jalview

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Friday 18 Dec 2020
11:37 am

Jim Procter

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.

Options
    • -9
    • +15
    /src/jalview/ws/AWSThread.java
Thursday 17 Dec 2020
4:31 pm

Jim Procter

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

Options
    • -8
    • +24
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 15 Dec 2020
7:04 pm

Jim Procter

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

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    • -4
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    /utils/jalviewjs/coretemplate.html
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    /utils/jalviewjs/template.html
6:46 pm

Jim Procter

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

Options
    • -0
    • +4
    /utils/jalviewjs/coretemplate.html
    • -0
    • +3
    /utils/jalviewjs/template.html
6:45 pm

Jim Procter

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

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    /src/jalview/ws/api/JobId.java
6:42 pm

Jim Procter

JAL-3690 patch out spinning animation for web service jobs

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    /src/jalview/gui/WebserviceInfo.java
11:53 am

Jim Procter

JAL-3690 disable proxy server for JalviewJS

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    /utils/jalviewjs/template.html
Monday 14 Dec 2020
7:58 pm

Jim Procter

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

Options
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    /src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
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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/AnnotationPanel.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/datamodel/Alignment.java
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    /src/jalview/gui/AlignFrame.java
    • -29
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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
  16. … 42 more files in changeset.
4:27 pm

Jim Procter

Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

Options
Friday 11 Dec 2020
2:33 pm

Mateusz Warowny

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

Options
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    /src/jalview/bin/Jalview.java
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    • +2
    /src/jalview/gui/AlignFrame.java
    • -0
    • +4
    /src/jalview/gui/Desktop.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /swingjs/README.txt
    • binary
    /swingjs/SwingJS-site.zip
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    /swingjs/differences.txt
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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.4/DEV_NOTES.txt
    • binary
    /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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    /swingjs/ver/3.2.4/timestamp
  16. … 27 more files in changeset.
Thursday 10 Dec 2020
5:50 pm

Jim Procter

JAL-3223 - update swingjs to 3.2.9-j11

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    /swingjs/SwingJS-site.zip
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    /swingjs/differences.txt
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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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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-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.9-j11/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/differences.txt
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.9/timestamp
Friday 27 Nov 2020
4:01 pm

Mateusz Warowny

JAL-3690 List.copyOf() workaround

Options
    • -1
    • +3
    /src/jalview/workers/AlignCalcManager2.java
Friday 13 Nov 2020
3:51 pm

Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

Options
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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    • +6
    /src/jalview/gui/AlignFrame.java
    • -0
    • +7
    /src/jalview/gui/Desktop.java
    • -0
    • +7
    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/PCAPanel.java
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    • +17
    /src/jalview/gui/ProgressBar.java
    • -0
    • +6
    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/WebserviceInfo.java
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    /src/jalview/workers/AlignCalcManager.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
Thursday 12 Nov 2020
3:13 pm

Mateusz Warowny

JAL-3690 - fixed state inconsistency when restarting the calcworker

Options
    • -54
    • +22
    /src/jalview/workers/AlignCalcManager2.java
Wednesday 11 Nov 2020
6:42 pm

Mateusz Warowny

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)

Options
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    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +18
    /src/jalview/api/PollableAlignCalcWorkerI.java
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    • +304
    /src/jalview/workers/AlignCalcManager2.java
Monday 26 Oct 2020
12:20 pm

Mateusz Warowny

JAL-3690 - introduce shutdown method that cleans up manager's resources.

Options
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    • +6
    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/bin/Jalview.java
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    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/workers/AlignCalcManager2.java
Wednesday 21 Oct 2020
3:18 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcListener

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    • +27
    /src/jalview/api/AlignCalcListener.java
2:54 pm

Mateusz Warowny

JAL-3690 Catch and notify about worker cancellation separately.

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    • +1
    /src/jalview/api/AlignCalcListener.java
    • -0
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    /src/jalview/workers/AlignCalcManager2.java
2:51 pm

Mateusz Warowny

JAL-3690 Fix concurrent modification exception when workers are cancelled

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    • -26
    • +32
    /src/jalview/workers/AlignCalcManager2.java
2:45 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcManagerI2

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    /src/jalview/api/AlignCalcManagerI2.java
Friday 25 Sep 2020
9:39 am

Ben Soares

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

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    /gradle.properties
Thursday 24 Sep 2020
6:16 pm

Ben Soares

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

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    /build.gradle
Friday 04 Sep 2020
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

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    /build.gradle
Sunday 02 Aug 2020
6:12 pm

Mateusz Warowny

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/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/workers/AlignCalcManager.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/AnnotationWorker.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
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    /src/jalview/workers/InformationThread.java
  16. … 5 more files in changeset.
Wednesday 22 Jul 2020
2:13 pm

Mateusz Warowny

JAL-3690 changed AWSThread to use Timer instead

Options
    • -135
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    /src/jalview/ws/AWSThread.java
Friday 17 Jul 2020
1:43 pm

Mateusz Warowny

JAL-3690 alternative servers menu fix

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws2/PreferredServiceChangeListener.java
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    /src/jalview/ws/jws2/PreferredServiceRegistry.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
11:59 am

Mateusz Warowny

JAL-3690 restore jws1 JPred

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws1/Discoverer.java
Thursday 16 Jul 2020
1:37 pm

Mateusz Warowny

JAL-3690 switching to CompletableFuture to allow chaining

Options
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/WSDiscovererI.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
Wednesday 15 Jul 2020
5:39 pm

Mateusz Warowny

JAL-3690 mark JalviewChangeSupport as deprecated

Options
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/JalviewChangeSupport.java
5:39 pm

Mateusz Warowny

JAL-3690 refactoring web-services discovery

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/ServiceChangeListener.java
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    /src/jalview/ws/WSDiscovererI.java
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    /src/jalview/ws/jws1/Discoverer.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
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    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java