jalview

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JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

JAL-3690 patch out spinning animation for web service jobs

JAL-3690 disable proxy server for JalviewJS

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    /src/jalview/analysis/AlignmentSorter.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/TitledPanel.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/JvSwingUtils.java
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    /src/jalview/gui/OverviewPanel.java
  1. … 42 more files in changeset.
Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

JAL-3690 Let's enable web services (seriously this time)

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
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JAL-3223 - update swingjs to 3.2.9-j11

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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.8/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/SwingJS-site.zip
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3690 List.copyOf() workaround

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-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

JAL-3679 Added externally specified plugins dir to J2sPlugin check

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