jalview

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JAL-3099 use Alignment.getVisibleWidth() where wanted

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/gui/AlignmentPanel.java
JAL-3099 new method AlignmentI.getVisibleWidth()

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentI.java
JAL-3097 adjust viewport width on hiding columns

JAL-3108 fix concurrency bug in Reveal action handler

JAL-3080 remove tree partition if no groups created

JAL-3078 reset Tree font (only!) on Cancel

Merge branch 'task/JAL-3047_clovercoverage' into develop

JAL-3047 don't set classes unconditionally (forgot to delete it in earlier patch)

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

Merge branch 'task/JAL-3047_clovercoverage' into develop

JAL-3047 don’t let the makedist task complete if a clover build was performed

JAL-3047 ‘cloverclasses’ build directory for instrumented classes (allow incremental compile and avoid releasing instrumented classes in production builds)

JAL-3047 enable clover for testng

JAL-3047 ignore clover output dir

JAL-3047 ant -Dclover.jar=../path/to/clover/lib/clover.jar to enable clover for testng ant task

Merge branch 'task/JAL-3042_remove_SimpleDocument_dependency' into develop

JAL-3042 remove mention of adjustable search box history length from docs

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    /help/html/features/searchclearhist.png
JAL-3035 removed jdas in libs documentation and noted spring modules as candidates for removal

Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

JAL-3035 documentation in 2.11 release notes (and 2.11 fictional release date)

JAL-3035 remove DAS UI documentation

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    /help/html/features/clarguments.html
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    /help/html/features/dasfeatures.html
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    /help/html/features/dassettings.html
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    /help/html/menus/alignmentMenu.html
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    /help/html/webServices/dbreffetcher.html
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

JAL-3035 - jalview-das is no more ! - jsdas lib removed - DAS settings panel deleted (Feature settings pane has no tabs now) - all code for wrapping DAS sources and retrieving sequences and features from them is gone - test methods/main methods have been de-dasified or removed if their only purpose was to test DAS source discovery - fancy sorting code to account for DAS sequence source names has been removed

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    /src/jalview/gui/DasSourceBrowser.java
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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/gui/JDatabaseTree.java
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    /src/jalview/gui/SequenceFetcher.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/ws/DBRefFetcher.java
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    /src/jalview/ws/SequenceFetcher.java
  1. … 8 more files in changeset.
JAL-3035 (unrelated) random XML error in nbbuild.xml

JAL-3042 don't allow user to change default history length for an input box

JAL-2755 correct Javadoc and error handling

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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
JAL-3013 ensure Chimera as a symlink gets resolved

JAL-2808 update test for revised treatment of 'mixed type' attribute values

JAL-3019 correctly form toRange of 'traversed' MapList

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    /test/jalview/util/MapListTest.java
JAL-3018 updated REST versions to 6.3