jalview

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

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    /src/jalview/datamodel/Mapping.java
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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
JAL-3779 apply properties to all groups with given name, not just first

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    /src/jalview/io/AnnotationFile.java
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    /test/jalview/io/AnnotationFileIOTest.java
JAL-3761 extra check that VCF feature is fully mappable to sequence

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

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    /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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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/project/Jalview2XML.java
JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/StructureChooser.java
JAL-3690 - fixed state inconsistency when restarting the calcworker

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

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    /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.

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    /src/jalview/gui/AlignFrame.java
JAL-3761 locateInFrom2 work in progress commit

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    /src/jalview/util/MapList.java
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    /src/jalview/util/MappingUtils.java
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    /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)

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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3609 formatting save after cherry-picks

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

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    /src/jalview/bin/Jalview.java
Merge branch 'releases/Release_2_11_1_Branch'

JAL-3766 what’s new and release notes for 2.11.1.3

JAL-3761 unit test for MapList.countPos()

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    /test/jalview/util/MapListTest.java
JAL-3759 fix compilation error for test

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    /test/jalview/analysis/GroupingTest.java
JAL-3766 release notes for JAL-3759

JAL-3759 exclude hidden columns when processing column selection

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    /src/jalview/analysis/Grouping.java
Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch

JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_11_1_Branch

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3700 mapped sequence group includes short (or all gapped) sequences

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    /test/jalview/io/EmblFlatFileTest.java