Branch: refs/heads/feature/json-support
Home: https://github.com/cytoscape/cytoscape-impl
Commit: 89c7ed8a8ca70647922397f533fbe24cefbc5a6f
https://github.com/cytoscape/cytoscape-impl/commit/89c7ed8a8ca70647922397f533fbe24cefbc5a6f
Author: Christian Lopes <[email protected]>
Date: 2013-09-06 (Fri, 06 Sep 2013)
Changed paths:
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VisualPropertySheetItem.java
Log Message:
-----------
Refs #1969: Adds icon to Remove Mapping button.
Commit: bc4726bf8948dea09a76f44a3b60ea1491a3ec41
https://github.com/cytoscape/cytoscape-impl/commit/bc4726bf8948dea09a76f44a3b60ea1491a3ec41
Author: Scooter Morris <[email protected]>
Date: 2013-09-07 (Sat, 07 Sep 2013)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/CyActivator.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ArbitraryGraphicsCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingVisualStyleRenderingEngineFactory.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationFactoryManager.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationManagerImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/CyAnnotator.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/AbstractAnnotation.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ArrowAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/BoundedTextAnnotationImpl.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/DingAnnotation.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GraphicsUtilities.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ImageAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ShapeAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/TextAnnotationImpl.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/Annotation.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ArrowAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/BoundedTextAnnotation.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ImageAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ShapeAnnotation.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/TextAnnotation.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/AnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/AnnotationFactoryManager.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ArrowAnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/BoundedTextAnnotationFactory.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/DingAnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ImageAnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ShapeAnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/TextAnnotationFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ArrowAnnotationDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ArrowAnnotationPanel.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/BoundedTextAnnotationDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ImageAnnotationDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ImageAnnotationPanel.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/LoadImageDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/PreviewPanel.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/SelectColor.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationPanel.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/TextAnnotationDialog.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/TextAnnotationPanel.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasKeyListener.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseListener.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseMotionListener.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseWheelListener.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddArrowTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddArrowTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ChangeAnnotationCanvasTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ChangeAnnotationCanvasTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/EditAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/EditAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/LayerAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/LayerAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/MoveAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/MoveAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ReloadImagesTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/RemoveAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/RemoveAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ResizeAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ResizeAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/SelectAnnotationTask.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/SelectAnnotationTaskFactory.java
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ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
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ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/DGraphViewApplyTest.java
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ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/DNodeViewTest.java
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ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/view/DNetworkViewTest.java
Log Message:
-----------
Significant modifications to expose annotations functionality through
annotations API.
Change-Id: I6f0984f839b182f692c12b94909627fb11dc81fb
Commit: 9f776b7b376a134685c94a34908e65a9e28ebe53
https://github.com/cytoscape/cytoscape-impl/commit/9f776b7b376a134685c94a34908e65a9e28ebe53
Author: rodche <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M biopax-impl/pom.xml
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyServices.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/LaunchExternalBrowser.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/NodeAttributesWrapper.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ParentFinder.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/StaxHack.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/VisualStyleUtil.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/WebFileConnect.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/AboutPanel.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainer.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxCytoPanelComponent.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
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biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/EdgeFilterUi.java
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biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java
R
biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
M cpath2-impl/pom.xml
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathException.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathFactory.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathNetworkImportTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathProperties.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathProtocol.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathResponseFormat.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathSearchTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebService.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebServiceImpl.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebServiceListener.java
M cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CyActivator.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CytoscapeCPathWebService.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/EmptySetException.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/MergeNetworkEdit.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTaskFactory.java
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/driver/Driver.java
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/driver/index.html
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/ChainedFilter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/DataSourceFilter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/EntityTypeFilter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/Filter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPConnectionHandler.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPEvent.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPReader.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPServer.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPServerListener.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPWriter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/mapping/MapCPathToCytoscape.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/plugin/CPathPlugIn2.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/CPathNetworkImportTask.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/CPathSearchTask.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecutePhysicalEntitySearch.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTaskFactory.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/SelectPhysicalEntity.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ViewNetworkNeighborhoodTask.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ViewNetworkNeighborhoodTaskFactory.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkGroupUtil.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkMergeUtil.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/ChainedFilter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/CheckNode.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/CheckNodeRenderer.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/DataSourceFilter.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/DownloadDetails.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/EntityTypeFilter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/ExtendedRecordWrapper.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/Filter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/InteractionBundleModel.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/InteractionBundlePanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/JListWithToolTips.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/JTreeWithCheckNodes.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/MergePanel.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/NetworkWrapper.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/Organism.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/PathwayTableModel.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/PhysicalEntityDetailsPanel.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/RecordList.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchDetailsPanel.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchHitsPanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/ExtendedRecordWrapper.java
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cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/InteractionBundleModel.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/NetworkWrapper.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/Organism.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/PathwayTableModel.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/RecordList.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/CheckNode.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/CheckNodeRenderer.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/JTreeWithCheckNodes.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/TreeDemo.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathException.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProtocol.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathResponseFormat.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebService.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebServiceImpl.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebServiceListener.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/EmptySetException.java
R cpath2-impl/src/test/java/TestCytoscapeCPathWebService.java
Log Message:
-----------
Polished and moved files in cpath2-impl and biopax-impl in preparing for
cpath2-impl removal and upgrading biopax reader plugin
(in Cy 3.1, biopax-impl will read BioPAX data and optionally convert to SIF or
SBGN and delegate to corresp. apps, if any…)
Commit: 51f4114b73e80c50aadd91b08fba226087618bd7
https://github.com/cytoscape/cytoscape-impl/commit/51f4114b73e80c50aadd91b08fba226087618bd7
Author: rodche <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CyActivator.java
Log Message:
-----------
Removed all services from the cpath2-impl bundle app (it's deprecated; will
remove from the impl-parent and features.xml and move the sources out later)
Commit: 589f68cc04658f21313747118ae63d228335b456
https://github.com/cytoscape/cytoscape-impl/commit/589f68cc04658f21313747118ae63d228335b456
Author: Scooter Morris <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/CyAnnotator.java
Log Message:
-----------
Make sure to test canvas when looking at position
Change-Id: I8617f9578858c84257bda68c5eddf0bcb54e3916
Commit: 9c545e453ebd535e62b513c276652949dff6a93a
https://github.com/cytoscape/cytoscape-impl/commit/9c545e453ebd535e62b513c276652949dff6a93a
Author: Samad Lotia <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/JDialogTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/TaskManagerImpl.java
Log Message:
-----------
Added support for TaskObserver's failed and cancelled methods
Commit: 1f8bdcf72252c9821ba761f685327da6be9539ed
https://github.com/cytoscape/cytoscape-impl/commit/1f8bdcf72252c9821ba761f685327da6be9539ed
Author: Samad Lotia <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/SyncTaskManager.java
Log Message:
-----------
Added support for cancelled() and failed() to task observers
Commit: e827101480b13193e4c03b29d7c35b1b985ef9de
https://github.com/cytoscape/cytoscape-impl/commit/e827101480b13193e4c03b29d7c35b1b985ef9de
Author: Samad Lotia <[email protected]>
Date: 2013-09-09 (Mon, 09 Sep 2013)
Changed paths:
M
command-dialog-impl/src/main/java/org/cytoscape/command-dialog/internal/handlers/CommandHandler.java
Log Message:
-----------
Added TaskObserver's cancelled() and failed() support to CommandHandler
Commit: 03e439e86206662d028216aa5c50154b90b1fa88
https://github.com/cytoscape/cytoscape-impl/commit/03e439e86206662d028216aa5c50154b90b1fa88
Author: Oriol Guitart <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/CyActivator.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/StringToModelImpl.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/available/BasicArgHandler.java
A
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/CyTableTunableHandler.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/ListMultipleTunableHandler.java
Log Message:
-----------
New StringHandler for CyTable. Fix issue with MultipleList tunable. Add help
string for CyTable tunable.
Change-Id: I68b16bdefa6a2b5744f8757db80100e668929797
Commit: 1e75d5744943bb1f21ee6de72c65d9fca79b46a5
https://github.com/cytoscape/cytoscape-impl/commit/1e75d5744943bb1f21ee6de72c65d9fca79b46a5
Author: Samad Lotia <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallAppsPanel.java
Log Message:
-----------
Fixed issue with App Manager -- http://code.cytoscape.org/redmine/issues/2089
Commit: ca87e09f00c90cf22623d3cdd5eed3361df91492
https://github.com/cytoscape/cytoscape-impl/commit/ca87e09f00c90cf22623d3cdd5eed3361df91492
Author: Samad Lotia <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/JDialogTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/TaskManagerImpl.java
Log Message:
-----------
Updated work-swing-impl's task managers to TaskObserve's FinishStatus
Commit: dda41735988d123d9e88c684d53c594ef5314fce
https://github.com/cytoscape/cytoscape-impl/commit/dda41735988d123d9e88c684d53c594ef5314fce
Author: Samad Lotia <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/SyncTaskManager.java
Log Message:
-----------
Updated work-impl to TaskObserver's FinishStatus
Commit: 3a3f8e8cae35f9cd1522c3603c6228d635b5b3eb
https://github.com/cytoscape/cytoscape-impl/commit/3a3f8e8cae35f9cd1522c3603c6228d635b5b3eb
Author: Samad Lotia <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M
command-dialog-impl/src/main/java/org/cytoscape/command-dialog/internal/handlers/CommandHandler.java
Log Message:
-----------
Updated command-dialog-impl to reflect changes to TaskObserver's FinishStatus
Commit: 77bf57f8a739912d00b0790cf61f924bfb31c1be
https://github.com/cytoscape/cytoscape-impl/commit/77bf57f8a739912d00b0790cf61f924bfb31c1be
Author: Samad Lotia <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/CyActivator.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/StringToModelImpl.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/available/BasicArgHandler.java
A
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/CyTableTunableHandler.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/ListMultipleTunableHandler.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/CyAnnotator.java
Log Message:
-----------
Merge branch 'develop' of https://github.com/cytoscape/cytoscape-impl into
develop
Commit: 3ac6f4161913fb7a44d67987adde62ab6ba615d0
https://github.com/cytoscape/cytoscape-impl/commit/3ac6f4161913fb7a44d67987adde62ab6ba615d0
Author: Scooter Morris <[email protected]>
Date: 2013-09-10 (Tue, 10 Sep 2013)
Changed paths:
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/CyActivator.java
M editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
Log Message:
-----------
Clean up node context edit menu a little. Move "Add Edge" and "Connect
Selected Nodes" to new "Add" menu and retitle appropriately
Change-Id: Iecebc683d697616f5b9666c12e7ad5376246f54b
Commit: dce6bc3e88640f02ed7c5e69902156ab06b3e381
https://github.com/cytoscape/cytoscape-impl/commit/dce6bc3e88640f02ed7c5e69902156ab06b3e381
Author: rodche <[email protected]>
Date: 2013-09-12 (Thu, 12 Sep 2013)
Changed paths:
M biopax-impl/pom.xml
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReader.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
A
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ClassLoaderHack.java
R biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/StaxHack.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
Log Message:
-----------
Fixed NPE in the BrowserTableModel. Continue updating biopax-impl (fixed JAXB
and StAX dependencies problems that came with added sbgn-converter)
Commit: 60ca10ba993885b0fd44df09f3381c57328596b9
https://github.com/cytoscape/cytoscape-impl/commit/60ca10ba993885b0fd44df09f3381c57328596b9
Author: Christian Lopes <[email protected]>
Date: 2013-09-12 (Thu, 12 Sep 2013)
Changed paths:
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
Log Message:
-----------
Just changed CyRootNetwork and CySubNetwork toString implementation so the
names of networks on the UI is more human readable (e.g. when using Tunables)
Commit: b0293de6d63a9b674dc84678c628aa8e5042a868
https://github.com/cytoscape/cytoscape-impl/commit/b0293de6d63a9b674dc84678c628aa8e5042a868
Author: David Welker <[email protected]>
Date: 2013-09-12 (Thu, 12 Sep 2013)
Changed paths:
M
core-task-impl/src/main/java/org/cytoscape/task/internal/export/ViewWriter.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/export/network/CyNetworkViewWriter.java
Log Message:
-----------
fixes #2112 so PNG is default
Commit: 6d44b0e889304d10ba5bd2ca1faafc84290fb629
https://github.com/cytoscape/cytoscape-impl/commit/6d44b0e889304d10ba5bd2ca1faafc84290fb629
Author: David Welker <[email protected]>
Date: 2013-09-12 (Thu, 12 Sep 2013)
Changed paths:
M biopax-impl/pom.xml
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReader.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
A
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ClassLoaderHack.java
R biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/StaxHack.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
Log Message:
-----------
Merge branch 'develop' of github.com:cytoscape/cytoscape-impl into develop
Commit: ea1ae46450e390fc35a3b0b05932f536367b7c51
https://github.com/cytoscape/cytoscape-impl/commit/ea1ae46450e390fc35a3b0b05932f536367b7c51
Author: rodche <[email protected]>
Date: 2013-09-12 (Thu, 12 Sep 2013)
Changed paths:
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReader.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ExternalLinkUtil.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/VisualStyleUtil.java
Log Message:
-----------
Polishing the BioPAX reader app: tuned the file filter, almost fixed custom
visual style and layout after network is created, etc…
Commit: d43b2394d33cf9730e5a5144404e28b665878c9a
https://github.com/cytoscape/cytoscape-impl/commit/d43b2394d33cf9730e5a5144404e28b665878c9a
Author: keiono <[email protected]>
Date: 2013-09-18 (Wed, 18 Sep 2013)
Changed paths:
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallAppsPanel.java
M biopax-impl/pom.xml
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReader.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
M biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
A biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyServices.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/DisplayBioPaxXmlTask.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/LaunchExternalBrowser.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxUtil.java
A
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ClassLoaderHack.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ExternalLinkUtil.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/NodeAttributesWrapper.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/ParentFinder.java
M
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/VisualStyleUtil.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/WebFileConnect.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/AboutPanel.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainer.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxCytoPanelComponent.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxDetailsPanel.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/EdgeFilterUi.java
R
biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/LegendPanel.java
R
biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
M
command-dialog-impl/src/main/java/org/cytoscape/command-dialog/internal/handlers/CommandHandler.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/CyActivator.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/StringToModelImpl.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/available/BasicArgHandler.java
A
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/CyTableTunableHandler.java
M
command-executor-impl/src/main/java/org/cytoscape/command/internal/tunables/ListMultipleTunableHandler.java
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/export/ViewWriter.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/export/network/CyNetworkViewWriter.java
M cpath2-impl/pom.xml
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathException.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathFactory.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathNetworkImportTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathProperties.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathProtocol.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathResponseFormat.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathSearchTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebService.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebServiceImpl.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CPathWebServiceListener.java
M cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CyActivator.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/CytoscapeCPathWebService.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/EmptySetException.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/MergeNetworkEdit.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTask.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/ViewNetworkNeighborhoodTaskFactory.java
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/driver/Driver.java
R cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/driver/index.html
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/ChainedFilter.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/DataSourceFilter.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/EntityTypeFilter.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/filters/Filter.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPConnectionHandler.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPEvent.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPReader.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPServer.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPServerListener.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/http/HTTPWriter.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/mapping/MapCPathToCytoscape.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/plugin/CPathPlugIn2.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/CPathNetworkImportTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/CPathSearchTask.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecutePhysicalEntitySearch.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTask.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/MergeNetworkTaskFactory.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/SelectPhysicalEntity.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ViewNetworkNeighborhoodTask.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ViewNetworkNeighborhoodTaskFactory.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/BioPaxUtil.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkGroupUtil.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkMergeUtil.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/util/NetworkUtil.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/ChainedFilter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/CheckNode.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/CheckNodeRenderer.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/DataSourceFilter.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/DownloadDetails.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/EntityTypeFilter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/ExtendedRecordWrapper.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/Filter.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/InteractionBundleModel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/InteractionBundlePanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/JListWithToolTips.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/JTreeWithCheckNodes.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/MergePanel.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/NetworkWrapper.java
A cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/Organism.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/PathwayTableModel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/PhysicalEntityDetailsPanel.java
A
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/RecordList.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchBoxPanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchDetailsPanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/SearchHitsPanel.java
M
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/cPathSearchPanel.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/ExtendedRecordWrapper.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/InteractionBundleModel.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/NetworkWrapper.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/Organism.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/PathwayTableModel.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/model/RecordList.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/CheckNode.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/CheckNodeRenderer.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/JTreeWithCheckNodes.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/view/tree/TreeDemo.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathException.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProperties.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathProtocol.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathResponseFormat.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebService.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebServiceImpl.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CPathWebServiceListener.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
R
cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/EmptySetException.java
R cpath2-impl/src/test/java/TestCytoscapeCPathWebService.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/CyActivator.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ArbitraryGraphicsCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingVisualStyleRenderingEngineFactory.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationFactoryManager.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationManagerImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/CyAnnotator.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/AbstractAnnotation.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ArrowAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/BoundedTextAnnotationImpl.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/DingAnnotation.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GraphicsUtilities.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ImageAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ShapeAnnotationImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/TextAnnotationImpl.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/Annotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ArrowAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/BoundedTextAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ImageAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/ShapeAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/api/TextAnnotation.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/AnnotationFactory.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/AnnotationFactoryManager.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ArrowAnnotationFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/BoundedTextAnnotationFactory.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/DingAnnotationFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ImageAnnotationFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/ShapeAnnotationFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/create/TextAnnotationFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ArrowAnnotationDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ArrowAnnotationPanel.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/BoundedTextAnnotationDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ImageAnnotationDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ImageAnnotationPanel.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/LoadImageDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/PreviewPanel.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/SelectColor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationPanel.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/TextAnnotationDialog.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/TextAnnotationPanel.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasKeyListener.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseListener.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseMotionListener.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/listeners/CanvasMouseWheelListener.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddArrowTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/AddArrowTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ChangeAnnotationCanvasTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ChangeAnnotationCanvasTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/EditAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/EditAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/LayerAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/LayerAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/MoveAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/MoveAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ReloadImagesTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/RemoveAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/RemoveAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ResizeAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ResizeAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/SelectAnnotationTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/SelectAnnotationTaskFactory.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/DGraphViewApplyTest.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/DNodeViewTest.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/view/DNetworkViewTest.java
M editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyRootNetworkImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CySubNetworkImpl.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VisualPropertySheetItem.java
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/SyncTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/JDialogTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/TaskManagerImpl.java
Log Message:
-----------
Merge branch 'develop' into feature/json-support
Commit: 614903b8991c4bb1f89772953e7f565c1a0bf1cf
https://github.com/cytoscape/cytoscape-impl/commit/614903b8991c4bb1f89772953e7f565c1a0bf1cf
Author: keiono <[email protected]>
Date: 2013-09-18 (Wed, 18 Sep 2013)
Changed paths:
M json-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
M
json-impl/src/main/java/org/cytoscape/io/internal/write/json/JSONNetworkWriterFactory.java
M
json-impl/src/main/java/org/cytoscape/io/internal/write/json/JSONVisualStyleWriterFactory.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/ColorSerializer.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsNetworkSerializer.java
M
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsStyleConverter.java
M
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsToken.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsViewSerializer.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsVisualStyleModule.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsVisualStyleSerializer.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapeJsVsiaulStyleSetSerializer.java
M
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/CytoscapejsModule.java
R
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/JsCyNetworkSerializer.java
R
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/JsCyNetworkViewSerializer.java
R
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/JsVisualStyleSerializer.java
R
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/JsVsiaulStyleSetSerializer.java
A
json-impl/src/main/java/org/cytoscape/io/internal/write/json/serializer/ShapeSerializer.java
A
json-impl/src/test/java/org/cytoscape/io/internal/write/json/AbstractJsonNetworkViewWriterTest.java
A
json-impl/src/test/java/org/cytoscape/io/internal/write/json/CytoscapeJsViewWriterTest.java
A
json-impl/src/test/java/org/cytoscape/io/internal/write/json/CytoscapeJsVisualStyleSerializerTest.java
R
json-impl/src/test/java/org/cytoscape/io/internal/write/json/JSONNetworkViewWriterTest.java
R
json-impl/src/test/java/org/cytoscape/io/internal/write/json/JsVisualStyleSerializerTest.java
M json-impl/src/test/resources/site/.idea/workspace.xml
A json-impl/src/test/resources/site/app/data/cytoscapeJsNetwork1.json
A json-impl/src/test/resources/site/app/data/cytoscapeJsStyle.json
M json-impl/src/test/resources/site/app/scripts/main.js
M json-impl/src/test/resources/site/bower.json
Log Message:
-----------
Adding serializers for visual properties. This version does not pass tests
yet.
Compare:
https://github.com/cytoscape/cytoscape-impl/compare/19e0eebdef03...614903b8991c
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