jalview

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JAL-3751 second occurrence of bug squashed

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    /test/jalview/util/MapListTest.java
JAL-3761 helper method reinstated to avoid code duplication

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-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-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-3761 unit test for MapList.countPos()

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    /test/jalview/util/MapListTest.java
JAL-3761 failing test, formatting, method renamed

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    /test/jalview/util/MapListTest.java
JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    /test/jalview/util/MapListTest.java
JAL-3751 only merge strictly contiguous ranges of mappings

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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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    /getdown/lib/getdown-launcher-local.jar
JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

Merge branch 'feature/JAL-3615gzipXfam' into develop

JAL-3746 bump release version for 2.11.2 series (currently on develop)

JAL-3679 Added externally specified plugins dir to J2sPlugin check

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3680 merged description of individual cursor key actions

JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow JAL-3733 TODO - provide an undo for sequence/group up/down moves

JAL-3518 removed unneeded override in ChimeraCommands

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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3018 Ensembl reviewed REST version updated to 13.0

JAL-1191 use Cache.log for logging

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    /src/jalview/ext/so/SequenceOntology.java
JAL-3018 updated reviewed REST version to 12.0

JAL-3615 code tidy, improve unit test

JAL-2656 better read of (potential) gzip magic bytes

JAL-2656 Java 8 compatible test for gzipped, refactored for unit test

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    /test/jalview/io/FileIOTester.java
Merge branch 'task/JAL-3597memoryLeakTest' into develop

JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size

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    /test/jalview/gui/FreeUpMemoryTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop