jalview

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JAL-3809 - Change CompletionStage to CompletableFuture.

Seems that swingjs doesn't have completion stages

properly implemented.

JAL-3809 - fixed param edit for msa but default is broken.

Edit settings dialog now works asynchronously. Everything

works properly in java. In javascript, edit settings dialog

works properly for msa services, but running without the

dialog does not work.

Annotation services do not add annotations to the seuqnces.

    • -39
    • +48
    /src/jalview/gui/AlignFrame.java
    • -71
    • +35
    /src/jalview/gui/WsJobParameters.java
    • -36
    • +35
    /src/jalview/ws/jws2/MsaWSClient.java
JAL-3809 - Fixed param edit dialog for jalviewjs.

Edit settings dialog now works asynchronously.

Annotation services still do not add annotations to the sequences.

    • -39
    • +48
    /src/jalview/gui/AlignFrame.java
    • -71
    • +35
    /src/jalview/gui/WsJobParameters.java
    • -36
    • +35
    /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

    • -22
    • +138
    /src/jalview/io/gff/ExonerateHelper.java
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

    • -0
    • +74
    /examples/testdata/test_cdna2genome_showquerygff.gff2
    • -0
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    /examples/testdata/test_cdna2genome_showtargetgff.gff2
    • -0
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    /examples/testdata/test_coding2genome_showquerygff.gff2
    • -0
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    /examples/testdata/test_coding2genome_showtargetgff.gff2
    • -0
    • +42
    /test/jalview/io/FeaturesFileTest.java
JAL-3878 Initial preparation.

    • -0
    • +67
    /src/jalview/ws2/JalviewWebServiceI.java
    • -0
    • +12
    /src/jalview/ws2/MenuEntryProviderI.java
    • -0
    • +211
    /src/jalview/ws2/MsaMenuEntryProvider.java
    • -0
    • +69
    /src/jalview/ws2/WSJobID.java
    • -0
    • +57
    /src/jalview/ws2/WSJobState.java
    • -0
    • +9
    /src/jalview/ws2/WSJobTrackerI.java
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    • +85
    /src/jalview/ws2/WebServiceExecutor.java
    • -0
    • +73
    /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

    • -11
    • +242
    /src/jalview/ws/JPredThread.java
Implementing JPredThread methods and SlivkaJPredServiceInstance

    • -11
    • +242
    /src/jalview/ws/JPredThread.java
    • -0
    • +47
    /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.

    • -0
    • +222
    /src/jalview/ws/JPredThread.java
    • -1
    • +1
    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
Some preliminary refactoring

    • -0
    • +44
    /src/jalview/ws/JPredClient.java
    • -0
    • +64
    /src/jalview/ws/JPredThread.java
    • -0
    • +13
    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
    • -1
    • +1
    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3690 Introduce AlignCalcManager2 tests.

    • -0
    • +7
    /src/jalview/api/AlignCalcManagerI2.java
    • -0
    • +377
    /test/jalview/workers/AlignCaclManager2Test.java
JAL-3521 Updating file opening marker to %u

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    • +1
    /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
    • binary
    /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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    • +13
    /utils/debian/debian/jalview.desktop
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    • +1
    /utils/debian/file_associations_template-mailcap.txt
    • -0
    • +6
    /utils/debian/file_associations_template-shared-mime-info.xml
    • -0
    • +249
    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

    • binary
    /utils/debian/debian/jalview-file.png
    • binary
    /utils/debian/debian/jalview-icon.png
    • -0
    • +22
    /utils/debian/debian/jalview-mailcap
    • -0
    • +143
    /utils/debian/debian/jalview-mime.xml
    • -0
    • +13
    /utils/debian/debian/jalview.desktop
    • -0
    • +1
    /utils/debian/file_associations_template-mailcap.txt
    • -0
    • +6
    /utils/debian/file_associations_template-shared-mime-info.xml
    • -0
    • +249
    /utils/debian/mime_types_for_debian.pl
JAL-2422 this is for testing only. do not merge.

    • -2
    • +13
    /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.

    • binary
    /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