jalview

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JAL=3121 more data format validation/tests, help text tweak

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    /help/help/html/features/featuresFormat.html
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    /src/jalview/io/gff/GffHelperBase.java
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    /test/jalview/io/gff/GffHelperBaseTest.java
JAL-3121 update help page for GFF column 9 nested attributes

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    /help/help/html/features/featuresFormat.html
JAL-3121 'attributes map' in GFF3 without special 'jvmap_' token

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    /src/jalview/io/gff/GffHelperBase.java
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    /test/jalview/io/FeaturesFileTest.java
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    /test/jalview/io/gff/GffHelperBaseTest.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
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    /test/jalview/util/StringUtilsTest.java
JAL-3121 slightly cleaner parsing of, and unit test for, map attributes

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    /src/jalview/io/gff/Gff2Helper.java
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    /src/jalview/io/gff/GffHelperBase.java
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    /test/jalview/io/FeaturesFileTest.java
Merge branch 'develop' into feature/JAL-3121gffAttributeMap

JAL-3187 case-insensitive codon variant calculation

JAL-3121 round trip GFF attributes including map-valued attributes

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/io/FeaturesFile.java
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    /src/jalview/io/gff/GffHelperBase.java
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    /src/jalview/util/StringUtils.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /test/jalview/io/FeaturesFileTest.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
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    /test/jalview/util/StringUtilsTest.java
JAL-3187 one more obsolete method removed

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3187 minor code tidying, todo removal

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
JAL-3375 format validate VCF Integer and Float fields

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3375 ignore '.' values for VCF data

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    /test/jalview/io/vcf/VCFLoaderTest.java
Merge branch 'develop' into feature/JAL-3187linkedFeatures

JAL-2987 tolerate null double values when formatting JTable

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

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/CrossRefAction.java
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    /test/jalview/gui/AlignFrameTest.java