jalview

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JAL-3502 improved fast paint of wrapped scales

JAL-2305 moved failing CrossRef tests to Functional_Failing group

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    /test/jalview/analysis/CrossRefTest.java
JAL-3407 update release date for Jalview 2.11.1

JAL-3473 Checked value of def and min. Set def to min if lower than min.

JAL-3407 update release date for Jalview 2.11.1

Merge branch 'develop' into documentation/JAL-3407_2.11.1_release

JAL-2481 remove code duplication left by merge

JAL-3441 action double-click in Feature Type column only

JAL-3141 correct cast of spinner value

JAL-3187 case-insensitive codon variant calculation

JAL-3187 minor code tidying, todo removal

JAL-2987 release notes

JAL-3407 update RELEASE and cut new release notes in releaseHistory.html

JAL-3407 JAL-3406 update credits in Jalview 2.11.1

JAL-3187 removal of variant feature (non-virtual) transfer to protein

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    /src/jalview/analysis/AlignmentUtils.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
JAL-3187 (fudge) look in both alignments for stored mappings

Merge branch 'develop' into feature/JAL-3187linkedFeatures

JAL-3389 add .py to restored Chimera session filename so it opens!

Merge branch 'bug/JAL-3388structureChooserSorting' into develop

JAL-3198 more efficient Sequence.getDisplayId()

JAL-3388 correct class for column 0 Ref Sequence

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    /src/jalview/fts/core/FTSRestResponse.java
JAL-3386 correct wrapped width calculation for headless image export

JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

JAL-3377 add seq-annotations gap to cheight not to hgap

JAL-3377 Javadoc added for getWrappedHeight()

JAL-3377 include seq-annotation spacing in getWrappedHeight()

JAL-3377 corrected wrapped widths height for IdCanvas

Merge branch 'features/JAL-3375vcfValidation' into feature/JAL-3187linkedFeatures

Conflicts:

src/jalview/io/vcf/VCFLoader.java

test/jalview/io/vcf/VCFLoaderTest.java

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-1793 only decode specific special characters in VCF data

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes

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    /test/jalview/io/vcf/VCFLoaderTest.java