jalview

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JAL-3594 very subtle grey tesselation of logo in the whitespace on getdown splashscreen added for release channel

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3907 changed two commented out lines to reflect location of future upgraded JRE zipfiles.

JAL-3907 added creation of symbolic links to workaround an install4j9 problem with parsing packed jre filenames with hyphens.

JAL-3830 forgot to uncheck this

JAL-3830 polished setup app for macos

JAL-3830 quick fix to installer text

JAL-3830 install4j9 tries to parse and can't cope with the hyphens and filename format of the jre-VERSION-OS-ARCH.tar.gz JRE tar files, so using underscores in symbolic links

JAL-3830 Added steps for install4j9 to create macOS symbolic link to wrapper script (link) at /Applications/Jalview.app/Contents/MacOS/jalview and to add icon to Dock

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    /utils/install4j/install4j9_template.install4j
JAL-3907 adjusted download_jdks.sh and download_jres.sh scripts to use adoptium and added Java 17 download. Added JAVA_VERSION=17 as a gradle build property option.

JAL-3878 Make interactive service arguments persistent between starts.

JAL-3878 Create proper menu for interactive services.

JAL-3878 Add methods to get and remove workers by their calc name.

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    /src/jalview/api/AlignCalcManagerI2.java
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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    /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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    /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