jalview

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Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

Merge branch 'develop' into task/JAL-3796_notarization

JAL-3807 JPred can now successfully submit and track the job.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
Some preliminary refactoring

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    /src/jalview/ws/JPredClient.java
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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3690 Introduce AlignCalcManager2 tests.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /test/jalview/workers/AlignCaclManager2Test.java
JAL-3521 Updating file opening marker to %u

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    /utils/debian/mime_types_for_debian.pl
JAL-3521 Updating file opening marker to %u

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    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    /utils/debian/debian/jalview-file.png
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    /utils/debian/debian/jalview-icon.png
    • -0
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    /utils/debian/debian/jalview-mailcap
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    /utils/debian/debian/jalview-mime.xml
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    /utils/debian/debian/jalview.desktop
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    /utils/debian/file_associations_template-mailcap.txt
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    /utils/debian/file_associations_template-shared-mime-info.xml
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    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    /utils/debian/debian/jalview-file.png
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    /utils/debian/debian/jalview-icon.png
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    /utils/debian/debian/jalview-mailcap
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    /utils/debian/debian/jalview-mime.xml
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    /utils/debian/debian/jalview.desktop
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    /utils/debian/file_associations_template-mailcap.txt
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    /utils/debian/file_associations_template-shared-mime-info.xml
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    • +249
    /utils/debian/mime_types_for_debian.pl
JAL-2422 this is for testing only. do not merge.

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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services

JAL-3805 Smaller DMG Finder windows for all DS_Store files in utils/channels/... . Removed no longer used DS_Store files from utils/install4j.

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    /utils/install4j/DS_Store-NON-RELEASE
    • binary
    /utils/install4j/DS_Store-TEST-RELEASE
JAL-3805 New DS_Store for smaller DMG Finder window

JAL-3805 New DS_Store for smaller DMG Finder window

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3038 corrected code that reads editable JComboBox text input

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AlignCalcManager - add full support for oneshot workers

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    • +124
    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AACon ws menu entry fix.

JAL-3690 AACon ws menu entry fix.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Fix typo in enum name in slivka client.

JAL-3690 Fix typo in enum name in slivka client.

    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

JAL-3690 Fixed slivka wsmenu categories.

JAL-3690 Fixed slivka wsmenu categories.

JAL-3796 update signature for uninstaller on OSX