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

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

author	jprocter <jprocter@compbio.dundee.ac.uk>
	Wed, 3 Oct 2012 10:49:43 +0000 (11:49 +0100)
committer	jprocter <jprocter@compbio.dundee.ac.uk>
	Wed, 3 Oct 2012 10:49:43 +0000 (11:49 +0100)
commit	b57a02c25e335d033c97f8a6bacd6b54f62bd2b6
tree	820c36b7c5cfbba54198cd2fc318d6b859578073	tree \| snapshot
parent	1cc81e06ac2faa5ee4b8879e9fa019956e34259f	commit \| diff

formatting

378 files changed:

src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.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/Rna.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/api/AlignCalcManagerI.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/AlignmentViewPanel.java		diff \| blob \| history
src/jalview/api/RotatableCanvasI.java		diff \| blob \| history
src/jalview/api/StructureSelectionManagerProvider.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/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.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/ExtJmol.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/IdPanel.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/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/binding/Alignment.java		diff \| blob \| history
src/jalview/binding/Annotation.java		diff \| blob \| history
src/jalview/binding/AnnotationElement.java		diff \| blob \| history
src/jalview/binding/Colour.java		diff \| blob \| history
src/jalview/binding/Feature.java		diff \| blob \| history
src/jalview/binding/FeatureSettings.java		diff \| blob \| history
src/jalview/binding/Features.java		diff \| blob \| history
src/jalview/binding/JGroup.java		diff \| blob \| history
src/jalview/binding/JSeq.java		diff \| blob \| history
src/jalview/binding/JalviewModel.java		diff \| blob \| history
src/jalview/binding/JalviewModelSequence.java		diff \| blob \| history
src/jalview/binding/JalviewUserColours.java		diff \| blob \| history
src/jalview/binding/Pdbentry.java		diff \| blob \| history
src/jalview/binding/PdbentryItem.java		diff \| blob \| history
src/jalview/binding/Pdbids.java		diff \| blob \| history
src/jalview/binding/Property.java		diff \| blob \| history
src/jalview/binding/Sequence.java		diff \| blob \| history
src/jalview/binding/SequenceSet.java		diff \| blob \| history
src/jalview/binding/SequenceType.java		diff \| blob \| history
src/jalview/binding/Setting.java		diff \| blob \| history
src/jalview/binding/Tree.java		diff \| blob \| history
src/jalview/binding/UserColourScheme.java		diff \| blob \| history
src/jalview/binding/UserColours.java		diff \| blob \| history
src/jalview/binding/VAMSAS.java		diff \| blob \| history
src/jalview/binding/VamsasModel.java		diff \| blob \| history
src/jalview/binding/Viewport.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.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/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/FeatureProperties.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceCollectionI.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/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/JmolCommands.java		diff \| blob \| history
src/jalview/ext/varna/JalviewVarnaBinding.java		diff \| blob \| history
src/jalview/ext/varna/VarnaCommands.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppJmolBinding.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/DasSourceBrowser.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/IProgressIndicator.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JalviewChangeSupport.java		diff \| blob \| history
src/jalview/gui/JalviewDialog.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PaintRefresher.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/RestInputParamEditDialog.java		diff \| blob \| history
src/jalview/gui/RestServiceEditorPane.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/TextColourChooser.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/ViewSelectionMenu.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AlignmentProperties.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/ClustalFile.java		diff \| blob \| history
src/jalview/io/FeaturesFile.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/PileUpfile.java		diff \| blob \| history
src/jalview/io/SequenceAnnotationReport.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/TCoffeeScoreFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/packed/DataProvider.java		diff \| blob \| history
src/jalview/io/packed/JalviewDataset.java		diff \| blob \| history
src/jalview/io/packed/ParsePackedSet.java		diff \| blob \| history
src/jalview/io/packed/SimpleDataProvider.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/javascript/JSFunctionExec.java		diff \| blob \| history
src/jalview/javascript/JalviewLiteJsApi.java		diff \| blob \| history
src/jalview/javascript/JsCallBack.java		diff \| blob \| history
src/jalview/javascript/JsSelectionSender.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GRestInputParamEditDialog.java		diff \| blob \| history
src/jalview/jbgui/GRestServiceEditorPane.java		diff \| blob \| history
src/jalview/jbgui/GRnaStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/jbgui/GWebserviceInfo.java		diff \| blob \| history
src/jalview/jbgui/GWsPreferences.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/AwtRenderPanelI.java		diff \| blob \| history
src/jalview/schemabinding/version2/AlcodMap.java		diff \| blob \| history
src/jalview/schemabinding/version2/Alcodon.java		diff \| blob \| history
src/jalview/schemabinding/version2/AlcodonFrame.java		diff \| blob \| history
src/jalview/schemabinding/version2/Annotation.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/AnnotationElement.java		diff \| blob \| history
src/jalview/schemabinding/version2/CalcIdParam.java		diff \| blob \| history
src/jalview/schemabinding/version2/Colour.java		diff \| blob \| history
src/jalview/schemabinding/version2/DBRef.java		diff \| blob \| history
src/jalview/schemabinding/version2/Feature.java		diff \| blob \| history
src/jalview/schemabinding/version2/FeatureSettings.java		diff \| blob \| history
src/jalview/schemabinding/version2/Features.java		diff \| blob \| history
src/jalview/schemabinding/version2/Group.java		diff \| blob \| history
src/jalview/schemabinding/version2/HiddenColumns.java		diff \| blob \| history
src/jalview/schemabinding/version2/JGroup.java		diff \| blob \| history
src/jalview/schemabinding/version2/JSeq.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewModel.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewModelSequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewUserColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListFrom.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListTo.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListType.java		diff \| blob \| history
src/jalview/schemabinding/version2/Mapping.java		diff \| blob \| history
src/jalview/schemabinding/version2/MappingChoice.java		diff \| blob \| history
src/jalview/schemabinding/version2/OtherData.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbentry.java		diff \| blob \| history
src/jalview/schemabinding/version2/PdbentryItem.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbids.java		diff \| blob \| history
src/jalview/schemabinding/version2/Property.java		diff \| blob \| history
src/jalview/schemabinding/version2/Sequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceSet.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceSetProperties.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceType.java		diff \| blob \| history
src/jalview/schemabinding/version2/Setting.java		diff \| blob \| history
src/jalview/schemabinding/version2/StructureState.java		diff \| blob \| history
src/jalview/schemabinding/version2/ThresholdLine.java		diff \| blob \| history
src/jalview/schemabinding/version2/Tree.java		diff \| blob \| history
src/jalview/schemabinding/version2/UserColourScheme.java		diff \| blob \| history
src/jalview/schemabinding/version2/UserColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/VAMSAS.java		diff \| blob \| history
src/jalview/schemabinding/version2/VamsasModel.java		diff \| blob \| history
src/jalview/schemabinding/version2/Viewport.java		diff \| blob \| history
src/jalview/schemabinding/version2/WebServiceParameterSet.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/Blosum62ColourScheme.java		diff \| blob \| history
src/jalview/schemes/BuriedColourScheme.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeI.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/CovariationColourScheme.java		diff \| blob \| history
src/jalview/schemes/HelixColourScheme.java		diff \| blob \| history
src/jalview/schemes/HydrophobicColourScheme.java		diff \| blob \| history
src/jalview/schemes/NucleotideColourScheme.java		diff \| blob \| history
src/jalview/schemes/PIDColourScheme.java		diff \| blob \| history
src/jalview/schemes/PurinePyrimidineColourScheme.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColourChooser.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/ScoreColourScheme.java		diff \| blob \| history
src/jalview/schemes/ScoreMatrix.java		diff \| blob \| history
src/jalview/schemes/StrandColourScheme.java		diff \| blob \| history
src/jalview/schemes/TCoffeeColourScheme.java		diff \| blob \| history
src/jalview/schemes/TurnColourScheme.java		diff \| blob \| history
src/jalview/schemes/ZappoColourScheme.java		diff \| blob \| history
src/jalview/structure/AlignmentViewPanelListener.java		diff \| blob \| history
src/jalview/structure/SecondaryStructureListener.java		diff \| blob \| history
src/jalview/structure/StructureListener.java		diff \| blob \| history
src/jalview/structure/StructureMappingcommandSet.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structure/VamsasListener.java		diff \| blob \| history
src/jalview/structure/VamsasSource.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/Comparison.java		diff \| blob \| history
src/jalview/util/ParseHtmlBodyAndLinks.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/PCAModel.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/workers/AlignCalcWorker.java		diff \| blob \| history
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/workers/ConservationThread.java		diff \| blob \| history
src/jalview/workers/StrucConsensusThread.java		diff \| blob \| history
src/jalview/ws/AWSThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/DasSequenceFeatureFetcher.java		diff \| blob \| history
src/jalview/ws/EnfinEnvision2OneWay.java		diff \| blob \| history
src/jalview/ws/JobStateSummary.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/WSMenuEntryProviderI.java		diff \| blob \| history
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src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java		diff \| blob \| history
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src/jalview/ws/io/mime/HttpContentHandler.java		diff \| blob \| history
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src/jalview/ws/io/mime/MimeTypes.java		diff \| blob \| history
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src/jalview/ws/jws2/JabawsAlignCalcWorker.java		diff \| blob \| history
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src/jalview/ws/rest/InputType.java		diff \| blob \| history
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src/jalview/ws/rest/RestJob.java		diff \| blob \| history
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src/jalview/ws/rest/RestServiceDescription.java		diff \| blob \| history
src/jalview/ws/rest/params/Alignment.java		diff \| blob \| history
src/jalview/ws/rest/params/AnnotationFile.java		diff \| blob \| history
src/jalview/ws/rest/params/JobConstant.java		diff \| blob \| history
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src/jalview/ws/seqfetcher/DbSourceProxy.java		diff \| blob \| history
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