jalview

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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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    • +15
    /src/jalview/gui/ChimeraViewFrame.java
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    • +7
    /src/jalview/gui/StructureViewerBase.java
JAL-3904 failing test

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    /src/jalview/gui/StructureViewerBase.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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    /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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    /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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    /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
JAL-3616 explicit configure external viewer config

JAL-3878 Fix workers done condition to account for broken jobs.

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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 3d beacons logo - misi varadi gave permission to re-use but most likely it is CC-0

    • binary
    /resources/images/3d-beacons-logo-transparent.png
Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added

Merge branch 'improvement/JAL-3594_logos_for_jalview_test' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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    /src/jalview/gui/StructureChooser.java
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    • +19
    /src/jalview/jbgui/GStructureChooser.java