jalview

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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    /.externalToolBuilders/Help Indices Jalview Release [Builder].launch
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    /.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch
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    /.externalToolBuilders/Jalview Release indices [Builder].launch
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    /.settings/org.eclipse.jdt.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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hard-codes workingDir for TestNG for unknown necessity.

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    /build.Bob-Windows.xml
developer note pnly

*

* BH Note: It is critical that any call to

* AlignViewportI.setGlobalColourScheme is followed closely, if not

* immediately, by a call to AlignPanel.repaint(true, true) so that

the

* overview is updated. When that happens, the sequence overview color

caches

* are cleared.

*

JAL-3397 JAL-3253-applet

TEMPORARY disabling of NCList due to incompatibility with API in TestNG.

JAL-3253-applet no-NCList IntervalStore fixes

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    /src/intervalstore/nonc/IntervalStore.java
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    /src/jalview/renderer/OverviewResColourFinder.java
JAL-3423 testNG fixes for Windows

- \r\n, slightly differerent font metrics

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    /test/jalview/analysis/TestAlignSeq.java
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    /test/jalview/gui/SeqCanvasTest.java
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    /test/jalview/math/RotatableMatrixTest.java
JAL-3423 testNG fix for revised tooltip html format

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    /test/jalview/gui/JvSwingUtilsTest.java
Transpiler update fixes nuisance null-pointer error message when .j2s is set to disabled.

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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3423 TestNG test bugs

PDBEntry needs to normalize file names under Windows, particularly for

TestNG tests.

JAL-3423 TestNG test bugs

Cache logger not initializing early enough for some TestNG tests.

JAL-3422 JAL-3253-applet

SwingJS-site.zip fix for FontChooser combobox missing all text and

dropdown.

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    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3417 prototype sdppred calculation as groovy script

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    /examples/groovy/sdppred_testing.groovy
JAL-3417 access to consensus,conservation,cdsprofile and rnastrucconsensus calculation objects moved from AlignViewportI to AnnotatedCollectionI. AlignViewport methods left, but profiles etc are now stored on Alignment. SequenceGroups can now have their own RNA structure consensus, etc, too.

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentI.java
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    /src/jalview/datamodel/SequenceGroup.java
JAL-3417 findOrCreateAnnotation is designed to make unique rows based on Label+calcId, not Label+description. Also pass in all refs to ensure they are preserved!

JAL-3141 correct cast of spinner value

JAL-3121 slightly cleaner parsing of, and unit test for, map attributes

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    /src/jalview/io/gff/Gff2Helper.java
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    /src/jalview/io/gff/GffHelperBase.java
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    /test/jalview/io/FeaturesFileTest.java
Merge branch 'develop' into feature/JAL-3121gffAttributeMap

JAL-3187 case-insensitive codon variant calculation

JAL-3121 round trip GFF attributes including map-valued attributes

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/io/FeaturesFile.java
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    /src/jalview/io/gff/GffHelperBase.java
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    /src/jalview/util/StringUtils.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /test/jalview/io/FeaturesFileTest.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
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    /test/jalview/util/StringUtilsTest.java
JAL-3187 one more obsolete method removed

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3187 one more obsolete method removed

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3187 minor code tidying, todo removal

JAL-3390 unit tests for buildShowStructuresCommand() (Jmol and Chimera)

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/util/StructureCommands.java
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    /test/jalview/ext/jmol/JalviewJmolBindingTest.java
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    /test/jalview/ext/rbvi/chimera/JalviewChimeraBindingTest.java
Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

JAL-3235 -Dtestng-verbosity=10 to trace execution of TestNG tests

JAL-3253 fix scrollTo termination check.

JAL-3390 JAL-3400 revised commands to show structure / hide chains

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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3418 debug testng execution - verbosity=10

JAL-3364 tweaks to override of FIGURE_FIXEDIDWIDTH for split frame image

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    /src/jalview/gui/AlignmentPanel.java
JAL-3364 align split frame sequence panels with wrapped view scale left

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    /src/jalview/gui/SplitFrame.java