source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	Jim Procter <jprocter@issues.jalview.org>
	Thu, 6 Oct 2016 00:13:56 +0000 (01:13 +0100)
committer	Jim Procter <jprocter@issues.jalview.org>
	Thu, 6 Oct 2016 00:15:35 +0000 (01:15 +0100)
commit	db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3
tree	49c7884f7cc079ddaa343ad566364673c87af099	tree \| snapshot
parent	a90e2fe3cc3b779521a81cf8de410936f3a777c1	commit \| diff
parent	4e1d9a661070768f2b74a8ef7925c38372ee83d6	commit \| diff

JAL-2089 Merge branch releases/Release_2_10_Branch to master

404 files changed:

build.xml	diff1 \|	diff2 \|	blob \| history
doc/AddingGroovySupport.html	diff1 \|	diff2 \|	blob \| history
doc/building.html	diff1 \|	diff2 \|	blob \| history
examples/appletParameters.html	diff1 \|	diff2 \|	blob \| history
examples/applets.html	diff1 \|	diff2 \|	blob \| history
examples/embedded.html	diff1 \|	diff2 \|	blob \| history
examples/formComplete.html	diff1 \|	diff2 \|	blob \| history
examples/groovy/printtitle.groovy	diff1 \|	diff2 \|	blob \| history
examples/includes/nav_jv.html	diff1 \|	diff2 \|	blob \| history
examples/javascriptLaunch.html	diff1 \|	diff2 \|	blob \| history
examples/linkedapplets_ng.html	diff1 \|	diff2 \|	blob \| history
help/help.jhm	diff1 \|	diff2 \|	blob \| history
help/helpTOC.xml	diff1 \|	diff2 \|	blob \| history
help/html/calculations/consensus.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/conservation.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/pca.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/quality.html	diff1 \|	diff2 \|	blob \| history
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help/html/calculations/referenceseq.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/scorematrices.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/sorting.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/structureconsensus.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/tree.html	diff1 \|	diff2 \|	blob \| history
help/html/calculations/treeviewer.html	diff1 \|	diff2 \|	blob \| history
help/html/colourSchemes/annotationColouring.html	diff1 \|	diff2 \|	blob \| history
help/html/colourSchemes/conservation.html	diff1 \|	diff2 \|	blob \| history
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help/html/colourSchemes/rnahelicesColouring.html	diff1 \|	diff2 \|	blob \| history
help/html/editing/index.html	diff1 \|	diff2 \|	blob \| history
help/html/features/annotation.html	diff1 \|	diff2 \|	blob \| history
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help/html/features/preferences.html	diff1 \|	diff2 \|	blob \| history
help/html/features/seqfeatures.html	diff1 \|	diff2 \|	blob \| history
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help/html/features/structurechooser.html	diff1 \|	diff2 \|	blob \| history
help/html/features/varna.html	diff1 \|	diff2 \|	blob \| history
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help/html/features/xsspannotation.html	diff1 \|	diff2 \|	blob \| history
help/html/index.html	diff1 \|	diff2 \|	blob \| history
help/html/io/export.html	diff1 \|	diff2 \|	blob \| history
help/html/io/exportseqreport.html	diff1 \|	diff2 \|	blob \| history
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help/html/io/index.html	diff1 \|	diff2 \|	blob \| history
help/html/io/modellerpir.html	diff1 \|	diff2 \|	blob \| history
help/html/io/tcoffeescores.html	diff1 \|	diff2 \|	blob \| history
help/html/keys.html	diff1 \|	diff2 \|	blob \| history
help/html/memory.html	diff1 \|	diff2 \|	blob \| history
help/html/menus/alignmentMenu.html	diff1 \|	diff2 \|	blob \| history
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help/html/menus/desktopMenu.html	diff1 \|	diff2 \|	blob \| history
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help/html/menus/wsmenu.html	diff1 \|	diff2 \|	blob \| history
help/html/na/index.html	diff1 \|	diff2 \|	blob \| history
help/html/privacy.html	diff1 \|	diff2 \|	blob \| history
help/html/releases.html	diff1 \|	diff2 \|	blob \| history
help/html/vamsas/index.html	diff1 \|	diff2 \|	blob \| history
help/html/webServices/AACon.html	diff1 \|	diff2 \|	blob \| history
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help/html/webServices/webServicesPrefs.html	diff1 \|	diff2 \|	blob \| history
help/html/whatsNew.html	diff1 \|	diff2 \|	blob \| history
resources/embl_mapping.xml	diff1 \|	diff2 \|	blob \| history
schemas/jalview.xsd	diff1 \|	diff2 \|	blob \| history
src/MCview/AppletPDBCanvas.java	diff1 \|	diff2 \|	blob \| history
src/MCview/Atom.java	diff1 \|	diff2 \|	blob \| history
src/MCview/PDBCanvas.java	diff1 \|	diff2 \|	blob \| history
src/MCview/PDBChain.java	diff1 \|	diff2 \|	blob \| history
src/MCview/PDBViewer.java	diff1 \|	diff2 \|	blob \| history
src/MCview/PDBfile.java	diff1 \|	diff2 \|	blob \| history
src/MCview/Residue.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AAFrequency.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AlignSeq.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AlignmentSorter.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AlignmentUtils.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/Conservation.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/CrossRef.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/Dna.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/Grouping.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/NJTree.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/Rna.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/SeqsetUtils.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/SequenceIdMatcher.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/StructureFrequency.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/scoremodels/FeatureScoreModel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/AlignCalcManagerI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/AlignCalcWorkerI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/AlignViewControllerI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/AlignViewportI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/FeatureRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/FeatureSettingsModelI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/FeaturesDisplayedI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/APopupMenu.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignViewport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignmentPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationColourChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationColumnChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationLabels.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationRowFilter.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AppletJmol.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/FeatureColourChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/FeatureRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/FeatureSettings.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/IdCanvas.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/IdPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/OverviewPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/ScalePanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/SeqCanvas.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/SeqPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/SequenceRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/SliderPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/TreeCanvas.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/UserDefinedColours.java	diff1 \|	diff2 \|	blob \| history
src/jalview/bin/Cache.java	diff1 \|	diff2 \|	blob \| history
src/jalview/bin/Jalview.java	diff1 \|	diff2 \|	blob \| history
src/jalview/bin/JalviewLite.java	diff1 \|	diff2 \|	blob \| history
src/jalview/bin/JalviewLiteURLRetrieve.java	diff1 \|	diff2 \|	blob \| history
src/jalview/commands/TrimRegionCommand.java	diff1 \|	diff2 \|	blob \| history
src/jalview/controller/AlignViewController.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/AlignedCodon.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/AlignedCodonFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/Alignment.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/AlignmentAnnotation.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/AlignmentI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/AlignmentView.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/CigarBase.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/ColumnSelection.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/DBRefEntry.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/DBRefSource.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/FeatureProperties.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/HiddenSequences.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/Mapping.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/PDBEntry.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SearchResults.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SeqCigar.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/Sequence.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceDummy.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceFeature.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceGroup.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/xdb/embl/EmblFeature.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/xdb/embl/EmblFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/xdb/embl/EmblSequence.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/jmol/JmolCommands.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/paradise/Annotate3D.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/rbvi/chimera/ChimeraCommands.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java	diff1 \|	diff2 \|	blob \| history
src/jalview/fts/api/FTSData.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AlignFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AlignViewport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AlignmentPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationColourChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationColumnChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationExporter.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationLabels.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationRowFilter.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AppJmol.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/BlogReader.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/ChimeraViewFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/DasSourceBrowser.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/FeatureSettings.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/FontChooser.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/SeqCanvas.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/SeqPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/SequenceFetcher.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/SliderPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/SplitFrame.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/TreeCanvas.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/gui/VamsasApplication.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/AlignFile.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/io/BioJsHTMLOutput.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/io/HtmlFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/HtmlSvgOutput.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/IdentifyFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/JSONFile.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/javascript/JSFunctionExec.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/renderer/AnnotationRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/renderer/seqfeatures/FeatureRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/schemes/RNAHelicesColour.java	diff1 \|	diff2 \|	blob \| history
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src/jalview/structures/models/AAStructureBindingModel.java	diff1 \|	diff2 \|	blob \| history
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