jalview

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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
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

Merge branch 'releases/Release_2_11_1_Branch'

JAL-3690 Documentation for AlignCalcListener

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Catch and notify about worker cancellation separately.

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Fix concurrent modification exception when workers are cancelled

JAL-3690 Documentation for AlignCalcManagerI2

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    /src/jalview/api/AlignCalcManagerI2.java
JAL-3765 fix test

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

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

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
not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

Merge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path

JAL-3763 unused method removed

JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3763 failsafe check for null

JAL-3763 failsafe check for null

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 refactored getCoveringMapping for virtual feature discovery