[med-svn] [libjloda-java] branch upstream updated (9771605 -> 1fe8384)
Andreas Tille
tille at debian.org
Wed May 3 10:44:55 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository libjloda-java.
from 9771605 New upstream version 0.0+20161018
new 1fe8384 New upstream version 0.0+20170502
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
antbuild/build.xml | 54 +--
jars/VectorGraphics2D-0.11.jar | Bin 0 -> 101185 bytes
jars/VectorGraphics2D-License.txt | 133 ++++++
jars/gnujpdf-license.txt | 460 ---------------------
jars/gnujpdf-src.jar | Bin 75488 -> 0 bytes
jars/gnujpdf.jar | Bin 59551 -> 0 bytes
src/com/apple/eawt/AboutHandler.java | 30 ++
src/com/apple/eawt/AppEvent.java | 40 ++
src/com/apple/eawt/Application.java | 48 +++
src/com/apple/eawt/PreferencesHandler.java | 29 ++
src/com/apple/eawt/QuitHandler.java | 29 ++
src/com/apple/eawt/QuitResponse.java | 29 ++
src/jloda/export/EPSExportType.java | 2 +-
src/jloda/export/EPSGraphics.java | 2 +-
src/jloda/export/ExportGraphicType.java | 2 +-
src/jloda/export/ExportImageDialog.java | 2 +-
src/jloda/export/ExportManager.java | 6 +-
src/jloda/export/GIFExportType.java | 2 +-
src/jloda/export/GraphicsFileFilters.java | 2 +-
src/jloda/export/JPGExportType.java | 2 +-
src/jloda/export/PDFExportType.java | 26 +-
src/jloda/export/PNGExportType.java | 4 +-
src/jloda/export/RenderedExportType.java | 2 +-
src/jloda/export/SVGExportType.java | 2 +-
src/jloda/export/SVGStringExportType.java | 2 +-
src/jloda/export/SaveImageDialog.java | 2 +-
src/jloda/export/TransferableGraphic.java | 2 +-
src/jloda/export/gifEncode/DirectGif89Frame.java | 2 +-
src/jloda/export/gifEncode/Gif89Encoder.java | 2 +-
src/jloda/export/gifEncode/Gif89Frame.java | 2 +-
src/jloda/export/gifEncode/IndexGif89Frame.java | 2 +-
src/jloda/export/gifEncode/Put.java | 2 +-
src/jloda/fx/ASelectionModel.java | 240 +++++++++++
src/jloda/fx/ExtendedFXMLLoader.java | 88 ++++
src/jloda/fx/JButtonWithFXAction.java | 53 +++
src/jloda/graph/Dijkstra.java | 2 +-
src/jloda/graph/Edge.java | 2 +-
src/jloda/graph/EdgeArray.java | 4 +-
src/jloda/graph/EdgeAssociation.java | 2 +-
src/jloda/graph/EdgeDoubleArray.java | 2 +-
src/jloda/graph/EdgeDoubleMap.java | 2 +-
src/jloda/graph/EdgeIntegerArray.java | 2 +-
src/jloda/graph/EdgeIntegerMap.java | 2 +-
src/jloda/graph/EdgeMap.java | 3 +-
src/jloda/graph/EdgeSet.java | 2 +-
src/jloda/graph/Graph.java | 28 +-
src/jloda/graph/GraphBase.java | 2 +-
src/jloda/graph/GraphUpdateAdapter.java | 2 +-
src/jloda/graph/GraphUpdateListener.java | 2 +-
src/jloda/graph/IllegalSelfEdgeException.java | 2 +-
src/jloda/graph/MaxClique.java | 2 +-
src/jloda/graph/Node.java | 8 +-
src/jloda/graph/NodeArray.java | 4 +-
src/jloda/graph/NodeAssociation.java | 2 +-
src/jloda/graph/NodeData.java | 42 +-
src/jloda/graph/NodeDoubleArray.java | 2 +-
src/jloda/graph/NodeDoubleMap.java | 2 +-
src/jloda/graph/NodeEdge.java | 4 +-
src/jloda/graph/NodeEdgeEnumeration.java | 2 +-
src/jloda/graph/NodeIntegerArray.java | 2 +-
src/jloda/graph/NodeIntegerMap.java | 2 +-
src/jloda/graph/NodeMap.java | 2 +-
src/jloda/graph/NodeSet.java | 2 +-
src/jloda/graph/Num2EdgeArray.java | 2 +-
src/jloda/graph/Num2NodeArray.java | 2 +-
src/jloda/graphview/DefaultGraphDrawer.java | 2 +-
src/jloda/graphview/DefaultNodeDrawer.java | 184 ++++++---
src/jloda/graphview/EdgeActionAdapter.java | 2 +-
src/jloda/graphview/EdgeActionListener.java | 2 +-
src/jloda/graphview/EdgeView.java | 11 +-
src/jloda/graphview/GraphEditor.java | 2 +-
src/jloda/graphview/GraphView.java | 22 +-
src/jloda/graphview/GraphViewBase.java | 2 +-
src/jloda/graphview/GraphViewListener.java | 2 +-
src/jloda/graphview/IGraphDrawer.java | 2 +-
src/jloda/graphview/IGraphViewListener.java | 2 +-
src/jloda/graphview/INodeDrawer.java | 2 +-
src/jloda/graphview/INodeEdgeFormatable.java | 2 +-
src/jloda/graphview/IPopupListener.java | 2 +-
src/jloda/graphview/ITransformChangeListener.java | 2 +-
src/jloda/graphview/LabelLayoutRTree.java | 2 +-
src/jloda/graphview/LabelLayouter.java | 2 +-
src/jloda/graphview/LabelOverlapAvoider.java | 2 +-
src/jloda/graphview/Magnifier.java | 2 +-
src/jloda/graphview/MagnifierUtil.java | 2 +-
src/jloda/graphview/NodeActionAdapter.java | 2 +-
src/jloda/graphview/NodeActionListener.java | 2 +-
src/jloda/graphview/NodeImage.java | 2 +-
src/jloda/graphview/NodeShape.java | 38 ++
src/jloda/graphview/NodeShapeIcon.java | 54 +++
src/jloda/graphview/NodeView.java | 72 ++--
src/jloda/graphview/PanelActionListener.java | 2 +-
src/jloda/graphview/ScrollPaneAdjuster.java | 2 +-
src/jloda/graphview/Transform.java | 2 +-
src/jloda/graphview/ViewBase.java | 2 +-
src/jloda/gui/About.java | 2 +-
src/jloda/gui/ActionJList.java | 2 +-
src/jloda/gui/AppleStuff.java | 2 +-
src/jloda/gui/ChooseColorDialog.java | 2 +-
src/jloda/gui/ChooseFileDialog.java | 25 +-
src/jloda/gui/ChooseFontDialog.java | 2 +-
src/jloda/gui/ColorTableManager.java | 5 +-
src/jloda/gui/DefaultLabelGetter.java | 2 +-
src/jloda/gui/GraphViewPopupListener.java | 14 +-
src/jloda/gui/HistogramPanel.java | 2 +-
src/jloda/gui/ILabelGetter.java | 2 +-
src/jloda/gui/IMenuModifier.java | 4 +-
src/jloda/gui/IPopMenuModifier.java | 31 ++
src/jloda/gui/IPopupMenuModifier.java | 2 +-
src/jloda/gui/IToolBarModifier.java | 4 +-
src/jloda/gui/ListTransferHandler.java | 2 +-
src/jloda/gui/MemoryUsageManager.java | 4 +-
src/jloda/gui/MenuBar.java | 7 +-
src/jloda/gui/MenuConfiguration.java | 2 +-
src/jloda/gui/Message.java | 2 +-
src/jloda/gui/PopupMenu.java | 45 +-
src/jloda/gui/ProgressDialog.java | 4 +-
src/jloda/gui/ReorderListDialog.java | 2 +-
src/jloda/gui/StatusBar.java | 167 ++++----
src/jloda/gui/ToolBar.java | 7 +-
src/jloda/gui/WindowListenerAdapter.java | 2 +-
src/jloda/gui/WrapLayout.java | 2 +-
src/jloda/gui/commands/CommandBase.java | 2 +-
src/jloda/gui/commands/CommandManager.java | 6 +-
src/jloda/gui/commands/ICheckBoxCommand.java | 2 +-
src/jloda/gui/commands/ICommand.java | 2 +-
src/jloda/gui/commands/MenuCreator.java | 8 +-
src/jloda/gui/commands/TeXGenerator.java | 2 +-
src/jloda/gui/commands/WrappedCheckBoxCommand.java | 2 +-
src/jloda/gui/commands/WrappedCommand.java | 2 +-
src/jloda/gui/director/IDirectableViewer.java | 2 +-
src/jloda/gui/director/IDirector.java | 2 +-
src/jloda/gui/director/IDirectorListener.java | 2 +-
src/jloda/gui/director/IMainViewer.java | 2 +-
.../gui/director/IProjectsChangedListener.java | 2 +-
src/jloda/gui/director/IUpdateableView.java | 2 +-
src/jloda/gui/director/IUsesHeatMapColors.java | 33 ++
src/jloda/gui/director/IViewerWithFindToolBar.java | 2 +-
src/jloda/gui/director/IViewerWithLegend.java | 2 +-
src/jloda/gui/director/ProjectManager.java | 9 +-
...Searchers.java => CompositeObjectSearcher.java} | 185 ++++-----
src/jloda/gui/find/EdgeLabelSearcher.java | 2 +-
src/jloda/gui/find/EmptySearcher.java | 2 +-
src/jloda/gui/find/FindToolBar.java | 2 +-
src/jloda/gui/find/FindWindow.java | 2 +-
src/jloda/gui/find/IFindDialog.java | 2 +-
src/jloda/gui/find/IObjectSearcher.java | 2 +-
src/jloda/gui/find/ISearcher.java | 2 +-
src/jloda/gui/find/ITextSearcher.java | 2 +-
src/jloda/gui/find/JListSearcher.java | 2 +-
src/jloda/gui/find/JTableSearcher.java | 2 +-
src/jloda/gui/find/JTreeSearcher.java | 2 +-
src/jloda/gui/find/NodeLabelSearcher.java | 2 +-
src/jloda/gui/find/SearchActions.java | 12 +-
src/jloda/gui/find/SearchManager.java | 4 +-
src/jloda/gui/find/SingleStringSearcher.java | 154 +++++++
src/jloda/gui/find/TableSearcher.java | 2 +-
src/jloda/gui/find/TextAreaSearcher.java | 2 +-
src/jloda/gui/format/Formatter.java | 31 +-
src/jloda/gui/format/FormatterActions.java | 20 +-
src/jloda/gui/format/FormatterMenuBar.java | 2 +-
src/jloda/gui/format/IFormatterListener.java | 2 +-
src/jloda/gui/message/MessageWindow.java | 2 +-
src/jloda/gui/message/MessageWindowActions.java | 2 +-
src/jloda/gui/message/MessageWindowMenuBar.java | 2 +-
src/jloda/phylo/HomoplasyScore.java | 2 +-
src/jloda/phylo/PhyloGraph.java | 10 +-
src/jloda/phylo/PhyloGraphView.java | 2 +-
src/jloda/phylo/PhyloTree.java | 52 ++-
src/jloda/phylo/PhyloTreeUtils.java | 2 +-
src/jloda/phylo/PhyloTreeView.java | 13 +-
src/jloda/phylo/TreeDrawerAngled.java | 2 +-
src/jloda/phylo/TreeDrawerCircular.java | 2 +-
src/jloda/phylo/TreeDrawerParallel.java | 2 +-
src/jloda/phylo/TreeDrawerRadial.java | 2 +-
src/jloda/phylo/TreeParseException.java | 2 +-
src/jloda/progs/ApproximateBinaryExpansion.java | 2 +-
src/jloda/progs/ApproximateSquareRootOf2.java | 2 +-
src/jloda/progs/CoverDigraph.java | 2 +-
src/jloda/progs/Date2Number.java | 2 +-
src/jloda/progs/GeneEvolutionSimulator.java | 2 +-
src/jloda/progs/GraphPather.java | 2 +-
src/jloda/progs/GraphViewDemo.java | 2 +-
src/jloda/progs/Gunzip.java | 2 +-
src/jloda/progs/ImageProcessor.java | 2 +-
src/jloda/progs/JTableWithRowHeaders.java | 2 +-
src/jloda/progs/Lines2FastA.java | 2 +-
src/jloda/progs/MABlocker.java | 2 +-
src/jloda/progs/MASampler.java | 2 +-
src/jloda/progs/NewMABlocker.java | 2 +-
src/jloda/progs/NextMABlocker.java | 2 +-
src/jloda/progs/QuasiMedianClosure.java | 2 +-
src/jloda/progs/QuasiMedianNetwork.java | 6 +-
src/jloda/progs/RandomDNAGenerator.java | 2 +-
src/jloda/progs/RandomizeLines.java | 2 +-
src/jloda/progs/ReadTrimmer.java | 2 +-
src/jloda/progs/SharedGenesDistance.java | 2 +-
src/jloda/progs/Tree2MeganCSV.java | 2 +-
src/jloda/progs/TreeViewDemo.java | 2 +-
src/jloda/util/Alert.java | 2 +-
src/jloda/util/ArgsOptions.java | 4 +-
src/jloda/util/Basic.java | 349 +++++++++++++---
src/jloda/util/BlastFileFilter.java | 2 +-
src/jloda/util/Cache.java | 2 +-
src/jloda/util/CanceledException.java | 2 +-
src/jloda/util/Colors.java | 2 +-
src/jloda/util/CommandLineOptions.java | 2 +-
src/jloda/util/ConvexHull.java | 4 +-
src/jloda/util/Counter.java | 2 +-
src/jloda/util/Cursors.java | 2 +-
src/jloda/util/DNAComplexityMeasure.java | 2 +-
src/jloda/util/DrawOval.java | 165 --------
src/jloda/util/EditDistance.java | 2 +-
src/jloda/util/FastA.java | 2 +-
src/jloda/util/FastaFileFilter.java | 25 +-
src/jloda/util/FileFilter.java | 2 +-
src/jloda/util/FileFilterBase.java | 2 +-
src/jloda/util/FileInputIterator.java | 4 +-
src/jloda/util/FileIterator.java | 2 +-
src/jloda/util/GZipUtils.java | 2 +-
src/jloda/util/Geometry.java | 2 +-
src/jloda/util/HeatSpectrum.java | 2 +-
src/jloda/util/ICloseableIterator.java | 2 +-
src/jloda/util/IFileIterator.java | 2 +-
src/jloda/util/IViewerWithJComponent.java | 35 ++
src/jloda/util/IteratorAdapter.java | 2 +-
src/jloda/util/JointIterators.java | 63 +++
src/jloda/util/License.java | 353 ----------------
src/jloda/util/ListOfLongs.java | 2 +-
src/jloda/util/MenuMnemonics.java | 2 +-
src/jloda/util/MultiIterator.java | 88 ++++
src/jloda/util/MultiLineCellRenderer.java | 2 +-
src/jloda/util/NexusFileFilter.java | 2 +-
src/jloda/util/NotOwnerException.java | 2 +-
src/jloda/util/Pair.java | 47 ++-
src/jloda/util/PeakMemoryUsageMonitor.java | 2 +-
src/jloda/util/PhylipUtils.java | 2 +-
src/jloda/util/PluginClassLoader.java | 31 +-
src/jloda/util/PolygonDouble.java | 2 +-
src/jloda/util/ProgramProperties.java | 5 +-
src/jloda/util/ProgressCmdLine.java | 2 +-
src/jloda/util/ProgressListener.java | 2 +-
src/jloda/util/ProgressPercentage.java | 2 +-
src/jloda/util/ProgressSilent.java | 2 +-
src/jloda/util/PropertiesListListener.java | 2 +-
src/jloda/util/ProteinComplexityMeasure.java | 2 +-
src/jloda/util/RTFFileFilter.java | 2 +-
src/jloda/util/RTree.java | 2 +-
src/jloda/util/RandomGaussian.java | 2 +-
src/jloda/util/RememberingComboBox.java | 2 +-
src/jloda/util/ResourceManager.java | 2 +-
src/jloda/util/RunLater.java | 2 +-
src/jloda/util/SequenceUtils.java | 5 +-
src/jloda/util/Shapes.java | 98 +++++
src/jloda/util/Signer.java | 2 +-
src/jloda/util/Single.java | 2 +-
src/jloda/util/State.java | 2 +-
src/jloda/util/Statistics.java | 86 +++-
src/jloda/util/StreamGobbler.java | 2 +-
src/jloda/util/StringParser.java | 2 +-
src/jloda/util/Task.java | 2 +-
src/jloda/util/TemporaryFileSet.java | 2 +-
src/jloda/util/TextFileFilter.java | 2 +-
src/jloda/util/TextPrinter.java | 2 +-
src/jloda/util/TextWindow.java | 2 +-
src/jloda/util/TimeStamp.java | 2 +-
src/jloda/util/ToolTipHelper.java | 2 +-
src/jloda/util/Triplet.java | 2 +-
src/jloda/util/UsageException.java | 2 +-
src/jloda/util/lang/Language.java | 2 +-
src/jloda/util/lang/Translator.java | 2 +-
src/jloda/util/parse/NexusStreamParser.java | 45 +-
src/jloda/util/parse/NexusStreamTokenizer.java | 2 +-
src/jloda/util/shapes/TaxaSetShape.java | 76 ----
274 files changed, 2634 insertions(+), 1850 deletions(-)
create mode 100644 jars/VectorGraphics2D-0.11.jar
create mode 100644 jars/VectorGraphics2D-License.txt
delete mode 100644 jars/gnujpdf-license.txt
delete mode 100644 jars/gnujpdf-src.jar
delete mode 100644 jars/gnujpdf.jar
create mode 100644 src/com/apple/eawt/AboutHandler.java
create mode 100644 src/com/apple/eawt/AppEvent.java
create mode 100644 src/com/apple/eawt/Application.java
create mode 100644 src/com/apple/eawt/PreferencesHandler.java
create mode 100644 src/com/apple/eawt/QuitHandler.java
create mode 100644 src/com/apple/eawt/QuitResponse.java
create mode 100644 src/jloda/fx/ASelectionModel.java
create mode 100644 src/jloda/fx/ExtendedFXMLLoader.java
create mode 100644 src/jloda/fx/JButtonWithFXAction.java
create mode 100644 src/jloda/graphview/NodeShape.java
create mode 100644 src/jloda/graphview/NodeShapeIcon.java
create mode 100644 src/jloda/gui/IPopMenuModifier.java
create mode 100644 src/jloda/gui/director/IUsesHeatMapColors.java
rename src/jloda/gui/find/{CompositeObjectSearchers.java => CompositeObjectSearcher.java} (54%)
create mode 100644 src/jloda/gui/find/SingleStringSearcher.java
delete mode 100644 src/jloda/util/DrawOval.java
create mode 100644 src/jloda/util/IViewerWithJComponent.java
create mode 100644 src/jloda/util/JointIterators.java
delete mode 100644 src/jloda/util/License.java
create mode 100644 src/jloda/util/MultiIterator.java
create mode 100644 src/jloda/util/Shapes.java
delete mode 100644 src/jloda/util/shapes/TaxaSetShape.java
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