jalview

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JAL-3806 fix and test for one-to-many sequence mapping case

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    /test/jalview/util/MappingUtilsTest.java
JAL-3806 more lax allowance (3 positions) for stop codon

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-3766 what’s new and release notes for 2.11.1.3

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

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-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

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

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-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-3766 release notes for JAL-3611 JAL-3765

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into releases/Release_2_11_1_Branch

JAL-3766 cut new patch release

JAL-3765 fix test

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    /test/jalview/analysis/FinderTest.java
fix for JAL-3765

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

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    /test/jalview/analysis/FinderTest.java
JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java