jalview

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Merge branch 'bug/JAL-2829deleteCharsWithGaps' into develop

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    /src/jalview/datamodel/Sequence.java
JAL-2822 verify start/end is correctly updated and restored after edit, undo, and redo

JAL-2822 stash start/end before setSequence (which will modify ‘end’) and catch cases when dataset sequence and start/end limits change

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    /src/jalview/commands/EditCommand.java
JAL-2541 JAL-2822 verify limits for edited sequence, undone edit, and redone edit.

JAL-2069 fix minor bugs in variable setting

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    /src/jalview/gui/FeatureColourChooser.java
Merge branch 'develop' into features/JAL-1793VCF

JAL-2805 made needed color set methods public

JAL-2831 Removed unwanted hidden sequences checks

JAL-2805 expanded tree and treenode interfaces

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    /src/jalview/ext/archaeopteryx/Tree.java
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    /src/jalview/ext/archaeopteryx/TreeNode.java
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    /src/jalview/ext/treeviewer/ExternalTree.java
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    /src/jalview/ext/treeviewer/ExternalTreeI.java
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    /src/jalview/ext/treeviewer/ExternalTreeNodeI.java
JAL-2805 loads of file reorganizing, interfaces expanded

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    /hs_err_pid28190.log
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    /src/jalview/ext/archaeopteryx/JalviewBinding.java
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    /src/jalview/ext/archaeopteryx/Tree.java
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    /src/jalview/ext/archaeopteryx/TreeNode.java
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    /src/jalview/ext/forester/DataConversions.java
  1. … 12 more files in changeset.
JAL-2069 removed unused and redundant thresholdIsMinMax

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    /src/jalview/api/FeatureColourI.java
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    /src/jalview/schemes/FeatureColour.java
JAL-2816 JAL-2835 additional tests to include colour/filter by attribute

JAL-2842 remove infinite loop in cursor move

JAL-2835 update test for array-valued attribute name

JAL-2835 update test for CSQ data held as a Map

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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-2835 test updated for colour by 'nested attribute'

JAL-2816 tests for findFeaturesAtColumn

in progress

added -rs option

added -rs option

JAL-2831 Don't show cursor if position in hidden region

Merge branch 'bug/JAL-2811' into bug/JAL-2831

JAL-2816 exclude filtered / thresholded out features when finding

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    /src/jalview/schemes/FeatureColour.java
JAL-2811 Updated following review

JAL-2840 fix wrapped scrolling when using cursor at a hidden region

JAL-2834 JAL-2836 temporarily disabled wrapped mode fastpaint

JAL-2835 spike updated with latest

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    /help/html/features/pdbseqfetcher.png
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    /help/html/features/uniprotseqfetcher.png
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    /lib/groovy-all-2.4.12-indy.jar
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    /resources/lang/Messages_es.properties
  1. … 40 more files in changeset.
JAL-2835 take all CSQ fields; catch invalid field match patterns

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    /src/jalview/io/vcf/VCFLoader.java
JAL-2835 support filter/colour by nested attribute names

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    /src/jalview/gui/FeatureColourChooser.java
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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/schemes/FeatureColour.java
JAL-2835 code tidy (generic type constructors)