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

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

author	Jim Procter <jprocter@issues.jalview.org>
	Tue, 25 Oct 2016 10:49:32 +0000 (11:49 +0100)
committer	Jim Procter <jprocter@issues.jalview.org>
	Tue, 25 Oct 2016 10:49:32 +0000 (11:49 +0100)
commit	37de9310bec3501cbc6381e0c3dcb282fcaad812
tree	a6902053b5eacb0ae2b639eeb17e24060e965f87	tree \| snapshot
parent	7deae742715932ec04121b96a7cac76d0fd31bdc	commit \| diff

JAL-2089 patch broken merge to master for Release 2.10.0b1

888 files changed:

build.xml		diff \| blob \| history
doc/AddingGroovySupport.html		diff \| blob \| history
doc/AnnotationPostAnalysis.txt		diff \| blob \| history
doc/JalviewRNASupport.html		diff \| blob \| history
doc/UnitTesting.html		diff \| blob \| history
doc/biojsmsa-templates.html		diff \| blob \| history
doc/building.html		diff \| blob \| history
doc/developing.html		diff \| blob \| history
doc/i18n.html		diff \| blob \| history
doc/index.html		diff \| blob \| history
doc/newdmobj.html		diff \| blob \| history
examples/appletParameters.html		diff \| blob \| history
examples/applets.html		diff \| blob \| history
examples/css/ie6.css		diff \| blob \| history
examples/css/ie7.css		diff \| blob \| history
examples/css/reset.css		diff \| blob \| history
examples/css/style.css		diff \| blob \| history
examples/embedded.html		diff \| blob \| history
examples/formComplete.html		diff \| blob \| history
examples/groovy/JvLoadTestHarness.groovy		diff \| blob \| history
examples/groovy/JvLoadTester.groovy		diff \| blob \| history
examples/groovy/alignLoadedFile.groovy		diff \| blob \| history
examples/groovy/annotationForSelectedSequence.groovy		diff \| blob \| history
examples/groovy/annotationsascsv.groovy		diff \| blob \| history
examples/groovy/closures.groovy		diff \| blob \| history
examples/groovy/iterateOverAlignments.groovy		diff \| blob \| history
examples/groovy/parseproperties.groovy		diff \| blob \| history
examples/groovy/printtitle.groovy		diff \| blob \| history
examples/groovy/removeFeaturesByGroup.groovy		diff \| blob \| history
examples/groovy/selectColumnsByFeatureAndGroup.groovy		diff \| blob \| history
examples/groovy/sitesForSelectedColumns.groovy		diff \| blob \| history
examples/groovy/stripUniprotPrefixes.groovy		diff \| blob \| history
examples/includes/footer_jv.html		diff \| blob \| history
examples/includes/header_jv.html		diff \| blob \| history
examples/includes/nav_jv.html		diff \| blob \| history
examples/jalviewLiteJs.html		diff \| blob \| history
examples/javascript/jalview.js		diff \| blob \| history
examples/javascript/jvcontroller.js		diff \| blob \| history
examples/javascriptLaunch.html		diff \| blob \| history
examples/linkedapplets_ng.html		diff \| blob \| history
help/help.hs		diff \| blob \| history
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/calculations/consensus.html		diff \| blob \| history
help/html/calculations/conservation.html		diff \| blob \| history
help/html/calculations/pairwise.html		diff \| blob \| history
help/html/calculations/pca.html		diff \| blob \| history
help/html/calculations/quality.html		diff \| blob \| history
help/html/calculations/recoverInputdata.html		diff \| blob \| history
help/html/calculations/redundancy.html		diff \| blob \| history
help/html/calculations/referenceseq.html		diff \| blob \| history
help/html/calculations/scorematrices.html		diff \| blob \| history
help/html/calculations/sorting.html		diff \| blob \| history
help/html/calculations/structureconsensus.html		diff \| blob \| history
help/html/calculations/tree.html		diff \| blob \| history
help/html/calculations/treeviewer.html		diff \| blob \| history
help/html/colourSchemes/abovePID.html		diff \| blob \| history
help/html/colourSchemes/annotationColouring.html		diff \| blob \| history
help/html/colourSchemes/blosum.html		diff \| blob \| history
help/html/colourSchemes/buried.html		diff \| blob \| history
help/html/colourSchemes/clustal.html		diff \| blob \| history
help/html/colourSchemes/conservation.html		diff \| blob \| history
help/html/colourSchemes/helix.html		diff \| blob \| history
help/html/colourSchemes/hydrophobic.html		diff \| blob \| history
help/html/colourSchemes/index.html		diff \| blob \| history
help/html/colourSchemes/nucleotide.html		diff \| blob \| history
help/html/colourSchemes/pid.html		diff \| blob \| history
help/html/colourSchemes/purinepyrimidine.html		diff \| blob \| history
help/html/colourSchemes/rnahelicesColouring.html		diff \| blob \| history
help/html/colourSchemes/strand.html		diff \| blob \| history
help/html/colourSchemes/taylor.html		diff \| blob \| history
help/html/colourSchemes/textcolour.html		diff \| blob \| history
help/html/colourSchemes/turn.html		diff \| blob \| history
help/html/colourSchemes/user.html		diff \| blob \| history
help/html/colourSchemes/zappo.html		diff \| blob \| history
help/html/editing/index.html		diff \| blob \| history
help/html/features/annotation.html		diff \| blob \| history
help/html/features/annotationsFormat.html		diff \| blob \| history
help/html/features/bioJsonFormat.html		diff \| blob \| history
help/html/features/biojsmsa.html		diff \| blob \| history
help/html/features/chimera.html		diff \| blob \| history
help/html/features/clarguments.html		diff \| blob \| history
help/html/features/codingfeatures.html		diff \| blob \| history
help/html/features/columnFilterByAnnotation.html		diff \| blob \| history
help/html/features/commandline.html		diff \| blob \| history
help/html/features/creatinFeatures.html		diff \| blob \| history
help/html/features/cursorMode.html		diff \| blob \| history
help/html/features/dasfeatures.html		diff \| blob \| history
help/html/features/dassettings.html		diff \| blob \| history
help/html/features/editingFeatures.html		diff \| blob \| history
help/html/features/featuresFormat.html		diff \| blob \| history
help/html/features/featureschemes.html		diff \| blob \| history
help/html/features/featuresettings.html		diff \| blob \| history
help/html/features/groovy.html		diff \| blob \| history
help/html/features/hiddenRegions.html		diff \| blob \| history
help/html/features/jalarchive.html		diff \| blob \| history
help/html/features/jmol.html		diff \| blob \| history
help/html/features/multipleViews.html		diff \| blob \| history
help/html/features/newkeystrokes.html		diff \| blob \| history
help/html/features/overview.html		diff \| blob \| history
help/html/features/pdbsequencefetcher.html		diff \| blob \| history
help/html/features/pdbviewer.html		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/search.html		diff \| blob \| history
help/html/features/seqfeatures.html		diff \| blob \| history
help/html/features/seqfetch.html		diff \| blob \| history
help/html/features/seqmappings.html		diff \| blob \| history
help/html/features/splitView.html		diff \| blob \| history
help/html/features/structurechooser.html		diff \| blob \| history
help/html/features/varna.html		diff \| blob \| history
help/html/features/viewingpdbs.html		diff \| blob \| history
help/html/features/wrap.html		diff \| blob \| history
help/html/features/xsspannotation.html		diff \| blob \| history
help/html/index.html		diff \| blob \| history
help/html/io/export.html		diff \| blob \| history
help/html/io/exportseqreport.html		diff \| blob \| history
help/html/io/fileformats.html		diff \| blob \| history
help/html/io/index.html		diff \| blob \| history
help/html/io/modellerpir.html		diff \| blob \| history
help/html/io/tcoffeescores.html		diff \| blob \| history
help/html/keys.html		diff \| blob \| history
help/html/memory.html		diff \| blob \| history
help/html/menus/alignmentMenu.html		diff \| blob \| history
help/html/menus/alwannotation.html		diff \| blob \| history
help/html/menus/alwannotationpanel.html		diff \| blob \| history
help/html/menus/alwcalculate.html		diff \| blob \| history
help/html/menus/alwcolour.html		diff \| blob \| history
help/html/menus/alwedit.html		diff \| blob \| history
help/html/menus/alwfile.html		diff \| blob \| history
help/html/menus/alwformat.html		diff \| blob \| history
help/html/menus/alwselect.html		diff \| blob \| history
help/html/menus/alwview.html		diff \| blob \| history
help/html/menus/desktopMenu.html		diff \| blob \| history
help/html/menus/index.html		diff \| blob \| history
help/html/menus/popupMenu.html		diff \| blob \| history
help/html/menus/wsmenu.html		diff \| blob \| history
help/html/misc/aaproperties.html		diff \| blob \| history
help/html/misc/aminoAcids.html		diff \| blob \| history
help/html/misc/geneticCode.html		diff \| blob \| history
help/html/na/index.html		diff \| blob \| history
help/html/privacy.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/vamsas/index.html		diff \| blob \| history
help/html/webServices/AACon.html		diff \| blob \| history
help/html/webServices/JABAWS.html		diff \| blob \| history
help/html/webServices/RNAalifold.html		diff \| blob \| history
help/html/webServices/dbreffetcher.html		diff \| blob \| history
help/html/webServices/index.html		diff \| blob \| history
help/html/webServices/jnet.html		diff \| blob \| history
help/html/webServices/msaclient.html		diff \| blob \| history
help/html/webServices/newsreader.html		diff \| blob \| history
help/html/webServices/proteinDisorder.html		diff \| blob \| history
help/html/webServices/shmr.html		diff \| blob \| history
help/html/webServices/urllinks.html		diff \| blob \| history
help/html/webServices/webServicesParams.html		diff \| blob \| history
help/html/webServices/webServicesPrefs.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
jalview-jalopy.xml		diff \| blob \| history
nbbuild.xml		diff \| blob \| history
nbproject/project.xml		diff \| blob \| history
resources/embl_mapping.xml		diff \| blob \| history
resources/uniprot_mapping.xml		diff \| blob \| history
schemas/JalviewWsParamSet.xsd		diff \| blob \| history
schemas/castor-mapping.xsd		diff \| blob \| history
schemas/jalview.nodesc.properties		diff \| blob \| history
schemas/jalview.properties		diff \| blob \| history
schemas/jalview.xsd		diff \| blob \| history
schemas/jalviewJvV1.xsd		diff \| blob \| history
schemas/vamsas.xsd		diff \| blob \| history
schemas/vamsasJvV1.xsd		diff \| blob \| history
src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/AppletPDBViewer.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/Bond.java		diff \| blob \| history
src/MCview/MCMatrix.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/MCview/Residue.java		diff \| blob \| history
src/MCview/Zsort.java		diff \| blob \| history
src/castor.properties		diff \| blob \| history
src/ext/vamsas/IRegistry.java		diff \| blob \| history
src/ext/vamsas/IRegistryService.java		diff \| blob \| history
src/ext/vamsas/IRegistryServiceLocator.java		diff \| blob \| history
src/ext/vamsas/Jpred.java		diff \| blob \| history
src/ext/vamsas/JpredService.java		diff \| blob \| history
src/ext/vamsas/JpredServiceLocator.java		diff \| blob \| history
src/ext/vamsas/JpredSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/MuscleWS.java		diff \| blob \| history
src/ext/vamsas/MuscleWSService.java		diff \| blob \| history
src/ext/vamsas/MuscleWSServiceLocator.java		diff \| blob \| history
src/ext/vamsas/MuscleWSSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/RegistryServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/SeqSearchI.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceLocator.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceService.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/ServiceHandle.java		diff \| blob \| history
src/ext/vamsas/ServiceHandles.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentAnnotationUtils.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/AnnotationSorter.java		diff \| blob \| history
src/jalview/analysis/CodingUtils.java		diff \| blob \| history
src/jalview/analysis/CodonComparator.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/Finder.java		diff \| blob \| history
src/jalview/analysis/Grouping.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/ParseProperties.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SecStrConsensus.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/SequenceIdMatcher.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/analysis/WUSSParseException.java		diff \| blob \| history
src/jalview/analysis/scoremodels/FeatureScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/PIDScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SWScoreModel.java		diff \| blob \| history
src/jalview/api/AlignCalcManagerI.java		diff \| blob \| history
src/jalview/api/AlignCalcWorkerI.java		diff \| blob \| history
src/jalview/api/AlignExportSettingI.java		diff \| blob \| history
src/jalview/api/AlignViewControllerGuiI.java		diff \| blob \| history
src/jalview/api/AlignViewControllerI.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/AlignmentViewPanel.java		diff \| blob \| history
src/jalview/api/BuildDetailsI.java		diff \| blob \| history
src/jalview/api/ComplexAlignFile.java		diff \| blob \| history
src/jalview/api/FeatureRenderer.java		diff \| blob \| history
src/jalview/api/FeatureSettingsControllerI.java		diff \| blob \| history
src/jalview/api/FeatureSettingsModelI.java		diff \| blob \| history
src/jalview/api/FeaturesDisplayedI.java		diff \| blob \| history
src/jalview/api/OOMHandlerI.java		diff \| blob \| history
src/jalview/api/RotatableCanvasI.java		diff \| blob \| history
src/jalview/api/SequenceRenderer.java		diff \| blob \| history
src/jalview/api/SequenceStructureBinding.java		diff \| blob \| history
src/jalview/api/SplitContainerI.java		diff \| blob \| history
src/jalview/api/StructureSelectionManagerProvider.java		diff \| blob \| history
src/jalview/api/ViewStyleI.java		diff \| blob \| history
src/jalview/api/analysis/ScoreModelI.java		diff \| blob \| history
src/jalview/api/analysis/ViewBasedAnalysisI.java		diff \| blob \| history
src/jalview/api/structures/JalviewStructureDisplayI.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColumnChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationRowFilter.java		diff \| blob \| history
src/jalview/appletgui/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/AppletJmolBinding.java		diff \| blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/EditNameDialog.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/ExtJmol.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureRenderer.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/Finder.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdCanvas.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/appletgui/JVDialog.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/PaintRefresher.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/RotatableCanvas.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SequenceRenderer.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/SplitFrame.java		diff \| blob \| history
src/jalview/appletgui/TitledPanel.java		diff \| blob \| history
src/jalview/appletgui/Tooltip.java		diff \| blob \| history
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/BuildDetails.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/JalviewLiteURLRetrieve.java		diff \| blob \| history
src/jalview/commands/ChangeCaseCommand.java		diff \| blob \| history
src/jalview/commands/CommandI.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/commands/OrderCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapColCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapsCommand.java		diff \| blob \| history
src/jalview/commands/SlideSequencesCommand.java		diff \| blob \| history
src/jalview/commands/TrimRegionCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/controller/FeatureSettingsController.java		diff \| blob \| history
src/jalview/controller/FeatureSettingsControllerGuiI.java		diff \| blob \| history
src/jalview/datamodel/ASequence.java		diff \| blob \| history
src/jalview/datamodel/ASequenceI.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodon.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentExportData.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/BinaryNode.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/CigarArray.java		diff \| blob \| history
src/jalview/datamodel/CigarBase.java		diff \| blob \| history
src/jalview/datamodel/CigarCigar.java		diff \| blob \| history
src/jalview/datamodel/CigarSimple.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/FeatureProperties.java		diff \| blob \| history
src/jalview/datamodel/GraphLine.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/IncompleteCodonException.java		diff \| blob \| history
src/jalview/datamodel/Mapping.java		diff \| blob \| history
src/jalview/datamodel/NodeTransformI.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/Provenance.java		diff \| blob \| history
src/jalview/datamodel/ProvenanceEntry.java		diff \| blob \| history
src/jalview/datamodel/RnaViewerModel.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/SecondaryStructureAnnotation.java		diff \| blob \| history
src/jalview/datamodel/SeqCigar.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceCollectionI.java		diff \| blob \| history
src/jalview/datamodel/SequenceDummy.java		diff \| blob \| history
src/jalview/datamodel/SequenceFeature.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/SequenceNode.java		diff \| blob \| history
src/jalview/datamodel/SequencePoint.java		diff \| blob \| history
src/jalview/datamodel/StructureViewerModel.java		diff \| blob \| history
src/jalview/datamodel/UniprotEntry.java		diff \| blob \| history
src/jalview/datamodel/UniprotFile.java		diff \| blob \| history
src/jalview/datamodel/UniprotProteinName.java		diff \| blob \| history
src/jalview/datamodel/UniprotSequence.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblError.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblFeature.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblFile.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblSequence.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/Qualifier.java		diff \| blob \| history
src/jalview/exceptions/JalviewException.java		diff \| blob \| history
src/jalview/exceptions/NoFileSelectedException.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/JmolCommands.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/ChimeraCommands.java		diff \| blob \| history
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