jalview

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JAL-2698 11th hour release today

Merge branch 'bug/JAL-2831' into develop

    • -69
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    /src/jalview/gui/SeqCanvas.java
JAL-2759 Move isVisible to use cursor

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    • +4
    /src/jalview/datamodel/HiddenColumns.java
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    • +0
    /src/jalview/datamodel/HiddenColumns.java
JAL-2759 Update tests

    • -0
    • +5
    /src/jalview/datamodel/HiddenColumns.java
JAL-2808 set (read-only) condition text field as disabled

JAL-2759 Convert reveal to use cursor

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    • +25
    /src/jalview/datamodel/HiddenColumns.java
JAL-2759 HiddenColumnsCursor tests

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    • +49
    /src/jalview/datamodel/HiddenColumns.java
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    • +114
    /test/jalview/datamodel/HiddenColumnsCursorTest.java
JAL-281 added menu items and listeners to load from URL/Db

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    • +37
    /src/jalview/jbgui/GAlignFrame.java
JAL-281 changed load associated tree GUI item to menu selection

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    /src/jalview/jbgui/GAlignFrame.java
JAL-2822 rejig new dataset after edit computation so it works for test cases

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    • +25
    /src/jalview/commands/EditCommand.java
JAL-2822 fix comedy typo in test

Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

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    • +0
    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
JAL-2541 JAL-2829 JAL-2830 JAL-2822 catch all release note entry for sequence feature relocation

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

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    • +50
    /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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    • +19
    /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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    • +19
    /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
    • -0
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    /src/jalview/ext/treeviewer/ExternalTreeI.java
    • -0
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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
    • -0
    • +36
    /src/jalview/ext/archaeopteryx/Tree.java
    • -0
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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

    • -22
    • +43
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-2835 test updated for colour by 'nested attribute'