jalview

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JAL-3201 restore group colours correctly from project

JAL-3201 JAL-2386 don't pre-select 'apply to all groups'

JAL-3201 group colour schemes distinct instances

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    /test/jalview/gui/AlignViewportTest.java
JAL-3200 fast lookup of DSSP3 notation

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    /test/jalview/schemes/ResiduePropertiesTest.java
JAL-3198 don't recalculate group conservation for Id Panel selection

JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2915 don't recalculate Overview on scroll to position, ever!

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    /src/jalview/gui/AlignmentPanel.java
JAL-2738 don't set AF as feature score

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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3018 Ensembl version updated to 9.0

JAL-3063 correct handling of absent choice element in DBRef Mapping

JAL-3116 clear out whitespace when materialising Sequence object from Uniprot XML

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/FeatureSettings.java
JAL-1767 test that changing view association for PCA panel can be restored

JAL-1767 refactor associated view logic to public method and synchronise PCAPanel.av/ap with RotateableCanvac.ap/av

JAL-1767 patch buggy PCA view association test

JAL-3186 remove Variable Colour from popup menu

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/FeatureSettings.java
JAL-3186 remove duplicate message keys

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    /resources/lang/Messages_es.properties
JAL-2069 clear any error colour when setting threshold from slider

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    /src/jalview/gui/FeatureTypeSettings.java
JAL-1767 failing test to check if the PCA view association is correctly saved and restored

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

JAL-3063 remove stale JAXB binding POJO

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

JAL-3063 - ant task for regenerating JAXB schema - could be optimised further

JAL-1889 additional test for clover-added fields

JAL-1889 ignore 'synthetic' fields added for jacoco

JAL-1767 minimise local variable scope

JAL-1767 port save/load PCA panel to JAXB - JAL-3063

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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/gui/RotatableCanvas.java
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/DoubleMatrix.java
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    /src/jalview/xml/binding/jalview/DoubleVector.java
  1. … 15 more files in changeset.
JAL-3171 JAL-3063 merge updates from JAL-1767

Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_across_views

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/gui/PCAPanel.java
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    /test/jalview/io/Jalview2xmlTests.java
JAL-2791 JAL-2808 correct Javadoc for api method