Branch: refs/heads/feature/renderer-upgrade
Home: https://github.com/cytoscape/cytoscape-impl
Commit: 877d9368d1e92f1df11944e4e51b8f8786abb5cc
https://github.com/cytoscape/cytoscape-impl/commit/877d9368d1e92f1df11944e4e51b8f8786abb5cc
Author: Christian Lopes <[email protected]>
Date: 2019-01-30 (Wed, 30 Jan 2019)
Changed paths:
M core-task-impl/pom.xml
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/FinalStatusMessageUpdateTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableFileTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableFileTaskFactoryImpl.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableURLTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableURLTaskFactoryImpl.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/ReaderTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/table/ImportTableDataTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/table/ImportTableDataTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/utils/DataUtils.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/utils/IconUtil.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/export/network/CyNetworkViewWriterTest.java
R
core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
R
core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/AbstractLoadTableTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/AddImportedTableTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineNetworkReaderAndMappingTask.java
R
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineReaderAndMappingTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineTableReaderAndMappingTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/FinalStatusMessageUpdateTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportAttributeTableReaderFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportAttributeTableReaderTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNetworkTableReaderFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNoGuiNetworkReaderFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNoGuiTableReaderFactory.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportTableDataTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportTableDataTaskFactoryImpl.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadNetworkReaderTask.java
R
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadNoGuiTableReaderFactory.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableFileTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableFileTaskFactoryImpl.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableReaderTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableURLTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableURLTaskFactoryImpl.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ReaderTableTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/TableImportContext.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/AttributeMappingParametersHandler.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/AttributeMappingParametersHandlerFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/NetworkTableMappingParametersHandler.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/NetworkTableMappingParametersHandlerFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/DataUtils.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/IconUtil.java
A
table-import-impl/src/test/java/org/cytoscape/tableimport/internal/task/LoadAttributesFileTaskFactoryImplTest.java
A
table-import-impl/src/test/java/org/cytoscape/tableimport/internal/task/LoadAttributesURLTaskFactoryImplTest.java
Log Message:
-----------
CSD-15 #comment Importing an unassigned table no longer requires a source key
column and uses the default 'SUID'.
Commit: 1d4f28c4f711158a116f30b186e8637c7af027e6
https://github.com/cytoscape/cytoscape-impl/commit/1d4f28c4f711158a116f30b186e8637c7af027e6
Author: Christian Lopes <[email protected]>
Date: 2019-01-31 (Thu, 31 Jan 2019)
Changed paths:
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
M
io-impl/impl/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
A io-impl/impl/src/test/resources/testData/sif/orphanFirst.sif
R io-impl/impl/src/test/resources/testData/sif/sample.sif
A io-impl/impl/src/test/resources/testData/sif/typical.sif
Log Message:
-----------
CYTOSCAPE-12483 #comment Importing SIF files that have TABs as separators is
now correct no matter where in the file the first TAB appears.
Commit: fd2b4093cbca4d9d8855da0b9b3129f9272167b3
https://github.com/cytoscape/cytoscape-impl/commit/fd2b4093cbca4d9d8855da0b9b3129f9272167b3
Author: Christian Lopes <[email protected]>
Date: 2019-02-04 (Mon, 04 Feb 2019)
Changed paths:
M swing-application-impl/src/main/java/org/cytoscape/internal/util/Util.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewComparisonPanel.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewContainer.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewFrame.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewMainPanel.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewMediator.java
Log Message:
-----------
CYTOSCAPE-12485 #comment Number of selected nodes/edges on view's info panel
no longer updated when hiddenness changes. Likewise, number of hidden elements
no longer updated when only selection changes. Also, it now checks for changes
to NODE_VISIBLE or EDGE_VISIBLE properties on ViewChangedEvents, to avoid
unnecessary updates to the hiddenness info.
Commit: 2b14b7df903268a19b1777c90b55cb4ff654f91c
https://github.com/cytoscape/cytoscape-impl/commit/2b14b7df903268a19b1777c90b55cb4ff654f91c
Author: Christian Lopes <[email protected]>
Date: 2019-02-19 (Tue, 19 Feb 2019)
Changed paths:
M equations-impl/pom.xml
M
equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/cose/CoSELayoutAlgorithmTask.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java
M
log-swing-impl/src/main/java/org/cytoscape/log/internal/AllLogMessagesProcesser.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/ConsoleDialog.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyActivator.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyStatusBar.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/LogViewer.java
M
manual-layout-impl/src/main/java/org/cytoscape/view/manual/internal/CyActivator.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkManagerImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
M model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
M presentation-impl/pom.xml
M
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/shutdown/ConfigDirPropertyWriter.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/undo/RedoAction.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/undo/UndoAction.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/BiModalJSplitPane.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeMenuBar.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkSearchMediator.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/StarterPanel.java
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/OpenBrowserImpl.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/io/TableColumnStatFileIO.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ExcelNetworkSheetReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationAction.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectFileTableTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectURLTableTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/OntologyPanelBuilder.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/OntologyUtil.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/action/EditSelectedDiscreteValuesAction.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/task/ImportDefaultVizmapTask.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/NumberSeriesMappingGenerator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/RandomNumberMappingGenerator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapPropertyBuilder.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapperMediator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/cellrenderer/NumberContinuousCellRenderer.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/mappingeditor/ContinuousMappingEditorPanel.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/propertyeditor/CyNumberPropertyEditor.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
M
webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/AboutDialog.java
M
webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
M work-impl/pom.xml
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/LoggingTaskMonitor.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/JPanelTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/BoundedHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JDialogTunableMutator.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JPanelTunableMutator.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/UserActionHandler.java
Log Message:
-----------
Minor refactoring (using constant CyUserLog.NAME when possible).
Commit: 1aa7535c9ed88f63439619af2b0fbb4081a72d26
https://github.com/cytoscape/cytoscape-impl/commit/1aa7535c9ed88f63439619af2b0fbb4081a72d26
Author: Christian Lopes <[email protected]>
Date: 2019-02-25 (Mon, 25 Feb 2019)
Changed paths:
M app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/AppManagerAction.java
A
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java
A
app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Adds app update notification icon to toolbar.
Commit: 6e742f8b4df2f179c9d749bac811dbabe222090c
https://github.com/cytoscape/cytoscape-impl/commit/6e742f8b4df2f179c9d749bac811dbabe222090c
Author: Christian Lopes <[email protected]>
Date: 2019-02-25 (Mon, 25 Feb 2019)
Changed paths:
M app-impl/pom.xml
M app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/CitationsAction.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
M
app-impl/src/main/java/org/cytoscape/app/internal/manager/ParseAppDependencies.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Range.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Version.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/InformationTask.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/ListAvailableTask.java
M app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java
M
app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java
A app-impl/src/main/java/org/cytoscape/app/internal/util/AppUtil.java
R app-impl/src/main/java/org/cytoscape/app/internal/util/Utils.java
R app-impl/src/main/resources/images/alert-red.gif
R app-impl/src/main/resources/images/alert-red2.gif
R app-impl/src/main/resources/images/check-mark.gif
A app-impl/src/test/java/org/cytoscape/app/internal/util/AppUtilTest.java
R app-impl/src/test/java/org/cytoscape/app/internal/util/UtilTest.java
Log Message:
-----------
Minor code cleanup, refactoring and reformatting.
Commit: 661a0f9362b5bb2cb351f4b3abacaba69e95f991
https://github.com/cytoscape/cytoscape-impl/commit/661a0f9362b5bb2cb351f4b3abacaba69e95f991
Author: Christian Lopes <[email protected]>
Date: 2019-02-25 (Mon, 25 Feb 2019)
Changed paths:
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeDesktop.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/MemStatusPanel.java
Log Message:
-----------
Using only an icon on the memory status button (removed the "Memory" label)
in order to save some space on the status bar.
Commit: e611c885984c2191e9f25d3e1ad6ad5e052db7bd
https://github.com/cytoscape/cytoscape-impl/commit/e611c885984c2191e9f25d3e1ad6ad5e052db7bd
Author: Christian Lopes <[email protected]>
Date: 2019-02-25 (Mon, 25 Feb 2019)
Changed paths:
M
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
Log Message:
-----------
Code cleanup only.
Commit: 711794e227aac4f3c66f491afb5daa44b8143b4a
https://github.com/cytoscape/cytoscape-impl/commit/711794e227aac4f3c66f491afb5daa44b8143b4a
Author: Christian Lopes <[email protected]>
Date: 2019-02-26 (Tue, 26 Feb 2019)
Changed paths:
M
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Adds 'notification badge' to app update notification
icon.
Commit: 360ebc8e9e1e42c7bab6c96598589cd72f8a3aec
https://github.com/cytoscape/cytoscape-impl/commit/360ebc8e9e1e42c7bab6c96598589cd72f8a3aec
Author: Christian Lopes <[email protected]>
Date: 2019-02-26 (Tue, 26 Feb 2019)
Changed paths:
M app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M app-impl/src/test/java/org/cytoscape/app/internal/net/WebQuerierTest.java
Log Message:
-----------
Minor code cleanup and refactoring.
Commit: e814f37b44c4ee66d110c73b10ca67896d06b645
https://github.com/cytoscape/cytoscape-impl/commit/e814f37b44c4ee66d110c73b10ca67896d06b645
Author: Christian Lopes <[email protected]>
Date: 2019-02-28 (Thu, 28 Feb 2019)
Changed paths:
A app-impl/src/main/java/org/cytoscape/app/internal/util/CoalesceTimer.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/help/HelpTask.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Fixes rounding errors to better center the badge
number. Debounces app update events to avoid calling checkForUpdates()
unnecessarily.
Commit: 058ba647396ce43e8497dc449de71af84ef9f9b4
https://github.com/cytoscape/cytoscape-impl/commit/058ba647396ce43e8497dc449de71af84ef9f9b4
Author: Christian Lopes <[email protected]>
Date: 2019-02-28 (Thu, 28 Feb 2019)
Changed paths:
M
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Missed a class in the previous commit...
Commit: 7f830c7e3101bdd1967e7789086f9c6d7b5694bd
https://github.com/cytoscape/cytoscape-impl/commit/7f830c7e3101bdd1967e7789086f9c6d7b5694bd
Author: Adam Treister <[email protected]>
Date: 2019-03-01 (Fri, 01 Mar 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GraphicsUtilities.java
Log Message:
-----------
adding Diamond and Vee, X-Arrow to GraphicsUtilities
Commit: bc5cc49506e07fd3e9446c94f8068c22d6e51614
https://github.com/cytoscape/cytoscape-impl/commit/bc5cc49506e07fd3e9446c94f8068c22d6e51614
Author: Adam Treister <[email protected]>
Date: 2019-03-01 (Fri, 01 Mar 2019)
Changed paths:
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/GraphicsUtilities.java
Log Message:
-----------
adding Node and Arrow types
Commit: 75649a0c04bee435b33946da1063afa225d81561
https://github.com/cytoscape/cytoscape-impl/commit/75649a0c04bee435b33946da1063afa225d81561
Author: Adam Treister <[email protected]>
Date: 2019-03-01 (Fri, 01 Mar 2019)
Changed paths:
M app-impl/pom.xml
M app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/AppManagerAction.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/CitationsAction.java
A
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
M
app-impl/src/main/java/org/cytoscape/app/internal/manager/ParseAppDependencies.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Range.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Version.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/InformationTask.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/ListAvailableTask.java
M app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java
A
app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java
A app-impl/src/main/java/org/cytoscape/app/internal/util/AppUtil.java
A app-impl/src/main/java/org/cytoscape/app/internal/util/CoalesceTimer.java
R app-impl/src/main/java/org/cytoscape/app/internal/util/Utils.java
R app-impl/src/main/resources/images/alert-red.gif
R app-impl/src/main/resources/images/alert-red2.gif
R app-impl/src/main/resources/images/check-mark.gif
M app-impl/src/test/java/org/cytoscape/app/internal/net/WebQuerierTest.java
A app-impl/src/test/java/org/cytoscape/app/internal/util/AppUtilTest.java
R app-impl/src/test/java/org/cytoscape/app/internal/util/UtilTest.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/help/HelpTask.java
M equations-impl/pom.xml
M
equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/cose/CoSELayoutAlgorithmTask.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java
M
log-swing-impl/src/main/java/org/cytoscape/log/internal/AllLogMessagesProcesser.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/ConsoleDialog.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyActivator.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyStatusBar.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/LogViewer.java
M
manual-layout-impl/src/main/java/org/cytoscape/view/manual/internal/CyActivator.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkManagerImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
M model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
M presentation-impl/pom.xml
M
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/shutdown/ConfigDirPropertyWriter.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/undo/RedoAction.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/undo/UndoAction.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/BiModalJSplitPane.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeDesktop.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeMenuBar.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/MemStatusPanel.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkSearchMediator.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/StarterPanel.java
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/OpenBrowserImpl.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/io/TableColumnStatFileIO.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ExcelNetworkSheetReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationAction.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectFileTableTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectURLTableTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/OntologyPanelBuilder.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/OntologyUtil.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/action/EditSelectedDiscreteValuesAction.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/task/ImportDefaultVizmapTask.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/NumberSeriesMappingGenerator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/RandomNumberMappingGenerator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapPropertyBuilder.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapperMediator.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/cellrenderer/NumberContinuousCellRenderer.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/mappingeditor/ContinuousMappingEditorPanel.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/propertyeditor/CyNumberPropertyEditor.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
M
vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
M
webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/AboutDialog.java
M
webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
M work-impl/pom.xml
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/LoggingTaskMonitor.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/JPanelTaskManager.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/BoundedHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JDialogTunableMutator.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JPanelTunableMutator.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/UserActionHandler.java
Log Message:
-----------
Merge branch 'develop' of github.com:cytoscape/cytoscape-impl into develop
Commit: 3c1f4b7fab22335cb7b04510bb9c12f921ae84a5
https://github.com/cytoscape/cytoscape-impl/commit/3c1f4b7fab22335cb7b04510bb9c12f921ae84a5
Author: Christian Lopes <[email protected]>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
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/DingCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
Log Message:
-----------
CYTOSCAPE-12468 #comment Adds 'Transparent Background' option to Bitmap
Writer.
Commit: 24b397572733fae1ba8c4df360c5b3b79aacd3e2
https://github.com/cytoscape/cytoscape-impl/commit/24b397572733fae1ba8c4df360c5b3b79aacd3e2
Author: Christian Lopes <[email protected]>
Date: 2019-03-05 (Tue, 05 Mar 2019)
Changed paths:
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/DingCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
Log Message:
-----------
Minor refactoring only.
Commit: 033d067eb8c8e21b5ff9b8386c1b0b9a23c2199f
https://github.com/cytoscape/cytoscape-impl/commit/033d067eb8c8e21b5ff9b8386c1b0b9a23c2199f
Author: Christian Lopes <[email protected]>
Date: 2019-03-06 (Wed, 06 Mar 2019)
Changed paths:
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriterFactory.java
A
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PNGWriter.java
Log Message:
-----------
CYTOSCAPE-12468 #comment The 'Transparent Background' option is now available
to the PNG format only.
Commit: eddf1c03903681803e9df63e2fec3ccae87e0212
https://github.com/cytoscape/cytoscape-impl/commit/eddf1c03903681803e9df63e2fec3ccae87e0212
Author: Christian Lopes <[email protected]>
Date: 2019-03-06 (Wed, 06 Mar 2019)
Changed paths:
M io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/AbstractCyWriterFactory.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
Log Message:
-----------
Minor refactoring only.
Commit: ac2ed1cc69f7be0405555c71722311e87752cc8b
https://github.com/cytoscape/cytoscape-impl/commit/ac2ed1cc69f7be0405555c71722311e87752cc8b
Author: Christian Lopes <[email protected]>
Date: 2019-03-07 (Thu, 07 Mar 2019)
Changed paths:
M
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Fixes badge position when the notification icon is
displayed on the toolbar customization menu.
Commit: b32909ee7d8b972012e52c915e8c197f45c2b72f
https://github.com/cytoscape/cytoscape-impl/commit/b32909ee7d8b972012e52c915e8c197f45c2b72f
Author: Christian Lopes <[email protected]>
Date: 2019-03-07 (Thu, 07 Mar 2019)
Changed paths:
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkMainPanel.java
Log Message:
-----------
Fixes a simple NPE.
Commit: 4be36a1a82cbfa941bbd3a6dd01dc9baaa976773
https://github.com/cytoscape/cytoscape-impl/commit/4be36a1a82cbfa941bbd3a6dd01dc9baaa976773
Author: Christian Lopes <[email protected]>
Date: 2019-03-08 (Fri, 08 Mar 2019)
Changed paths:
M
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
Log Message:
-----------
CYTOSCAPE-11351 #comment Reduces the size of the notification icon (32px) to
fix its alignment on the toolbar customization menu.
Commit: e0ceba883913dbb367a389539e5750dddc393471
https://github.com/cytoscape/cytoscape-impl/commit/e0ceba883913dbb367a389539e5750dddc393471
Author: Christian Lopes <[email protected]>
Date: 2019-03-13 (Wed, 13 Mar 2019)
Changed paths:
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/IconManagerImpl.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/FileHandlerFactory.java
A
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/utils/ColorUtil.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/utils/GUIDefaults.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/view/TaskHistoryWindow.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/view/TaskStatusBar.java
R work-swing-impl/impl/src/main/resources/images/cancelled-icon.png
R work-swing-impl/impl/src/main/resources/images/error-icon.png
R work-swing-impl/impl/src/main/resources/images/finished-icon.png
R work-swing-impl/impl/src/main/resources/images/info-icon.png
R work-swing-impl/impl/src/main/resources/images/warn-icon.png
Log Message:
-----------
Replaces FileHandler and TaskHistory PNG icons with FontAwesome ones. Task
History has better font and text spacing.
Commit: e24116742bbab9d60ecec57fa2b12349365fa7e7
https://github.com/cytoscape/cytoscape-impl/commit/e24116742bbab9d60ecec57fa2b12349365fa7e7
Author: Christian Lopes <[email protected]>
Date: 2019-03-14 (Thu, 14 Mar 2019)
Changed paths:
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/CyUserLogAppender.java
Log Message:
-----------
CYTOSCAPE-12507 #comment Fixes mapping from Pax Level codes to Cy Level types.
Commit: 7e5926b37d271c9dc68343969279452cf4a1dc01
https://github.com/cytoscape/cytoscape-impl/commit/7e5926b37d271c9dc68343969279452cf4a1dc01
Author: Christian Lopes <[email protected]>
Date: 2019-03-14 (Thu, 14 Mar 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/DVisualLexicon.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTaskFactory.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/CyUserLogAppender.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/view/TaskStatusBar.java
Log Message:
-----------
Very minor refactoring.
Commit: dc487b2867a78db10521673f575df33c180ab23d
https://github.com/cytoscape/cytoscape-impl/commit/dc487b2867a78db10521673f575df33c180ab23d
Author: Christian Lopes <[email protected]>
Date: 2019-03-14 (Thu, 14 Mar 2019)
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/DVisualLexicon.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/action/GraphicsDetailAction.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/util/IconUtil.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/util/SimpleToolBarToggleButton.java
M swing-application-impl/src/main/java/org/cytoscape/internal/util/Util.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewContainer.java
M swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf
Log Message:
-----------
CYTOSCAPE-12231 #comment LOD menu is now a Checkbox Menu and is called "Force
High Graphics Details". Adds the same action to the View's toolbar as a toggle
button. Had to create the Visual Property NETWORK_FORCE_HIGH_DETAIL, because
the View UI cannot access DingGraphLOD objects.
Commit: b18fe1a7a25ddcab3de4553a6b3e03dcdbf50684
https://github.com/cytoscape/cytoscape-impl/commit/b18fe1a7a25ddcab3de4553a6b3e03dcdbf50684
Author: Scooter Morris <[email protected]>
Date: 2019-03-14 (Thu, 14 Mar 2019)
Changed paths:
M
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTask.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTaskFactory.java
M swing-util-impl/pom.xml
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/CyActivator.java
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/OpenBrowserImpl.java
M
swing-util-impl/src/test/java/org/cytoscape/util/swing/internal/OpenBrowserImplTest.java
Log Message:
-----------
Add link to tutorials.cytoscape.org in Help menu
(CYTOSCAPE-12497) and provide better integration with CyBrowser. By
default, OpenBrowser not opens the URL in CyBrowser. The previous
behavior can be restored by changing a cytoscape3 property.
Commit: 0858d6f8f4ab2c685abe3a563797ec6bb20092df
https://github.com/cytoscape/cytoscape-impl/commit/0858d6f8f4ab2c685abe3a563797ec6bb20092df
Author: Mike Kucera <[email protected]>
Date: 2019-03-21 (Thu, 21 Mar 2019)
Changed paths:
M app-impl/pom.xml
M app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/AppManagerAction.java
M
app-impl/src/main/java/org/cytoscape/app/internal/action/CitationsAction.java
A
app-impl/src/main/java/org/cytoscape/app/internal/action/UpdateNotificationAction.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java
M
app-impl/src/main/java/org/cytoscape/app/internal/manager/ParseAppDependencies.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Range.java
M app-impl/src/main/java/org/cytoscape/app/internal/manager/Version.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/UpdateManager.java
M app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/InformationTask.java
M
app-impl/src/main/java/org/cytoscape/app/internal/task/ListAvailableTask.java
M app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java
A
app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerMediator.java
A app-impl/src/main/java/org/cytoscape/app/internal/util/AppUtil.java
A app-impl/src/main/java/org/cytoscape/app/internal/util/CoalesceTimer.java
R app-impl/src/main/java/org/cytoscape/app/internal/util/Utils.java
R app-impl/src/main/resources/images/alert-red.gif
R app-impl/src/main/resources/images/alert-red2.gif
R app-impl/src/main/resources/images/check-mark.gif
M app-impl/src/test/java/org/cytoscape/app/internal/net/WebQuerierTest.java
A app-impl/src/test/java/org/cytoscape/app/internal/util/AppUtilTest.java
R app-impl/src/test/java/org/cytoscape/app/internal/util/UtilTest.java
M core-task-impl/pom.xml
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/help/HelpTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AbstractLoadTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/AddImportedTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/CombineReaderAndMappingTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/FinalStatusMessageUpdateTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableFileTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableFileTaskFactoryImpl.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableURLTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/LoadTableURLTaskFactoryImpl.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/loaddatatable/ReaderTableTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/table/ImportTableDataTask.java
R
core-task-impl/src/main/java/org/cytoscape/task/internal/table/ImportTableDataTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/utils/DataUtils.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/utils/IconUtil.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/export/network/CyNetworkViewWriterTest.java
R
core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesFileTaskFactoryImplTest.java
R
core-task-impl/src/test/java/org/cytoscape/task/internal/loaddatatable/LoadAttributesURLTaskFactoryImplTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.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/DVisualLexicon.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTaskFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/action/GraphicsDetailAction.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/DRenderingEngine.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/ArrowAnnotationImpl.java
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GraphicsUtilities.java
M equations-impl/pom.xml
M
equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
M io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/AbstractCyWriterFactory.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriterFactory.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PNGWriter.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
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io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
M
io-impl/impl/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
A io-impl/impl/src/test/resources/testData/sif/orphanFirst.sif
R io-impl/impl/src/test/resources/testData/sif/sample.sif
A io-impl/impl/src/test/resources/testData/sif/typical.sif
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/cose/CoSELayoutAlgorithmTask.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java
M linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java
M
log-swing-impl/src/main/java/org/cytoscape/log/internal/AllLogMessagesProcesser.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/ConsoleDialog.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyActivator.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/CyStatusBar.java
M log-swing-impl/src/main/java/org/cytoscape/log/internal/LogViewer.java
M
manual-layout-impl/src/main/java/org/cytoscape/view/manual/internal/CyActivator.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/AbstractTableFacade.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
M
model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkManagerImpl.java
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model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
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model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableManagerImpl.java
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model-impl/impl/src/main/java/org/cytoscape/model/internal/DefaultTablesNetwork.java
M model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
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model-impl/impl/src/main/java/org/cytoscape/model/internal/LocalTableFacade.java
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model-impl/impl/src/main/java/org/cytoscape/model/internal/SharedTableFacade.java
M presentation-impl/pom.xml
M
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
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swing-application-impl/src/main/java/org/cytoscape/internal/shutdown/ConfigDirPropertyWriter.java
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swing-application-impl/src/main/java/org/cytoscape/internal/undo/RedoAction.java
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swing-application-impl/src/main/java/org/cytoscape/internal/undo/UndoAction.java
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swing-application-impl/src/main/java/org/cytoscape/internal/util/IconUtil.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/util/SimpleToolBarToggleButton.java
M swing-application-impl/src/main/java/org/cytoscape/internal/util/Util.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/BiModalJSplitPane.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeDesktop.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeMenuBar.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/MemStatusPanel.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkMainPanel.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkSearchMediator.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewComparisonPanel.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewContainer.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewFrame.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewMainPanel.java
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swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewMediator.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/StarterPanel.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTask.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTaskFactory.java
M swing-util-impl/pom.xml
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/CyActivator.java
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/IconManagerImpl.java
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/OpenBrowserImpl.java
M swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf
M
swing-util-impl/src/test/java/org/cytoscape/util/swing/internal/OpenBrowserImplTest.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/io/TableColumnStatFileIO.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/CyActivator.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeLineParser.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/AttributeMappingParameters.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/DefaultAttributeTableReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ExcelNetworkSheetReader.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/AbstractLoadTableTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/AddImportedTableTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineNetworkReaderAndMappingTask.java
R
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineReaderAndMappingTask.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/CombineTableReaderAndMappingTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/FinalStatusMessageUpdateTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportAttributeTableReaderFactory.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportAttributeTableReaderTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNetworkTableReaderFactory.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNoGuiNetworkReaderFactory.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportNoGuiTableReaderFactory.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationAction.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportTableDataTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportTableDataTaskFactoryImpl.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadNetworkReaderTask.java
R
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadNoGuiTableReaderFactory.java
A
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableFileTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableFileTaskFactoryImpl.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableReaderTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableURLTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/LoadTableURLTaskFactoryImpl.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/MapGeneAssociationTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ReaderTableTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/RegisterOntologyTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectFileTableTask.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/SelectURLTableTask.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/TableImportContext.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/AttributeMappingParametersHandler.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/AttributeMappingParametersHandlerFactory.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/NetworkTableMappingParametersHandler.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/tunable/NetworkTableMappingParametersHandlerFactory.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/OntologyPanelBuilder.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/DataUtils.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/IconUtil.java
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table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/OntologyUtil.java
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table-import-impl/src/test/java/org/cytoscape/tableimport/internal/task/LoadAttributesFileTaskFactoryImplTest.java
A
table-import-impl/src/test/java/org/cytoscape/tableimport/internal/task/LoadAttributesURLTaskFactoryImplTest.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewManagerImpl.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/action/EditSelectedDiscreteValuesAction.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/task/ImportDefaultVizmapTask.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/NumberSeriesMappingGenerator.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/mapgenerator/RandomNumberMappingGenerator.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapPropertyBuilder.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/VizMapperMediator.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/cellrenderer/NumberContinuousCellRenderer.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/mappingeditor/ContinuousMappingEditorPanel.java
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vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/propertyeditor/CyNumberPropertyEditor.java
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vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/ApplyToNetworkHandler.java
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vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
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vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
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vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
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webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/AboutDialog.java
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webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
M work-impl/pom.xml
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work-impl/src/main/java/org/cytoscape/work/internal/sync/LoggingTaskMonitor.java
M
work-impl/src/main/java/org/cytoscape/work/internal/sync/SyncTaskManager.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/CyUserLogAppender.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/task/JPanelTaskManager.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/BoundedHandler.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/FileHandlerFactory.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JDialogTunableMutator.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/JPanelTunableMutator.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/UserActionHandler.java
A
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/utils/ColorUtil.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/tunables/utils/GUIDefaults.java
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work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/view/TaskHistoryWindow.java
M
work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/view/TaskStatusBar.java
R work-swing-impl/impl/src/main/resources/images/cancelled-icon.png
R work-swing-impl/impl/src/main/resources/images/error-icon.png
R work-swing-impl/impl/src/main/resources/images/finished-icon.png
R work-swing-impl/impl/src/main/resources/images/info-icon.png
R work-swing-impl/impl/src/main/resources/images/warn-icon.png
Log Message:
-----------
Merge branch 'develop' into feature/renderer-upgrade
Conflicts:
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/CyActivator.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTask.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ShowGraphicsDetailsTaskFactory.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/action/GraphicsDetailAction.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ArbitraryGraphicsCanvas.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingCanvas.java
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
Compare:
https://github.com/cytoscape/cytoscape-impl/compare/416c83b1519b...0858d6f8f4ab
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