jalview

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JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

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    /src/jalview/gui/WebServicesMenuBuilder.java
JAL-3878 Annotation comments and questions

JAL-3878 Add annotation operations to slivka discoverer.

JAL-3878 Fix sequences not being gathered when submitting without gaps.

JAL-3878 Rename annotation provider method to getAnnotations

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    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Set job status to cancelled on job cancellation.

Despite job cancellation not being implemented in slivka client,

the job status should be updated to cancelled for the event to

be emitted to the ui updater.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Start interactive job by registering them with calcManager

JAL-3878 Fix progress updater bar to account for cancelled state.

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    /src/jalview/ws2/gui/ProgressBarUpdater.java
JAL-3878 Refactoring SeqAnnotationServiceCalcWorker.

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    • +47
    /src/jalview/ws2/gui/ProgressBarUpdater.java
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    /src/jalview/ws2/operations/AnnotationServiceWorker.java
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    • +6
    /src/jalview/ws2/operations/Operation.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop

JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution

JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3904 failing test

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    /src/jalview/gui/StructureViewerBase.java
JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

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    • +15
    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/workers/ConsensusThread.java
JAL-3878 Rename web service worker to more generic pollable task.

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    /src/jalview/ws2/PollableTaskI.java
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    /src/jalview/ws2/PollableTaskListenerI.java
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    /src/jalview/ws2/PollingTaskExecutor.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
Update annotation operation WIP

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3899 Replace prints with logger messages.

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    • +17
    /src/jalview/analysis/SeqsetUtils.java
JAL-3899 Update usages of uniquify and deuniquify.

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    /src/jalview/io/packed/JalviewDataset.java
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    /src/jalview/ws/jws1/JPredThread.java
tmp

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    • +5
    /src/jalview/io/packed/JalviewDataset.java
JAL-3899 Refactor sequence de/uniquification.

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    /src/jalview/analysis/SeqsetUtils.java
JAL-3416 make flat default laf for linux

JAL-3878 Annotation operation skeleton.

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    • +261
    /src/jalview/ws2/operations/AnnotationOperation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties

    • binary
    /j11lib/flatlaf-1.6.jar
    • binary
    /j8lib/flatlaf-1.6.jar
Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

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    /src/jalview/datamodel/CigarParser.java
Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3616 show name of structure viewer in ‘new view’ button

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    /src/jalview/jbgui/GStructureChooser.java