jalview

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Revert "JAL-3690 for a laugh, lets enable web services!"

This reverts commit 026057e76ba227a13968eb0ff3c01dc6b87145f4.

JAL-3690 update to swingjs patch 3.2.9

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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/differences.txt
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    /swingjs/ver/3.2.9-j11/net.sf.j2s.core-j11.jar
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JAL-3690 for a laugh, lets enable web services!

JAL-3690 update to next patched 3.2.9 j2s c336e447

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    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3690 update j2s from hanson1 branch 0b8b02bb

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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/StructureChooser.java
JAL-3690 - fixed state inconsistency when restarting the calcworker

JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 - introduce shutdown method that cleans up manager's resources.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 Documentation for AlignCalcListener

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Catch and notify about worker cancellation separately.

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Fix concurrent modification exception when workers are cancelled

JAL-3690 Documentation for AlignCalcManagerI2

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    /src/jalview/api/AlignCalcManagerI2.java
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
JAL-3690 changed AWSThread to use Timer instead

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    /src/jalview/ws/AWSThread.java
JAL-3690 alternative servers menu fix

JAL-3690 restore jws1 JPred

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    /src/jalview/gui/AlignFrame.java
JAL-3690 switching to CompletableFuture to allow chaining

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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3690 mark JalviewChangeSupport as deprecated

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    /src/jalview/gui/JalviewChangeSupport.java
JAL-3690 refactoring web-services discovery

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/ServiceChangeListener.java
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    /src/jalview/ws/jws1/Discoverer.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112

Conflicts:

src/jalview/gui/Desktop.java

src/jalview/gui/Preferences.java

src/jalview/jbgui/GPreferences.java

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3683 retrieve job status to output stream

JAL-6386 update slivka client for j2s compatibility

Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/appletgui/TitledPanel.java
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    /src/jalview/datamodel/Alignment.java
  1. … 60 more files in changeset.
JAL-3529 test updated for revised signature of getDBRefs()

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    /test/jalview/io/StockholmFileTest.java
Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/gui/IdPanel.java
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    /src/jalview/gui/PopupMenu.java
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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/io/StockholmFile.java
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    /src/jalview/util/DBRefUtils.java
  1. … 5 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3613 check sequence overlap when matching search results

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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/util/BrowserLauncher.java
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/CalculationChooser.java
  1. … 28 more files in changeset.
Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalview_212_alpha