jalview

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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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    /src/jalview/jbgui/GStructureChooser.java
Merge branch 'develop' into improvement/JAL-3594_logos_for_jalview_test

JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

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    /doc/README-DMG_background_image_creation.md
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    /doc/README-DMG_creation.md
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    /doc/README_convert_PNG_to_ICNS_and_ICO
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    /utils/channels/release/images/jalview_logo.svg
  1. … 15 more files in changeset.
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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    /src/jalview/gui/StructureChooser.java
JAL-3594 Changed logo for Jalview Test

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    /utils/channels/test-release/images/jalview_test-release_logo.svg
  1. … 21 more files in changeset.
JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer.

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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
JAL-3878 Skip getting results of failed jobs.

JAL-3878 Add job log messages reporting.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Fix null pointer exception when preparing empty sequences for job.

JAL-3878 Fetch sequences for alignment on menu action, not creation.

JAL-3878 Split web services menu entries by programs and hosts.

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    /src/jalview/ws2/operations/Operation.java
Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop