jalview

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JAL-3143 update unit test for ID -> id change

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    /test/jalview/analysis/AlignmentUtilsTests.java
JAL-3143 format alleles array for feature description

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    /src/jalview/ext/ensembl/EnsemblFeatures.java
JAL-3143 'id' not 'ID' attribute drives generation of variant link

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3143 unit tests updated for code changes!

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    /test/jalview/ext/ensembl/EnsemblCdsTest.java
JAL-3143 comma-delimited feature attributes for alleles, clinical_significance

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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/util/JSONUtils.java
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    /test/jalview/util/JSONUtilsTest.java
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF

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    /src/jalview/ext/ensembl/EnsemblCdna.java
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    /src/jalview/ext/ensembl/EnsemblCds.java
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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblGenome.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-2843 tweaks to help text for filters

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    /help/html/features/featuresFormat.html
JAL-2843 help text for colour by attribute, feature filters

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    /help/html/features/featuresFormat.html
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    /src/jalview/schemes/FeatureColour.java
Merge branch 'bug/JAL-3120restoreFeatureColour' into develop

JAL-3120 preserve plain colour value when changing to Colour by Label

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

Merge branch 'cherrypick/JAL-2808_notabs' into develop

JAL-2865 release notes

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

Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

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

JAL-1551 reinstated Save actions

JAL-3112 increased TEST_TIMEOUT to 9000ms - needed after inclusion discovered class path entries

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    /test/jalview/bin/CommandLineOperations.java
JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview

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    /test/jalview/bin/CommandLineOperations.java
    • binary
    /utils/classgraph-4.1.6.jar
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

Merge branch 'releases/Release_2_11_Branch' into merge/JAL-3091_develop_211

Merge branch 'develop' into releases/Release_2_11_Branch JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge

JAL-3091 changed release date to 10th September - tweaked release notes.

JAL-3106 normalise extension before checking if it is '.jar' when constructing fileformat/extension name index

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    /src/jalview/io/JalviewFileChooser.java
JAL-3107 update any group associated annotation rows when a new group is created

JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar

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    /doc/patching-vaqua.txt
    • binary
    /lib/VAqua5-patch.jar
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    /utils/InstallAnywhere/Jalview.iap_xml
JAL-2988 if selected file is null (On Java 10/OSX - happens if user has entered text after selecting a file), try and get the filename from the UI. If no file can be gotten, cancel the save operation

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    /src/jalview/io/JalviewFileChooser.java
JAL-2988 workaround: overload getSelectedFile() because calling setSelectedFile(..) results in getSelectedFile()==null on OSX/Java 10/VAqua4/5.

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    /src/jalview/io/JalviewFileChooser.java