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jim procter <j.procter@dundee.ac.uk> in jalview

JAL-4071 colour rows according to simple/graduated feature colour, beginning of support for complement features

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    /examples/groovy/featuresCounter.groovy
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/FeatureSetCounterI.java
JAL-4071 first working prototype

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    /src/jalview/api/FeatureRenderer.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/VisibleFeaturesAnnotationTracks.java
JAL-4071 boring GUI bits - add togglable menu item for show/hide sequence feature counts and viewModel/viewStyleI methods

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/jbgui/GAlignFrame.java
JAL-518 refactored groovy script into main codebase as an Edit Command and alignment view controller method. Left and Right Justify operations now in Edit menu on alignment window and selection popup.

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    /src/jalview/api/AlignViewControllerI.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/commands/JustifyLeftOrRightCommand.java
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    /src/jalview/jbgui/GAlignFrame.java
Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

JAL-4065 release notes for JAL-4061 JAL-4062

JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke

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    /help/help/html/menus/alignmentMenu.html
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    /src/jalview/jbgui/GAlignFrame.java
JAL-4061 JAL-4062 documentation and button labels.. will need revising !

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    /help/help/html/features/search.html
JAL-4061 use alignment panel’s feature renderer to limit search to just the visible features

JAL-4061 support incremental search of features

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    /test/jalview/analysis/FinderTest.java
JAL-4061 tests, bugfixes and TODOs for matching feature(s) and descriptions incrementally

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    /test/jalview/analysis/FinderTest.java
JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequences() to clipboard

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    /src/jalview/api/AlignViewControllerI.java
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    /src/jalview/datamodel/SearchResults.java
Merge branch 'develop' into features/JAL-4061_and_JAL-4062_findselectfeatures

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4065 release notes for JAL-4014 and JAL-4063 in 2.11.2.5

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4065 - new release notes featuring JAL-3612 fix

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    /help/markdown/releases/release-2_11_2_5.md
Merge branch 'bug/JAL-3612_overviewFeatureOrdering' into develop

JAL-4061 JAL-4062 button in Find dialog to copy highlighted regions to clipboard

JAL-4061 JAL-4062 Find can now search features

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    /src/jalview/analysis/Finder.java
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    /test/jalview/analysis/FinderTest.java
JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with Jmol API to handle double precision structure data

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    /j11lib/Jmol-15.2.69-NOLOG4J.jar
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    /j8lib/Jmol-15.2.69-NOLOG4J.jar
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolParser.java
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    /src/mc_view/AppletPDBCanvas.java
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    /utils/jalviewjs/libjs/jmol-app.zip
JAL-3059 upgrade Jmol from 14.31.53 to 15.2.69 (double precision) - required patches to structure data related classes and Jmol API implementors for float->double

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    /j11lib/Jmol-15.2.69-NOLOG4J.jar
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    /j8lib/Jmol-15.2.69-NOLOG4J.jar
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolParser.java
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    /src/mc_view/AppletPDBCanvas.java
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    /test/jalview/ext/jmol/JmolViewerTest.java
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    /utils/jalviewjs/libjs/jmol-app.zip
JAL-3059 bump version and Upgrade swingjs to 3.3.1

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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt~merged
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt~merged_0
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    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
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    /swingjs/ver/3.3.1/SwingJS-site.zip
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    /swingjs/ver/3.3.1/net.sf.j2s.core.jar
JAL-4059 bump version and Upgrade swingjs to 3.3.1

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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt~merged
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt~merged_0
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    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
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    /swingjs/ver/3.3.1/SwingJS-site.zip
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    /swingjs/ver/3.3.1/net.sf.j2s.core.jar
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4046 release on 9th August 2022

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4046 JAL-3993 imports reformatting

JAL-4046 JAL-3993 patch for 2.11.2.4 release

JAL-4046 release notes for JAL-3991