Branch: refs/heads/CYTOSCAPE-12532
Home: https://github.com/cytoscape/cytoscape-impl
Commit: 7cf8940b0ea7119caad3d7cfdf6bda72a3aafe26
https://github.com/cytoscape/cytoscape-impl/commit/7cf8940b0ea7119caad3d7cfdf6bda72a3aafe26
Author: Alexander Pico <[email protected]>
Date: 2019-11-01 (Fri, 01 Nov 2019)
Changed paths:
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpContactHelpDeskTask.java
Log Message:
-----------
Changing landing page for helpdesk link
Per https://cytoscape.atlassian.net/browse/CYTOSCAPE-12587
Commit: d8f190ed295c9d6c52ffecbad2b470b5c8bd78b3
https://github.com/cytoscape/cytoscape-impl/commit/d8f190ed295c9d6c52ffecbad2b470b5c8bd78b3
Author: Alexander Pico <[email protected]>
Date: 2019-11-01 (Fri, 01 Nov 2019)
Changed paths:
M
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
Log Message:
-----------
Checking help desk menu item
Per https://cytoscape.atlassian.net/browse/CYTOSCAPE-12587
Commit: 78c329ca734f8c81d72456df8d6f93529061eddb
https://github.com/cytoscape/cytoscape-impl/commit/78c329ca734f8c81d72456df8d6f93529061eddb
Author: Alexander Pico <[email protected]>
Date: 2019-11-01 (Fri, 01 Nov 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/HelpVideosTask.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpVideosTaskFactory.java
Log Message:
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added help link to video demos
Commit: abc6ddee000baee3fb3f28bd2be724ccfebe046a
https://github.com/cytoscape/cytoscape-impl/commit/abc6ddee000baee3fb3f28bd2be724ccfebe046a
Author: Mike Kucera <[email protected]>
Date: 2019-11-03 (Sun, 03 Nov 2019)
Changed paths:
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeTask.java
Log Message:
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Fix exception in AddEdgeTask
Commit: b88ef9b55e87d28dc7d64531963270aabd28bddb
https://github.com/cytoscape/cytoscape-impl/commit/b88ef9b55e87d28dc7d64531963270aabd28bddb
Author: Mike Kucera <[email protected]>
Date: 2019-11-04 (Mon, 04 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendStore.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.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/DingGraphLOD.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleInfo.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/NetworkPicker.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewFactoryFactoryImpl.java
Log Message:
-----------
Simplify BendStore and fix some bugs with bend handles.
Commit: 58502a58ecce38616ee5dda11521280a7ffeb1b3
https://github.com/cytoscape/cytoscape-impl/commit/58502a58ecce38616ee5dda11521280a7ffeb1b3
Author: Christian Lopes <[email protected]>
Date: 2019-11-05 (Tue, 05 Nov 2019)
Changed paths:
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layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayoutTask.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
A layout-prefuse-impl/src/main/java/prefuse/util/force/StateMonitor.java
Log Message:
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ForceDirectedLayoutTask (Prefuse FDL) can now be canceled.
Commit: 4c830d5e3a15a8296fe69d52f68163d8e2924cd5
https://github.com/cytoscape/cytoscape-impl/commit/4c830d5e3a15a8296fe69d52f68163d8e2924cd5
Author: Christian Lopes <[email protected]>
Date: 2019-11-05 (Tue, 05 Nov 2019)
Changed paths:
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layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayoutTask.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/Integrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
Log Message:
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Better TaskMonitor messages. Code reformatting and minor refactoring.
Commit: 5575374c7141fee9c17bc9f15f573a5500c92730
https://github.com/cytoscape/cytoscape-impl/commit/5575374c7141fee9c17bc9f15f573a5500c92730
Author: Mike Kucera <[email protected]>
Date: 2019-11-05 (Tue, 05 Nov 2019)
Changed paths:
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ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendStore.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleInfo.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/NetworkPicker.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/graph/render/stateful/EdgeDetails.java
Log Message:
-----------
Fix bend handles.
Commit: fdbc14abb27c342a145130c966ce4f965ffec3cf
https://github.com/cytoscape/cytoscape-impl/commit/fdbc14abb27c342a145130c966ce4f965ffec3cf
Author: Mike Kucera <[email protected]>
Date: 2019-11-05 (Tue, 05 Nov 2019)
Changed paths:
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayoutTask.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/Integrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
A layout-prefuse-impl/src/main/java/prefuse/util/force/StateMonitor.java
Log Message:
-----------
Merge branch 'develop' into feature/handle-optimize
Commit: b1e21bb78f86af7e519d245d367b02982c8634b4
https://github.com/cytoscape/cytoscape-impl/commit/b1e21bb78f86af7e519d245d367b02982c8634b4
Author: Mike Kucera <[email protected]>
Date: 2019-11-06 (Wed, 06 Nov 2019)
Changed paths:
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/DingNetworkViewFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/undo/ViewState.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewContainer.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewFactoryFactoryImpl.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/NetworkViewImplTest.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/SpacialIndex2DTest.java
Log Message:
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Remove CyNetworkViewConfig key fields from API.
Commit: 9d73b4837cae9b8faa66c81dd902aba5c079bd38
https://github.com/cytoscape/cytoscape-impl/commit/9d73b4837cae9b8faa66c81dd902aba5c079bd38
Author: Mike Kucera <[email protected]>
Date: 2019-11-06 (Wed, 06 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendStore.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DRenderingEngine.java
Log Message:
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Update vizmapper when manually adding or removing bend handles.
Commit: 316bbaec9c0764201e7cb690018a59cbe1ed65e2
https://github.com/cytoscape/cytoscape-impl/commit/316bbaec9c0764201e7cb690018a59cbe1ed65e2
Author: Christian Lopes <[email protected]>
Date: 2019-11-07 (Thu, 07 Nov 2019)
Changed paths:
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
Log Message:
-----------
It's now easier to cancel the BioLayout Task and its progress bar has been
fixed.
Commit: 108e0329252b6630dad226dc4d759e3d99a80493
https://github.com/cytoscape/cytoscape-impl/commit/108e0329252b6630dad226dc4d759e3d99a80493
Author: Mike Kucera <[email protected]>
Date: 2019-11-08 (Fri, 08 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/SimpleRootPaneContainer.java
Log Message:
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Renderer: enable glass pane in EdgeBendValueEditor
Commit: 2f9cb6beb8ef4e82f2e25e2825d3c6c7595474c3
https://github.com/cytoscape/cytoscape-impl/commit/2f9cb6beb8ef4e82f2e25e2825d3c6c7595474c3
Author: Mike Kucera <[email protected]>
Date: 2019-11-08 (Fri, 08 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingNetworkViewFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditorDialog.java
Log Message:
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Fix memory leak in EdgeBendValueEditor
Commit: 9adc3d76100f6dbe101e2ad0741e929dad751320
https://github.com/cytoscape/cytoscape-impl/commit/9adc3d76100f6dbe101e2ad0741e929dad751320
Author: Mike Kucera <[email protected]>
Date: 2019-11-08 (Fri, 08 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditorDialog.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EditMode.java
Log Message:
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CYTOSCAPE-12599 Fix edge bend editor.
Commit: 1984d8fe95e22ba32b01d64c4fb21e8bd2739afd
https://github.com/cytoscape/cytoscape-impl/commit/1984d8fe95e22ba32b01d64c4fb21e8bd2739afd
Author: Mike Kucera <[email protected]>
Date: 2019-11-08 (Fri, 08 Nov 2019)
Changed paths:
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
Log Message:
-----------
Merge branch 'develop' into feature/bend-editor-fix
Commit: 4b24cddbdbf5b8908c8651ac4e256bf743c4303b
https://github.com/cytoscape/cytoscape-impl/commit/4b24cddbdbf5b8908c8651ac4e256bf743c4303b
Author: Mike Kucera <[email protected]>
Date: 2019-11-08 (Fri, 08 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationPanel.java
Log Message:
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CYTOSCAPE-12597 Fix color buttons in shape annotation dialog.
Commit: fab6ebfb5d23dbcb9085a4f4f380a31d5c2f5b0d
https://github.com/cytoscape/cytoscape-impl/commit/fab6ebfb5d23dbcb9085a4f4f380a31d5c2f5b0d
Author: Mike Kucera <[email protected]>
Date: 2019-11-11 (Mon, 11 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NetworkTransform.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/AnnotationSelection.java
Log Message:
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CYTOSCAPE-12598 Fix moving annotations using the keyboard.
Commit: 9c1038ae41bb16dfcd20f5784c03801688e2f8b4
https://github.com/cytoscape/cytoscape-impl/commit/9c1038ae41bb16dfcd20f5784c03801688e2f8b4
Author: Mike Kucera <[email protected]>
Date: 2019-11-11 (Mon, 11 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GroupAnnotationImpl.java
Log Message:
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CYTOSCAPE-12598 Fix moving group annotations.
Commit: 8819ebf3df5a46f3b50e05e54349fca718c7daef
https://github.com/cytoscape/cytoscape-impl/commit/8819ebf3df5a46f3b50e05e54349fca718c7daef
Author: Mike Kucera <[email protected]>
Date: 2019-11-11 (Mon, 11 Nov 2019)
Changed paths:
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/snapshot/CyEdgeViewSnapshotImpl.java
Log Message:
-----------
Revert previous commit to CyEdgeViewSnapshotImpl, was causing NPE in
renderer.
Commit: 652430a7125bf71a31a93d9d88613fa1ea0e06d8
https://github.com/cytoscape/cytoscape-impl/commit/652430a7125bf71a31a93d9d88613fa1ea0e06d8
Author: Mike Kucera <[email protected]>
Date: 2019-11-12 (Tue, 12 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/AnnotationCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/AnnotationSelectionCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/ColorCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/CompositeImageCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/EdgeCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NodeCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/DiscreteProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/NoOutputProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/ProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/SubProgressMonitor.java
A
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/work/ProgressMonitorTest.java
Log Message:
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Fix network view progress bar.
Commit: 54be65c612d17e739ab774b5dbe4bfe51ee7bd8e
https://github.com/cytoscape/cytoscape-impl/commit/54be65c612d17e739ab774b5dbe4bfe51ee7bd8e
Author: Christian Lopes <[email protected]>
Date: 2019-11-12 (Tue, 12 Nov 2019)
Changed paths:
M
application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.java
Log Message:
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Preventing unnecessary events when setting selected networks, specially from
the UI.
Commit: b01ddcddbb68b1002d585dd5ab9e031f7a90f145
https://github.com/cytoscape/cytoscape-impl/commit/b01ddcddbb68b1002d585dd5ab9e031f7a90f145
Author: Mike Kucera <[email protected]>
Date: 2019-11-13 (Wed, 13 Nov 2019)
Changed paths:
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/canvas/ColorCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NetworkImageBuffer.java
Log Message:
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Fix nested networks.
Commit: e190e0df0eb1898b814c236b55627c4f97728494
https://github.com/cytoscape/cytoscape-impl/commit/e190e0df0eb1898b814c236b55627c4f97728494
Author: Mike Kucera <[email protected]>
Date: 2019-11-15 (Fri, 15 Nov 2019)
Changed paths:
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/undo/AddEdgeEdit.java
Log Message:
-----------
Fix undo manually add edge.
Commit: 75cdd551250a0b92cc4a5c3383bbda24d5c22539
https://github.com/cytoscape/cytoscape-impl/commit/75cdd551250a0b92cc4a5c3383bbda24d5c22539
Author: Christian Lopes <[email protected]>
Date: 2019-11-15 (Fri, 15 Nov 2019)
Changed paths:
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
Log Message:
-----------
It's now possible to cancel the Hierarchical Layout at any moment and its
progress bar has been fixed. Minor refactoring.
Commit: 7c649d834ae4ee7e1d7acad6267ae5157293060c
https://github.com/cytoscape/cytoscape-impl/commit/7c649d834ae4ee7e1d7acad6267ae5157293060c
Author: Christian Lopes <[email protected]>
Date: 2019-11-20 (Wed, 20 Nov 2019)
Changed paths:
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
A
table-browser-impl/src/main/java/org/cytoscape/browser/internal/task/HideColumnTask.java
A
table-browser-impl/src/main/java/org/cytoscape/browser/internal/task/HideColumnTaskFactory.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTableModel.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/TableBrowserMediator.java
Log Message:
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CYTOSCAPE-9381 #comment Adds "Hide Column" option to each column's context
menu in the Table Browser.
Commit: 42fe9a8f51b7967a69263a78bca06138b0c136dd
https://github.com/cytoscape/cytoscape-impl/commit/42fe9a8f51b7967a69263a78bca06138b0c136dd
Author: Christian Lopes <[email protected]>
Date: 2019-11-20 (Wed, 20 Nov 2019)
Changed paths:
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTableModel.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/PopupMenuHelper.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/TableBrowserToolBar.java
Log Message:
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Minor code refactoring and reformatting.
Commit: fd5fec47ac1abc19ad2df0b8b2c6f1d005134210
https://github.com/cytoscape/cytoscape-impl/commit/fd5fec47ac1abc19ad2df0b8b2c6f1d005134210
Author: Christian Lopes <[email protected]>
Date: 2019-11-22 (Fri, 22 Nov 2019)
Changed paths:
M swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/util/IconUtil.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/TableBrowserToolBar.java
Log Message:
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CYTOSCAPE-9381 #comment Changes icons for "Show|Create|Delete Column" buttons
in the Table Browser's tool bar.
Commit: 42be8cb686b935300a27f1d5b7c53eab77cf3dc9
https://github.com/cytoscape/cytoscape-impl/commit/42be8cb686b935300a27f1d5b7c53eab77cf3dc9
Author: Christian Lopes <[email protected]>
Date: 2019-11-22 (Fri, 22 Nov 2019)
Changed paths:
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeMenuPopulator.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/PopupMenuHelper.java
Log Message:
-----------
Minor code refactoring only.
Commit: a5c4857b1a3e4e0ce7597df71dcd772a7a066040
https://github.com/cytoscape/cytoscape-impl/commit/a5c4857b1a3e4e0ce7597df71dcd772a7a066040
Author: Christian Lopes <[email protected]>
Date: 2019-11-25 (Mon, 25 Nov 2019)
Changed paths:
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/CloneNetworkTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/RegisterNetworkTask.java
Log Message:
-----------
CYTOSCAPE-12065 #comment Adds 'cloneView' option (as Tunable) to
CloneNetworkTask. Fixes a related NPE.
Commit: 6420f1c65887c27f6bbd65b892c978d56718f4e5
https://github.com/cytoscape/cytoscape-impl/commit/6420f1c65887c27f6bbd65b892c978d56718f4e5
Author: Christian Lopes <[email protected]>
Date: 2019-11-25 (Mon, 25 Nov 2019)
Changed paths:
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/AbstractCreationTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/AbstractNetworkFromSelectionTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/CloneNetworkTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/CloneNetworkTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkCommandTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkCommandTaskFactory.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/RegisterNetworkTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/view/CopyExistingViewTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/view/CreateNetworkViewTask.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/CloneNetworkTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MergeDataTableTaskTest.java
Log Message:
-----------
Code refactoring only.
Commit: 939c92798024eb66357162949e96625bd3429861
https://github.com/cytoscape/cytoscape-impl/commit/939c92798024eb66357162949e96625bd3429861
Author: Christian Lopes <[email protected]>
Date: 2019-11-25 (Mon, 25 Nov 2019)
Changed paths:
M core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddEdgeTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddEdgeTaskFactory.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddNodeTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddNodeTaskFactory.java
Log Message:
-----------
Code refactoring only.
Commit: 20ae0f79906a10bc284d773a9b7c261ca9d9601d
https://github.com/cytoscape/cytoscape-impl/commit/20ae0f79906a10bc284d773a9b7c261ca9d9601d
Author: Jing Chen <[email protected]>
Date: 2019-11-25 (Mon, 25 Nov 2019)
Changed paths:
M
application-impl/src/main/java/org/cytoscape/application/internal/CyApplicationManagerImpl.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/edit/ConnectSelectedNodesTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/AbstractCreationTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/AbstractNetworkFromSelectionTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/CloneNetworkTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/CloneNetworkTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkCommandTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkCommandTaskFactory.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskFactoryImpl.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/network/RegisterNetworkTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddEdgeTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddEdgeTaskFactory.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddNodeTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/AddNodeTaskFactory.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/view/CopyExistingViewTask.java
M
core-task-impl/src/main/java/org/cytoscape/task/internal/view/CreateNetworkViewTask.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/CloneNetworkTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesEdgesTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskFactoryTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/network/NewNetworkSelectedNodesOnlyTaskTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MappingIntegrationTest.java
M
core-task-impl/src/test/java/org/cytoscape/task/internal/table/MergeDataTableTaskTest.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeTask.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendImpl.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/BendStore.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.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/DingGraphLOD.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingNetworkViewFactory.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleInfo.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/NetworkPicker.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/AnnotationCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/AnnotationSelectionCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/ColorCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/CompositeImageCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/EdgeCanvas.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NetworkImageBuffer.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NetworkTransform.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/NodeCanvas.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/AnnotationSelection.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/annotations/GroupAnnotationImpl.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/editor/EdgeBendValueEditor.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditorDialog.java
R
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EditMode.java
A
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/SimpleRootPaneContainer.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/undo/AddEdgeEdit.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/undo/ViewState.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/DiscreteProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/NoOutputProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/ProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/work/SubProgressMonitor.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/graph/render/stateful/EdgeDetails.java
A
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/work/ProgressMonitorTest.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
M
layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
M
layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayoutTask.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/BackwardEulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/EulerIntegrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/ForceSimulator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/Integrator.java
M layout-prefuse-impl/src/main/java/prefuse/util/force/NBodyForce.java
M
layout-prefuse-impl/src/main/java/prefuse/util/force/RungeKuttaIntegrator.java
A layout-prefuse-impl/src/main/java/prefuse/util/force/StateMonitor.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
M
swing-application-impl/src/main/java/org/cytoscape/internal/view/CytoscapeMenuPopulator.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/help/HelpContactHelpDeskTask.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpVideosTask.java
A
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpVideosTaskFactory.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/CyActivator.java
A
table-browser-impl/src/main/java/org/cytoscape/browser/internal/task/HideColumnTask.java
A
table-browser-impl/src/main/java/org/cytoscape/browser/internal/task/HideColumnTaskFactory.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/util/IconUtil.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTable.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/BrowserTableModel.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/PopupMenuHelper.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/TableBrowserMediator.java
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/TableBrowserToolBar.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewFactoryFactoryImpl.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/snapshot/CyEdgeViewSnapshotImpl.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/NetworkViewImplTest.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/SpacialIndex2DTest.java
Log Message:
-----------
Merge branch 'develop' into CYTOSCAPE-12532
# Conflicts:
#
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
#
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/NetworkPicker.java
# swing-util-impl/src/main/resources/fonts/cytoscape-3.ttf
Compare:
https://github.com/cytoscape/cytoscape-impl/compare/3c67aa1e6502...20ae0f79906a
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