Dashboard

Merge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch

JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting

    • -0
    • +116
    /test/jalview/bin/HiDPISettingTest1.java
    • -0
    • +223
    /test/jalview/bin/HiDPISettingTest2.java
    • -0
    • +15
    /test/jalview/bin/hidpiTestProps.jvprops
JAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display can be mocked in tests by Mockito

    • -0
    • +21
    /src/jalview/bin/ScreenInfo.java
JAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1

    • binary
    /utils/testnglibs/byte-buddy-1.10.15.jar
    • binary
    /utils/testnglibs/byte-buddy-agent-1.10.15.jar
    • binary
    /utils/testnglibs/mockito-core-3.6.0.jar
    • binary
    /utils/testnglibs/objenesis-3.1.jar
JAL-3774 better translation

    • -1
    • +1
    /resources/lang/Messages_es.properties
JAL-3530 Added a -nowebservicediscovery command line argument.

JAL-3774 missing i18n added, overlong translation shortened

    • -1
    • +2
    /resources/lang/Messages_es.properties
JAL-3690 for a laugh, lets enable web services!

JAL-3690 update to next patched 3.2.9 j2s c336e447

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3690 update j2s from hanson1 branch 0b8b02bb

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3774 fixed focus Finder from split frame

    • -0
    • +1
    /resources/lang/Messages_es.properties
    • -13
    • +17
    /src/jalview/gui/SplitFrame.java
JAL-3660 Fix for specified output format when using command line arg to convert a file

JAL-3660 Fix for specified output format when using command line arg to convert a file

JAL-3761 locateInFrom/To revised with tests; unused methods removed

    • -20
    • +3
    /src/jalview/datamodel/Mapping.java
    • -318
    • +198
    /src/jalview/util/MapList.java
    • -141
    • +199
    /test/jalview/util/MapListTest.java
JAL-3779 apply properties to all groups with given name, not just first

    • -105
    • +114
    /src/jalview/io/AnnotationFile.java
    • -5
    • +51
    /test/jalview/io/AnnotationFileIOTest.java
JAL-3761 extra check that VCF feature is fully mappable to sequence

    • -24
    • +29
    /src/jalview/io/vcf/VCFLoader.java
JAL-3761 debugged and working (but not tidied) locateInFrom2/To2

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    • +281
    /test/jalview/util/MapListTest.java
JAL-3521 removed unnecessary parts of the ext project in build.gradle

JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar

JAL-3775 Re-compiled Getdown jars

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3775 Eclipse re-formatting commit

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    /src/jalview/gui/Preferences.java
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    • +26
    /src/jalview/jbgui/GPreferences.java
    • -155
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    /src/jalview/project/Jalview2XML.java
JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

    • -0
    • +7
    /src/jalview/gui/IProgressIndicator.java
    • -0
    • +6
    /src/jalview/gui/StructureChooser.java
JAL-3690 - fixed state inconsistency when restarting the calcworker

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.

    • -18
    • +14
    /src/jalview/gui/AlignFrame.java
JAL-3761 locateInFrom2 work in progress commit

    • -10
    • +254
    /src/jalview/util/MapList.java
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    • +35
    /src/jalview/util/MappingUtils.java
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    • +128
    /test/jalview/util/MapListTest.java
JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

    • -14
    • +3
    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +18
    /src/jalview/api/PollableAlignCalcWorkerI.java
    • -183
    • +304
    /src/jalview/workers/AlignCalcManager2.java
JAL-3609 formatting save after cherry-picks

    • -46
    • +46
    /src/jalview/bin/MemorySetting.java
JAL-3608 cherry pick of 92cb745e7

    • -104
    • +141
    /src/jalview/bin/Jalview.java