jalview

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JAL-3809 - Fixed param edit dialog for jalviewjs.

Edit settings dialog now works asynchronously.

Annotation services still do not add annotations to the sequences.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/MsaWSClient.java
JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

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    /src/jalview/io/gff/ExonerateHelper.java
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

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    /examples/testdata/test_cdna2genome_showquerygff.gff2
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    /examples/testdata/test_cdna2genome_showtargetgff.gff2
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    /examples/testdata/test_coding2genome_showquerygff.gff2
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    /examples/testdata/test_coding2genome_showtargetgff.gff2
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    /test/jalview/io/FeaturesFileTest.java
JAL-3878 Initial preparation.

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    /src/jalview/ws2/JalviewWebServiceI.java
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    /src/jalview/ws2/MenuEntryProviderI.java
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    /src/jalview/ws2/MsaMenuEntryProvider.java
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    /src/jalview/ws2/WSJobID.java
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    /src/jalview/ws2/WSJobState.java
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    /src/jalview/ws2/WSJobTrackerI.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
JAL-3807 JPred can now successfully submit and track the job.

This one should be compiling

JAL-3806 more lax allowance (3 positions) for stop codon

Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
Merge branch 'task/JAL-3796_notarization_no_uninstaller' into develop

Merge branch 'task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch' into task/JAL-3796_notarization_no_uninstaller

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
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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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    /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