jalview

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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-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
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)

Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

update test for JAL-3763 redact shared DS sequences for contiguous CDS

JAL-3768 noticed failure of test when run as part of suite via gradle - whilst patching JAL-3700 JAL-3748 JAL-3763 for 2.11.1.3

JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3690 - introduce shutdown method that cleans up manager's resources.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3763 Javadoc, check for null, additional tests

JAL-3763 Javadoc, check for null, additional tests

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java