Branch: refs/heads/develop
Home: https://github.com/cytoscape/cytoscape-impl
Commit: fec31ae8068d135945cec6e8bbad2478801f352d
https://github.com/cytoscape/cytoscape-impl/commit/fec31ae8068d135945cec6e8bbad2478801f352d
Author: Chris Churas <[email protected]>
Date: 2019-09-24 (Tue, 24 Sep 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
M search-impl/src/main/java/org/cytoscape/search/internal/SearchResults.java
M
search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
M
search-impl/src/main/java/org/cytoscape/search/internal/util/CustomMultiFieldQueryParser.java
Log Message:
-----------
Fix for CYTOSCAPE-12553 by adding logic to catch ParseException and report
information to user. Also set hard limit of query to 65k and added timing
values to log messages for user
Commit: 9a318512f12830330191799e724a6025d5d254ae
https://github.com/cytoscape/cytoscape-impl/commit/9a318512f12830330191799e724a6025d5d254ae
Author: Chris Churas <[email protected]>
Date: 2019-09-25 (Wed, 25 Sep 2019)
Changed paths:
A
search-impl/src/test/java/org/cytoscape/search/internal/SearchResultsTest.java
Log Message:
-----------
initial revision
Commit: 5bd8c5bc3fb281339e249192648a3e3a0943830a
https://github.com/cytoscape/cytoscape-impl/commit/5bd8c5bc3fb281339e249192648a3e3a0943830a
Author: Chris Churas <[email protected]>
Date: 2019-09-25 (Wed, 25 Sep 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
M search-impl/src/main/java/org/cytoscape/search/internal/SearchResults.java
M
search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
M
search-impl/src/test/java/org/cytoscape/search/internal/SearchResultsTest.java
Log Message:
-----------
refactored SearchResults to hold business logic of the message so its easier
to test. Fix for CYTOSTCAPE-12553
Commit: 3d8b8b942c71833c891a954e00dbd0db29a28018
https://github.com/cytoscape/cytoscape-impl/commit/3d8b8b942c71833c891a954e00dbd0db29a28018
Author: Chris Churas <[email protected]>
Date: 2019-09-25 (Wed, 25 Sep 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
M
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
M
search-impl/src/main/java/org/cytoscape/search/internal/ui/EnhancedSearchPanel.java
Log Message:
-----------
Put index and query under separate threads so they can be quickly killed. Fix
for CYTOSCAPE-12553
Commit: 377482f9504f8c9d1960038ec4cd700eb829f1b6
https://github.com/cytoscape/cytoscape-impl/commit/377482f9504f8c9d1960038ec4cd700eb829f1b6
Author: Chris Churas <[email protected]>
Date: 2019-09-26 (Thu, 26 Sep 2019)
Changed paths:
M search-impl/pom.xml
Log Message:
-----------
added mockito
Commit: 17d18f5811dca5cad9e5757dfcfcc5b9d4594e74
https://github.com/cytoscape/cytoscape-impl/commit/17d18f5811dca5cad9e5757dfcfcc5b9d4594e74
Author: Chris Churas <[email protected]>
Date: 2019-09-27 (Fri, 27 Sep 2019)
Changed paths:
A
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndexFactory.java
M
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQuery.java
A
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchQueryFactory.java
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
A
search-impl/src/main/java/org/cytoscape/search/internal/NodeAndEdgeSelector.java
A
search-impl/src/main/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImpl.java
M search-impl/src/main/java/org/cytoscape/search/internal/ReindexTask.java
M
search-impl/src/main/java/org/cytoscape/search/internal/SearchTaskFactory.java
A search-impl/src/main/java/org/cytoscape/search/internal/ViewUpdator.java
A
search-impl/src/main/java/org/cytoscape/search/internal/ViewUpdatorImpl.java
A
search-impl/src/test/java/org/cytoscape/search/internal/IndexAndSearchTaskTest.java
A
search-impl/src/test/java/org/cytoscape/search/internal/ViewUpdatorImplTest.java
Log Message:
-----------
Added unset of nodes and edges in case where no matches were found. Also
refactored the code to make it easier to test and added a couple new test
classes. Fix for CSD-168
Commit: 01c115e8e21303c1262ccea4dd270e70a35f09e3
https://github.com/cytoscape/cytoscape-impl/commit/01c115e8e21303c1262ccea4dd270e70a35f09e3
Author: Chris Churas <[email protected]>
Date: 2019-09-27 (Fri, 27 Sep 2019)
Changed paths:
A
search-impl/src/test/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImplTest.java
Log Message:
-----------
initial revision
Commit: 15b100294f375e81aa98262c05cdabcb707b73dd
https://github.com/cytoscape/cytoscape-impl/commit/15b100294f375e81aa98262c05cdabcb707b73dd
Author: Chris Churas <[email protected]>
Date: 2019-09-27 (Fri, 27 Sep 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImpl.java
Log Message:
-----------
improved javadoc for selectNodesAndEdges method
Commit: ecdea78cfb99b289ace7535061f777f6290b028b
https://github.com/cytoscape/cytoscape-impl/commit/ecdea78cfb99b289ace7535061f777f6290b028b
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
A
search-impl/src/test/java/org/cytoscape/search/internal/util/AttributeFieldsTest.java
A
search-impl/src/test/java/org/cytoscape/search/internal/util/EnhancedSearchUtilsTest.java
Log Message:
-----------
initial revision
Commit: 7e787d742db6f84d45f2143c6717f2cb53dafe47
https://github.com/cytoscape/cytoscape-impl/commit/7e787d742db6f84d45f2143c6717f2cb53dafe47
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M search-impl/pom.xml
Log Message:
-----------
added needed dependencies to use NetworkTestSupport class in model-impl
Commit: 0178af2517dde0d668734afcd35353d9d185d9fe
https://github.com/cytoscape/cytoscape-impl/commit/0178af2517dde0d668734afcd35353d9d185d9fe
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
Log Message:
-----------
put license above imports
Commit: 09a0da1b2ea5549da8f60038a282e982061addc3
https://github.com/cytoscape/cytoscape-impl/commit/09a0da1b2ea5549da8f60038a282e982061addc3
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImpl.java
Log Message:
-----------
added javadoc and bypassed CyTableUtil to get selected nodes and edges since
there for improved speed with very large networks
Commit: 468b722151c6c04fb0af02b94189e17b03133b53
https://github.com/cytoscape/cytoscape-impl/commit/468b722151c6c04fb0af02b94189e17b03133b53
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M search-impl/src/main/java/org/cytoscape/search/internal/SearchResults.java
Log Message:
-----------
simplified the code that generates the selected nodes/edges message
Commit: 51902180143966446edcb60deda1f48a861a92fa
https://github.com/cytoscape/cytoscape-impl/commit/51902180143966446edcb60deda1f48a861a92fa
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/util/EnhancedSearchUtils.java
Log Message:
-----------
switched code to use StringBuilder which is more efficient
Commit: d124bf5c4501b17deace5cceb79867f7a70cedd9
https://github.com/cytoscape/cytoscape-impl/commit/d124bf5c4501b17deace5cceb79867f7a70cedd9
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M
search-impl/src/test/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImplTest.java
Log Message:
-----------
added more tests
Commit: 6d74bfbf717a9bb30f82a7e7cda65fceaffdb750
https://github.com/cytoscape/cytoscape-impl/commit/6d74bfbf717a9bb30f82a7e7cda65fceaffdb750
Author: Chris Churas <[email protected]>
Date: 2019-10-03 (Thu, 03 Oct 2019)
Changed paths:
M
core-task-impl/src/main/java/org/cytoscape/task/internal/export/ViewWriter.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/PrintLOD.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/debug/DebugEntry.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/debug/DebugFrameType.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/debug/DingDebugPanel.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/InputHandlerGlassPane.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/MainRenderComponent.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/canvas/RenderComponent.java
M
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/dialogs/ShapeAnnotationPanel.java
M
equations-impl/src/main/java/org/cytoscape/equations/internal/builtins/If.java
M
equations-impl/src/test/java/org/cytoscape/equations/internal/builtins/IfTest.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/write/AbstractWriterManager.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/PresentationWriterManagerImpl.java
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/PDFWriter.java
M
io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PNGWriter.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
M
table-browser-impl/src/main/java/org/cytoscape/browser/internal/view/PopupMenuHelper.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/NullCyNetworkViewImpl.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/CyNetworkViewImpl.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/CyViewBase.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/ViewLock.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/snapshot/CyViewSnapshotBase.java
A
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/NetworkViewBatchTest.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/NetworkViewTestUtils.java
M
work-impl/src/main/java/org/cytoscape/work/internal/properties/BoundedPropertyHandler.java
Log Message:
-----------
Merge branch 'develop' into csd-168
Commit: ce25deb64703a3046771d3c66f232a07a3086ed0
https://github.com/cytoscape/cytoscape-impl/commit/ce25deb64703a3046771d3c66f232a07a3086ed0
Author: Chris Churas <[email protected]>
Date: 2019-10-04 (Fri, 04 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
Log Message:
-----------
added real progress values for indexing step
Commit: 49d68587c1aa1e26527269220136aa6780c1f2f5
https://github.com/cytoscape/cytoscape-impl/commit/49d68587c1aa1e26527269220136aa6780c1f2f5
Author: Chris Churas <[email protected]>
Date: 2019-10-07 (Mon, 07 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/IndexAndSearchTask.java
Log Message:
-----------
log the time it takes to update any views
Commit: 481a8700dfa0c6093de93de0c132a99525f6fe06
https://github.com/cytoscape/cytoscape-impl/commit/481a8700dfa0c6093de93de0c132a99525f6fe06
Author: Chris Churas <[email protected]>
Date: 2019-10-07 (Mon, 07 Oct 2019)
Changed paths:
M
search-impl/src/main/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImpl.java
M
search-impl/src/test/java/org/cytoscape/search/internal/NodeAndEdgeSelectorImplTest.java
Log Message:
-----------
updated code to properly track progress of unsetting and setting node and
edge selection
Commit: bab404e42e0c4ff09ee3ce526f14f17ce5c47b60
https://github.com/cytoscape/cytoscape-impl/commit/bab404e42e0c4ff09ee3ce526f14f17ce5c47b60
Author: Chris Churas <[email protected]>
Date: 2019-10-08 (Tue, 08 Oct 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/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/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/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/DingAnnotation.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/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/DGraphViewApplyTest.java
M
ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/impl/cyannotator/AbstractAnnotationTest.java
M
table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/TypeUtil.java
M viewmodel-impl/impl/pom.xml
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyActivator.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/CyNetworkViewConfigImpl.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/CyNetworkViewImpl.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/CyNodeViewImpl.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/snapshot/CyNetworkViewSnapshotImpl.java
R
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/RTreeSpacialIndex2DBase.java
R
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/RTreeSpacialIndex2DFactoryImpl.java
R
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/RTreeSpacialIndex2DImpl.java
R
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/RTreeSpacialIndex2DSnapshotImpl.java
R
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/RTreeSpacialIndexStore.java
M
viewmodel-impl/impl/src/main/java/org/cytoscape/view/model/internal/model/spacial/SimpleSpacialIndex2DSnapshotImpl.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/NetworkViewFactoryTestSupport.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/NetworkViewTestUtils.java
M
viewmodel-impl/impl/src/test/java/org/cytoscape/view/model/SpacialIndex2DTest.java
M
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/valueeditor/CyColorChooser.java
Log Message:
-----------
Merge branch 'develop' into csd-168
Commit: e722fbd79f9d612b9050fc797e64c9f048fb1912
https://github.com/cytoscape/cytoscape-impl/commit/e722fbd79f9d612b9050fc797e64c9f048fb1912
Author: Chris Churas <[email protected]>
Date: 2019-10-09 (Wed, 09 Oct 2019)
Changed paths:
M
swing-util-impl/src/main/java/org/cytoscape/util/swing/internal/CyColorPaletteChooserImpl.java
Log Message:
-----------
Merge branch 'develop' into csd-168
Commit: 233b4cc468be63fb96c3f506945a178d04d4ab8f
https://github.com/cytoscape/cytoscape-impl/commit/233b4cc468be63fb96c3f506945a178d04d4ab8f
Author: Chris Churas <[email protected]>
Date: 2019-10-09 (Wed, 09 Oct 2019)
Changed paths:
Log Message:
-----------
Fixes for search issues CYTOSCAPE-12553 and CSD-168
Compare:
https://github.com/cytoscape/cytoscape-impl/compare/ddbe3d2fadb9...233b4cc468be
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To view this discussion on the web visit
https://groups.google.com/d/msgid/cytoscape-cvs/cytoscape/cytoscape-impl/push/refs/heads/develop/ddbe3d-233b4c%40github.com.
