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Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka

JAL-3807 Fix SlivkaWSInstance not fetching alignments.

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    /src/jalview/ws/api/JPredServiceI.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Move new JPred client to the jws2 package.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.java
JAL-3807 JPred can now successfully submit and track the job.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3690 Introduce AlignCalcManager2 tests.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /test/jalview/workers/AlignCaclManager2Test.java
Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AACon ws menu entry fix.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Fix typo in enum name in slivka client.

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    /utils/jalviewjs/libjs/slivka-client-site.zip
Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

JAL-3690 Fixed slivka wsmenu categories.

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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    /swingjs/ver/3.2.10/differences.txt
  1. … 24 more files in changeset.
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
  1. … 27 more files in changeset.
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