jalview

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JAL-2745 update www.ebi.ac.uk to https

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    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2738 separate thread to load VCF; update FeatureSettings when done

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    /src/jalview/io/vcf/VCFLoader.java
Merge branch 'develop' into features/JAL-1793VCF

JAL-2647 more iterators

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/gui/VamsasApplication.java
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    /test/jalview/analysis/DnaTest.java
JAL-2036 set menus after fully loading AlignFrame

JAL-1796 GeneLociI as distinguished DBRefEntry

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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/datamodel/GeneLoci.java
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    /src/jalview/datamodel/GeneLociI.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-2744 simple Feature Details report from Popup menu

JAL-2744 refactor PopupMenu constructor to enable adding feature details

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    /test/jalview/gui/PopupMenuTest.java
proof of concept for passing tree data to archaeopteryx

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    /.settings/org.eclipse.jdt.core.prefs
JAL-2674 Removing most calls to getHiddenColumnsCopy

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    /src/jalview/datamodel/HiddenColumns.java
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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-2674 tidied up CigarArray

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    /src/jalview/datamodel/CigarArray.java
Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

JAL-2742 uncomment test

JAL-2674 uncomment test

Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

Conflicts:

src/jalview/datamodel/CigarArray.java

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    /src/jalview/datamodel/CigarArray.java
JAL-2742 fixed

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    /src/jalview/datamodel/CigarArray.java
JAL-2742 CigarArray constructor unit test

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    /test/jalview/datamodel/CigarArrayTest.java
JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator

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    /src/jalview/datamodel/CigarArray.java
JAL-2674 more List<int[]> -> HiddenColumns copy changes

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    /src/jalview/gui/AnnotationLabels.java
JAL-2674 Unit test for new copy constructor.

JAL-2674 Changes to pasting

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2738 transfer VCF variant features to CDS sequences

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    /src/jalview/io/vcf/VCFLoader.java
JAL-2738 JAL-2154 add DBRef from transcript to synthesized CDS and vice versa

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    /src/jalview/analysis/AlignmentUtils.java
Merge remote-tracking branch 'origin/bug/JAL-2740' into feature/JAL-2674take2

JAL-2740 additional unit testing

Merge remote-tracking branch 'origin/bug/JAL-2740' into feature/JAL-2674take2

JAL-2740 removed unwanted code, added unit test

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    /src/jalview/gui/AnnotationColumnChooser.java
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    /test/jalview/gui/AnnotationColumnChooserTest.java
JAL-2674 HiddenColumns interface tidies

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 Added iterators and associated tests and benchmarks

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2738 unit test for reverse strand gene

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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /test/jalview/io/vcf/VCFLoaderTest.java