658 +
.../main/java/cytoscape/groups/CyGroupManager.java | 659 +
.../main/java/cytoscape/groups/CyGroupViewer.java | 102 +
.../groups/GroupPropertyChangeListener.java | 70 +
.../src/main/java/cytoscape/init/CyInitParams.java | 165 +
.../main/java/cytoscape/layout/AbstractLayout.java | 399 +
.../java/cytoscape/layout/CyLayoutAlgorithm.java | 212 +
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.../src/main/java/cytoscape/layout/CyLayouts.java | 139 +
.../main/java/cytoscape/layout/LayoutAdapter.java | 215 +
.../java/cytoscape/layout/LayoutAlgorithm.java | 56 +
.../java/cytoscape/layout/LayoutProperties.java | 137 +
.../src/main/java/cytoscape/layout/LayoutTask.java | 131 +
.../src/main/java/cytoscape/layout/Tunable.java | 1322 +
.../java/cytoscape/layout/TunableListener.java | 23 +
.../layout/algorithms/GridNodeLayout.java | 190 +
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.../cytoscape/layout/ui/DynamicLayoutMenu.java | 250 +
.../main/java/cytoscape/layout/ui/LayoutMenu.java | 161 +
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.../cytoscape/layout/ui/LayoutSettingsDialog.java | 324 +
.../java/cytoscape/layout/ui/SettingsAction.java | 62 +
.../java/cytoscape/layout/ui/StaticLayoutMenu.java | 86 +
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.../main/java/cytoscape/logger/CyLogHandler.java | 55 +
.../src/main/java/cytoscape/logger/CyLogger.java | 398 +
.../src/main/java/cytoscape/logger/LogLevel.java | 45 +
application/src/main/java/cytoscape/overview.html | 23 +
application/src/main/java/cytoscape/package.html | 49 +
.../src/main/java/cytoscape/plugin/Category.java | 27 +
.../java/cytoscape/plugin/CytoscapePlugin.java | 225 +
.../java/cytoscape/plugin/DownloadableInfo.java | 568 +
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.../main/java/cytoscape/plugin/Installable.java | 39 +
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.../main/java/cytoscape/util/CytoscapeAction.java | 381 +
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.../cytoscape/util/CytoscapeProgressMonitor.java | 193 +
.../main/java/cytoscape/util/CytoscapeToolBar.java | 169 +
application/src/main/java/cytoscape/util/Exec.java | 303 +
.../src/main/java/cytoscape/util/FileUtil.java | 544 +
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.../main/java/cytoscape/util/GraphSetUtils.java | 528 +
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.../main/java/cytoscape/util/JnlpWriterUtil.java | 385 +
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.../src/main/java/cytoscape/util/MinMaxDouble.java | 110 +
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application/src/main/java/cytoscape/util/Misc.java | 181 +
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.../java/cytoscape/util/ModulePropertiesImpl.java | 277 +
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.../images/versioned-svg/CytoscapeCredits.svg | 3258 +
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application/src/main/resources/vizmap.props | 602 +
application/src/main/resources/xsd/bookmarks.xsd | 38 +
application/src/main/resources/xsd/cysession.xsd | 210 +
application/src/main/resources/xsd/xlinks-2001.xsd | 127 +
application/src/test/java/cytoscape/AllTests.java | 182 +
.../src/test/java/cytoscape/BugGetCyNodeTest.java | 70 +
.../java/cytoscape/BugHideNodeEventFiringTest.java | 111 +
application/src/test/java/cytoscape/BugTest1.java | 102 +
application/src/test/java/cytoscape/CoreSuite.java | 63 +
.../src/test/java/cytoscape/CyNodeTest.java | 143 +
.../src/test/java/cytoscape/CytoscapeTest.java | 288 +
.../test/java/cytoscape/data/CyAttributesTest.java | 440 +
.../java/cytoscape/data/CyAttributesUtilsTest.java | 436 +
.../java/cytoscape/data/CyNetworkEventTest.java | 139 +
.../test/java/cytoscape/data/CyNetworkTest.java | 369 +
.../java/cytoscape/data/ExpressionDataTest.java | 175 +
.../java/cytoscape/data/ImportHandlerTest.java | 374 +
.../test/java/cytoscape/data/InteractionTest.java | 155 +
.../test/java/cytoscape/data/NetworkDataTest.java | 227 +
.../test/java/cytoscape/data/SelectEventTest.java | 169 +
.../test/java/cytoscape/data/SelectFilterTest.java | 473 +
.../annotation/AnnotationAndOntologyFullTest.java | 149 +
.../data/annotation/AnnotationDescriptionTest.java | 129 +
.../cytoscape/data/annotation/AnnotationTest.java | 195 +
.../data/annotation/OntologyTermTest.java | 154 +
.../cytoscape/data/annotation/OntologyTest.java | 256 +
.../test/java/cytoscape/data/annotation/Utils.java | 133 +
.../cytoscape/data/attr/util/MultiHashMapTest.java | 149 +
.../java/cytoscape/data/mRNAMeasurementTest.java | 100 +
.../test/java/cytoscape/data/networkProject.pro | 6 +
.../java/cytoscape/data/ontology/OntologyTest.java | 274 +
.../readers/DBCrossReferenceReaderTest.java | 175 +
.../ontology/readers/OBOFlatFileReaderTest.java | 151 +
.../cytoscape/data/readers/BookmarkReaderTest.java | 98 +
.../data/readers/CyAttributesReaderTest.java | 270 +
.../data/readers/CytoscapeSessionReaderTest.java | 184 +
.../cytoscape/data/readers/FileImporterTest.java | 150 +
.../java/cytoscape/data/readers/GMLReaderTest.java | 189 +
.../data/readers/InteractionsReaderTest.java | 279 +
.../cytoscape/data/readers/MetadataParserTest.java | 99 +
.../java/cytoscape/data/readers/NNFReaderTest.java | 195 +
.../cytoscape/data/readers/TextFileReaderTest.java | 112 +
.../cytoscape/data/readers/TextJarReaderTest.java | 140 +
.../cytoscape/data/readers/XGMMLReaderTest.java | 163 +
.../java/cytoscape/data/readers/degenerate.sif | 9 +
.../cytoscape/data/readers/multiWordProteins.sif | 30 +
.../multiWordProteinsFileTrailingSpaces.sif | 30 +
.../test/java/cytoscape/data/readers/sample.sif | 25 +
.../cytoscape/data/servers/BioDataServerTest.java | 377 +
.../java/cytoscape/data/synonyms/AliasesTest.java | 109 +
.../cytoscape/data/synonyms/ThesaurusTest.java | 263 +
.../readers/ThesaurusFlatFileReaderTest.java | 144 +
.../data/writers/CyAttributesWriterTest.java | 201 +
.../data/writers/CytoscapeSessionWriterTest.java | 70 +
.../data/writers/InteractionWriterTest.java | 160 +
.../cytoscape/data/writers/XGMMLWriterTest.java | 227 +
.../cytoscape/giny/CytoscapeFingRootGraphTest.java | 133 +
.../cytoscape/plugin/DownloadableInfoTest.java | 290 +
.../cytoscape/plugin/PluginFileReaderTest.java | 167 +
.../java/cytoscape/plugin/PluginIndexTest.java | 126 +
.../java/cytoscape/plugin/PluginManagerTest.java | 744 +
.../cytoscape/plugin/PluginPropertiesTest.java | 51 +
.../test/java/cytoscape/plugin/PluginTestXML.java | 84 +
.../java/cytoscape/plugin/PluginTrackerTest.java | 440 +
.../cytoscape/plugin/PluginVersionUtilsTest.java | 72 +
.../src/test/java/cytoscape/sampleProject.pro | 18 +
application/src/test/java/cytoscape/test1.cpr | 10 +
application/src/test/java/cytoscape/test2.cpr | 9 +
.../java/cytoscape/util/BookmarksUtilTest.java | 109 +
.../test/java/cytoscape/util/ColorUtilTest.java | 45 +
.../test/java/cytoscape/util/CyFileFilterTest.java | 312 +
.../src/test/java/cytoscape/util/FileUtilTest.java | 66 +
.../java/cytoscape/util/GMLFileFilterTest.java | 86 +
.../java/cytoscape/util/GraphSetUtilsTest.java | 254 +
.../test/java/cytoscape/util/LinearScalerTest.java | 26 +
.../src/test/java/cytoscape/util/MathUtilTest.java | 24 +
.../src/test/java/cytoscape/util/MinMaxTest.java | 146 +
.../src/test/java/cytoscape/util/MiscTest.java | 264 +
.../util/NestedNetworkImageManagerTest.java | 36 +
.../src/test/java/cytoscape/util/PropUtilTest.java | 147 +
.../test/java/cytoscape/util/RankScalerTest.java | 38 +
.../java/cytoscape/util/SIFFileFilterTest.java | 86 +
.../java/cytoscape/util/ScalerFactoryTest.java | 24 +
.../src/test/java/cytoscape/util/TestUtil.java | 20 +
.../java/cytoscape/util/TopologicalSortTest.java | 187 +
.../java/cytoscape/util/XGMMLFileFilterTest.java | 86 +
.../java/cytoscape/view/CytoscapeViewTest.java | 193 +
.../view/FlagAndSelectionHandlerTest.java | 217 +
.../java/cytoscape/visual/BypassHelperTest.java | 165 +
.../cytoscape/visual/CalculatorPropertiesTest.java | 203 +
.../visual/EdgeAppearanceCalculatorTest.java | 168 +
.../java/cytoscape/visual/LabelPositionTest.java | 147 +
.../visual/NodeAppearanceCalculatorTest.java | 448 +
.../java/cytoscape/visual/NodeAppearanceTest.java | 141 +
.../test/java/cytoscape/visual/NodeShapeTest.java | 46 +
.../test/java/cytoscape/visual/TestEdgeView.java | 246 +
.../src/test/java/cytoscape/visual/TestLabel.java | 191 +
.../java/cytoscape/visual/TestNetworkView.java | 255 +
.../test/java/cytoscape/visual/TestNodeView.java | 558 +
.../cytoscape/visual/VisualMappingManagerTest.java | 174 +
.../visual/VisualPropertyDependencyTest.java | 88 +
.../cytoscape/visual/VizMapPropertiesTest.java | 276 +
.../visual/mappings/BoundaryRangeValuesTest.java | 120 +
.../visual/mappings/FlatInterpolatorTest.java | 127 +
.../LinearNumberToColorInterpolatorTest.java | 126 +
.../LinearNumberToNumberInterpolatorTest.java | 117 +
.../cytoscape/visual/mappings/MappingUtilTest.java | 224 +
.../visual/mappings/PassthroughMappingTest.java | 97 +
.../TestContinuousColorRangeCalculator.java | 210 +
.../continuous/TestContinuousMappingReader.java | 141 +
.../continuous/TestContinuousMappingWriter.java | 104 +
.../discrete/DiscreteMappingReaderTest.java | 169 +
.../discrete/DiscreteMappingWriterTest.java | 184 +
.../testData/NNFData/1000SmallNetworks.nnf | 38139 ++++++++
.../testData/NNFData/100SmallNetworks.nnf | 3728 +
.../resources/testData/NNFData/10LargeNetworks.nnf | 87381 ++++++++++++++++++
.../testData/NNFData/300SmallNetworks.nnf | 6396 ++
.../test/resources/testData/NNFData/5Nested.nnf | 50 +
.../src/test/resources/testData/NNFData/bad1.nnf | 9 +
.../src/test/resources/testData/NNFData/bad2.nnf | 9 +
.../resources/testData/NNFData/calc_network_size | 47 +
.../testData/NNFData/generate_multi_level_networks | 117 +
.../resources/testData/NNFData/generate_networks | 78 +
.../src/test/resources/testData/NNFData/good1.nnf | 9 +
.../src/test/resources/testData/NNFData/good2.nnf | 9 +
.../src/test/resources/testData/NNFData/good3.nnf | 9 +
.../src/test/resources/testData/NNFData/good4.nnf | 18 +
.../src/test/resources/testData/NNFData/good5.nnf | 11 +
.../src/test/resources/testData/NNFData/good6.nnf | 2 +
.../resources/testData/NNFData/intermediate.nnf | 11195 +++
.../src/test/resources/testData/NNFData/large.nnf | 89514 +++++++++++++++++++
.../src/test/resources/testData/NNFData/loop.nnf | 2 +
.../src/test/resources/testData/NNFData/loop1.nnf | 2 +
.../src/test/resources/testData/NNFData/small.nnf | 5560 ++
.../src/test/resources/testData/NNFData/t3.cys | Bin 0 -> 12558 bytes
.../src/test/resources/testData/NNFData/t4.cys | Bin 0 -> 13000 bytes
.../testData/XGMMLWriterTestFile01a.xgmml | 40 +
.../testData/XGMMLWriterTestFile01b.xgmml | 33 +
.../testData/XGMMLWriterTestFile02a.xgmml | 22 +
.../testData/XGMMLWriterTestFile02b.xgmml | 22 +
.../testData/XGMMLWriterTestFile02c.xgmml | 22 +
.../testData/XGMMLWriterTestFile02d.xgmml | 22 +
.../testData/annotation/goslim_generic.obo | 1754 +
.../src/test/resources/testData/broken_t.gml | 1031 +
.../src/test/resources/testData/bug1565.gml | 1639 +
.../src/test/resources/testData/bug_839.sif | 6 +
.../src/test/resources/testData/degenerate.sif | 9 +
.../src/test/resources/testData/directedGraph.sif | 5 +
.../resources/testData/explicitDouble.attribute | 4 +
application/src/test/resources/testData/gal.gml | 303 +
.../src/test/resources/testData/gal1.22x5.mRNA | 23 +
.../resources/testData/gal1.22x5.mRNA_wo_descript | 23 +
.../test/resources/testData/galFiltered.edgeAttrs2 | 354 +
.../test/resources/testData/galFiltered.nodeAttrs1 | 329 +
.../src/test/resources/testData/galFiltered.sif | 362 +
.../src/test/resources/testData/galFiltered2.xgmml | 17902 ++++
.../resources/testData/haloMetabolicPathway.xml | 4740 +
.../resources/testData/humanKeggAndGO/bioproc.anno | 40 +
.../testData/humanKeggAndGO/cellcomp.anno | 40 +
.../test/resources/testData/humanKeggAndGO/go.onto | 13108 +++
.../resources/testData/humanKeggAndGO/human.syno | 17 +
.../resources/testData/humanKeggAndGO/kegg.anno | 40 +
.../resources/testData/humanKeggAndGO/kegg.onto | 196 +
.../testData/humanKeggAndGO/manifest.both | 7 +
.../resources/testData/humanKeggAndGO/molfunc.anno | 40 +
.../testData/implicitStringArray.attribute | 6 +
.../testData/implicitStringArrayEnc.attribute | 6 +
.../testData/metabolicPathwayOntology.xml | 1174 +
.../test/resources/testData/multiWordProteins.sif | 30 +
.../multiWordProteinsFileTrailingSpaces.sif | 30 +
.../src/test/resources/testData/noLabels.gml | 8613 ++
.../src/test/resources/testData/old_vizmap.props | 436 +
.../test/resources/testData/plugins/BadPlugin.jar | Bin 0 -> 1780 bytes
.../test/resources/testData/plugins/GoodPlugin.jar | Bin 0 -> 1858 bytes
.../test/resources/testData/plugins/GoodPlugin.zip | Bin 0 -> 1214 bytes
.../resources/testData/plugins/MCODE_broken.jar | Bin 0 -> 1896 bytes
.../test/resources/testData/plugins/license.txt | 2 +
.../testData/plugins/partial_plugin_file.xml | 45 +
.../resources/testData/plugins/test_plugin.props | 34 +
.../resources/testData/plugins/test_plugin.xml | 390 +
.../testData/plugins/test_plugin_no_themes.xml | 183 +
.../resources/testData/plugins/test_plugins.xsl | 96 +
.../resources/testData/plugins/track_plugins.xml | 430 +
.../testData/plugins/track_plugins_c1.xml | 429 +
.../testData/plugins/track_plugins_c2.xml | 430 +
.../src/test/resources/testData/randomTextFile.txt | 6 +
application/src/test/resources/testData/sample.sif | 25 +
.../src/test/resources/testData/small.edgeAttr | 5 +
.../src/test/resources/testData/small.nodeAttr | 5 +
application/src/test/resources/testData/small.sif | 4 +
.../src/test/resources/testData/small.vizmap.props | 136 +
.../src/test/resources/testData/yeastSmall.txt | 10 +
archetypes/ant-sample-plugin/pom.xml | 36 +
.../ant-sample-plugin/src/main/assembly/src.xml | 14 +
.../ant-sample-plugin/src/main/resources/README | 11 +
.../ant-sample-plugin/src/main/resources/build.xml | 258 +
.../src/main/resources/resources/plugin.props | 26 +
.../src/main/resources/src/example/MyAction.java | 32 +
.../src/main/resources/src/example/MyPlugin.java | 23 +
.../main/resources/tests/example/MyActionTest.java | 17 +
archetypes/pom.xml | 55 +
archetypes/sample-plugin/pom.xml | 88 +
.../src/it/projects/firsttest/test.properties | 4 +
.../src/it/projects/firsttest/verify.bsh | 7 +
.../META-INF/maven/archetype-metadata.xml | 23 +
.../main/resources/META-INF/maven/archetype.xml | 13 +
.../src/main/resources/archetype-resources/pom.xml | 88 +
.../src/main/java/MyAction.java | 34 +
.../src/main/java/MyPlugin.java | 26 +
.../src/main/resources/plugin.props | 26 +
.../src/test/java/MyActionTest.java | 20 +
.../CYTOSCAPE_README | 11 +
.../commons-cli-1.x-cytocape-custom/LICENSE.txt | 202 +
.../commons-cli-1.x-cytocape-custom/NOTICE.txt | 2 +
.../commons-cli-1.x-cytocape-custom/README.txt | 42 +
.../RELEASE-NOTES.txt | 26 +
corelibs/commons-cli-1.x-cytocape-custom/pom.xml | 49 +
.../src/conf/MANIFEST.MF | 11 +
.../commons/cli/AlreadySelectedException.java | 36 +
.../java/org/apache/commons/cli/BasicParser.java | 44 +
.../java/org/apache/commons/cli/CommandLine.java | 295 +
.../org/apache/commons/cli/CommandLineParser.java | 86 +
.../java/org/apache/commons/cli/GnuParser.java | 134 +
.../java/org/apache/commons/cli/HelpFormatter.java | 801 +
.../commons/cli/MissingArgumentException.java | 36 +
.../apache/commons/cli/MissingOptionException.java | 35 +
.../main/java/org/apache/commons/cli/Option.java | 541 +
.../java/org/apache/commons/cli/OptionBuilder.java | 345 +
.../java/org/apache/commons/cli/OptionGroup.java | 144 +
.../org/apache/commons/cli/OptionValidator.java | 86 +
.../main/java/org/apache/commons/cli/Options.java | 266 +
.../org/apache/commons/cli/ParseException.java | 35 +
.../main/java/org/apache/commons/cli/Parser.java | 343 +
.../apache/commons/cli/PatternOptionBuilder.java | 180 +
.../java/org/apache/commons/cli/PosixParser.java | 265 +
.../java/org/apache/commons/cli/TypeHandler.java | 209 +
.../commons/cli/UnrecognizedOptionException.java | 36 +
.../src/main/java/org/apache/commons/cli/Util.java | 63 +
.../commons/cli/avalon/AbstractParserControl.java | 38 +
.../apache/commons/cli/avalon/CLArgsParser.java | 661 +
.../org/apache/commons/cli/avalon/CLOption.java | 158 +
.../commons/cli/avalon/CLOptionDescriptor.java | 208 +
.../java/org/apache/commons/cli/avalon/CLUtil.java | 106 +
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distribution/src/main/sampleData/galFiltered.xls | Bin 0 -> 59392 bytes
.../src/main/sampleData/galFiltered2.xgmml | 17902 ++++
distribution/src/main/sampleData/galFiltered25.cys | Bin 0 -> 168690 bytes
.../src/main/sampleData/galFilteredAnnotated.xgmml | 14663 +++
.../main/sampleData/galFiltered_int_edge_attr.ea | 363 +
.../main/sampleData/galFiltered_list_edge_attr.ea | 15 +
.../src/main/sampleData/galFilteredintAttr.xls | Bin 0 -> 38912 bytes
.../human_interactome_may07_small.tab.gz | Bin 0 -> 535386 bytes
.../src/main/sampleData/sampleStyles.props | 1063 +
.../src/main/sampleData/yeastHighQuality.sif | 6888 ++
javadoc/pom.xml | 177 +
legacy/build.xml | 1122 +
legacy/resources/Gene_Ontology_Wizard.html | 90 +
.../resources/cytoscape_jalopy_code_convention.xml | 434 +
legacy/resources/javax.imageio.spi.ImageWriterSpi | 1 +
.../org.freehep.util.export.ExportFileType | 5 +
.../resources/plugin_website/CyPluginDB_schema.sql | 135 +
.../plugin_website/generate_plugin_xml.pl | 501 +
.../resources/plugin_website/plugin.props.example | 43 +
legacy/resources/plugin_website/plugin.xml | 40 +
legacy/resources/schema/binding.xjb | 15 +
legacy/resources/schema/dcmes-xml-dtd.xsd | 200 +
legacy/resources/schema/plugins.xsd | 57 +
legacy/resources/schema/rdf.xsd | 29 +
legacy/resources/schema/readme.txt | 15 +
legacy/resources/schema/xgmml.xsd | 461 +
legacy/resources/schema/xml.xsd | 146 +
packaging/README.txt | 6 +
packaging/pom.xml | 140 +
packaging/src/main/images/cytoscape.icns | Bin 0 -> 46545 bytes
packaging/src/main/images/cytoscape_file.icns | Bin 0 -> 45977 bytes
packaging/src/main/images/gml.icns | Bin 0 -> 49342 bytes
packaging/src/main/images/icon16x16.png | Bin 0 -> 761 bytes
packaging/src/main/images/icon32x32.png | Bin 0 -> 2251 bytes
packaging/src/main/images/sif.icns | Bin 0 -> 48940 bytes
packaging/src/main/install4j/Cytoscape.install4j | 931 +
pom.xml | 225 +
webstart/README.txt | 17 +
webstart/pom.xml | 222 +
webstart/src/main/jnlp/template.vm | 57 +
3030 files changed, 1168151 insertions(+)
--
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