JAL-1517 fix copyright for 2.8.2
authorJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Jun 2014 08:52:38 +0000 (09:52 +0100)
committerJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Jun 2014 08:52:38 +0000 (09:52 +0100)
commit47168f025aefdaa044802bd5f8f510ffe43a4808
treef3b85e7987241b636560e28ed319eb69e1de27a9
parenta8f483d04205bb8273ee311c12968b7e86d205fa
JAL-1517 fix copyright for 2.8.2
663 files changed:
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/Atom.java
src/MCview/Bond.java
src/MCview/MCMatrix.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/MCview/Residue.java
src/MCview/Zsort.java
src/ext/vamsas/IRegistry.java
src/ext/vamsas/IRegistryService.java
src/ext/vamsas/IRegistryServiceLocator.java
src/ext/vamsas/Jpred.java
src/ext/vamsas/JpredService.java
src/ext/vamsas/JpredServiceLocator.java
src/ext/vamsas/JpredSoapBindingStub.java
src/ext/vamsas/MuscleWS.java
src/ext/vamsas/MuscleWSService.java
src/ext/vamsas/MuscleWSServiceLocator.java
src/ext/vamsas/MuscleWSSoapBindingStub.java
src/ext/vamsas/RegistryServiceSoapBindingStub.java
src/ext/vamsas/SeqSearchI.java
src/ext/vamsas/SeqSearchServiceLocator.java
src/ext/vamsas/SeqSearchServiceService.java
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
src/ext/vamsas/ServiceHandle.java
src/ext/vamsas/ServiceHandles.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/Finder.java
src/jalview/analysis/Grouping.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/ParseProperties.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SecStrConsensus.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/WUSSParseException.java
src/jalview/analysis/scoremodels/PIDScoreModel.java
src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
src/jalview/analysis/scoremodels/SWScoreModel.java
src/jalview/api/AlignCalcManagerI.java
src/jalview/api/AlignCalcWorkerI.java
src/jalview/api/AlignViewControllerGuiI.java
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/OOMHandlerI.java
src/jalview/api/RotatableCanvasI.java
src/jalview/api/SequenceRenderer.java
src/jalview/api/SequenceStructureBinding.java
src/jalview/api/StructureSelectionManagerProvider.java
src/jalview/api/analysis/ScoreModelI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/EditNameDialog.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/IdwidthAdjuster.java
src/jalview/appletgui/JVDialog.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PaintRefresher.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/binding/Alignment.java
src/jalview/binding/Annotation.java
src/jalview/binding/AnnotationElement.java
src/jalview/binding/Colour.java
src/jalview/binding/Feature.java
src/jalview/binding/FeatureSettings.java
src/jalview/binding/Features.java
src/jalview/binding/JGroup.java
src/jalview/binding/JSeq.java
src/jalview/binding/JalviewModel.java
src/jalview/binding/JalviewModelSequence.java
src/jalview/binding/JalviewUserColours.java
src/jalview/binding/Pdbentry.java
src/jalview/binding/PdbentryItem.java
src/jalview/binding/Pdbids.java
src/jalview/binding/Property.java
src/jalview/binding/Sequence.java
src/jalview/binding/SequenceSet.java
src/jalview/binding/SequenceType.java
src/jalview/binding/Setting.java
src/jalview/binding/Tree.java
src/jalview/binding/UserColourScheme.java
src/jalview/binding/UserColours.java
src/jalview/binding/VAMSAS.java
src/jalview/binding/VamsasModel.java
src/jalview/binding/Viewport.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/CommandI.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
src/jalview/commands/RemoveGapColCommand.java
src/jalview/commands/RemoveGapsCommand.java
src/jalview/commands/SlideSequencesCommand.java
src/jalview/commands/TrimRegionCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AnnotatedCollectionI.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/BinaryNode.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/CigarBase.java
src/jalview/datamodel/CigarCigar.java
src/jalview/datamodel/CigarSimple.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/FeatureProperties.java
src/jalview/datamodel/GraphLine.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/NodeTransformI.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/Provenance.java
src/jalview/datamodel/ProvenanceEntry.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SecondaryStructureAnnotation.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/SequenceNode.java
src/jalview/datamodel/SequencePoint.java
src/jalview/datamodel/UniprotEntry.java
src/jalview/datamodel/UniprotFile.java
src/jalview/datamodel/UniprotProteinName.java
src/jalview/datamodel/UniprotSequence.java
src/jalview/datamodel/xdb/embl/BasePosition.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/datamodel/xdb/embl/EmblError.java
src/jalview/datamodel/xdb/embl/EmblFeature.java
src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
src/jalview/datamodel/xdb/embl/EmblFile.java
src/jalview/datamodel/xdb/embl/EmblSequence.java
src/jalview/datamodel/xdb/embl/Qualifier.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/jmol/PDBFileWithJmol.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/BlogReader.java
src/jalview/gui/Console.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IProgressIndicator.java
src/jalview/gui/IProgressIndicatorHandler.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JalviewAppender.java
src/jalview/gui/JalviewChangeSupport.java
src/jalview/gui/JalviewDialog.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/MenuChooser.java
src/jalview/gui/OOMWarning.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OptsParametersContainerI.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/PromptUserConfig.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/RestInputParamEditDialog.java
src/jalview/gui/RestServiceEditorPane.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/ScriptWindow.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/ViewSelectionMenu.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsParamSetManager.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AMSAFile.java
src/jalview/io/AlignFile.java
src/jalview/io/AlignmentProperties.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BLCFile.java
src/jalview/io/ClansFile.java
src/jalview/io/ClustalFile.java
src/jalview/io/DBRefFile.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/InputStreamParser.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/JalviewFileFilter.java
src/jalview/io/JalviewFileView.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/MSFfile.java
src/jalview/io/MatrixFile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/RnamlFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/SimpleBlastFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/io/packed/DataProvider.java
src/jalview/io/packed/JalviewDataset.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/packed/SimpleDataProvider.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/DatastoreItem.java
src/jalview/io/vamsas/DatastoreRegistry.java
src/jalview/io/vamsas/Dbref.java
src/jalview/io/vamsas/LocalDocSyncObject.java
src/jalview/io/vamsas/Rangetype.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JalviewLiteJsApi.java
src/jalview/javascript/JsCallBack.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/javascript/MouseOverListener.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GAlignmentPanel.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDasSourceBrowser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GFontChooser.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPairwiseAlignPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GRestInputParamEditDialog.java
src/jalview/jbgui/GRestServiceEditorPane.java
src/jalview/jbgui/GRnaStructureViewer.java
src/jalview/jbgui/GSequenceLink.java
src/jalview/jbgui/GSliderPanel.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/jbgui/GTreePanel.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/jbgui/GWebserviceInfo.java
src/jalview/jbgui/GWsPreferences.java
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.java
src/jalview/schemabinding/version2/AlcodMap.java
src/jalview/schemabinding/version2/Alcodon.java
src/jalview/schemabinding/version2/AlcodonFrame.java
src/jalview/schemabinding/version2/Annotation.java
src/jalview/schemabinding/version2/AnnotationColourScheme.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/AnnotationElement.java
src/jalview/schemabinding/version2/CalcIdParam.java
src/jalview/schemabinding/version2/Colour.java
src/jalview/schemabinding/version2/DBRef.java
src/jalview/schemabinding/version2/Feature.java
src/jalview/schemabinding/version2/FeatureSettings.java
src/jalview/schemabinding/version2/Features.java
src/jalview/schemabinding/version2/Group.java
src/jalview/schemabinding/version2/HiddenColumns.java
src/jalview/schemabinding/version2/JGroup.java
src/jalview/schemabinding/version2/JSeq.java
src/jalview/schemabinding/version2/JalviewModel.java
src/jalview/schemabinding/version2/JalviewModelSequence.java
src/jalview/schemabinding/version2/JalviewUserColours.java
src/jalview/schemabinding/version2/MapListFrom.java
src/jalview/schemabinding/version2/MapListTo.java
src/jalview/schemabinding/version2/MapListType.java
src/jalview/schemabinding/version2/Mapping.java
src/jalview/schemabinding/version2/MappingChoice.java
src/jalview/schemabinding/version2/OtherData.java
src/jalview/schemabinding/version2/Pdbentry.java
src/jalview/schemabinding/version2/PdbentryItem.java
src/jalview/schemabinding/version2/Pdbids.java
src/jalview/schemabinding/version2/Property.java
src/jalview/schemabinding/version2/Sequence.java
src/jalview/schemabinding/version2/SequenceSet.java
src/jalview/schemabinding/version2/SequenceSetProperties.java
src/jalview/schemabinding/version2/SequenceType.java
src/jalview/schemabinding/version2/Setting.java
src/jalview/schemabinding/version2/StructureState.java
src/jalview/schemabinding/version2/ThresholdLine.java
src/jalview/schemabinding/version2/Tree.java
src/jalview/schemabinding/version2/UserColourScheme.java
src/jalview/schemabinding/version2/UserColours.java
src/jalview/schemabinding/version2/VAMSAS.java
src/jalview/schemabinding/version2/VamsasModel.java
src/jalview/schemabinding/version2/Viewport.java
src/jalview/schemabinding/version2/WebServiceParameterSet.java
src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/BuriedColourScheme.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/Consensus.java
src/jalview/schemes/CovariationColourScheme.java
src/jalview/schemes/FollowerColourScheme.java
src/jalview/schemes/GraduatedColor.java
src/jalview/schemes/HelixColourScheme.java
src/jalview/schemes/HydrophobicColourScheme.java
src/jalview/schemes/NucleotideColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/PurinePyrimidineColourScheme.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/schemes/RNAInteractionColourScheme.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreColourScheme.java
src/jalview/schemes/ScoreMatrix.java
src/jalview/schemes/StrandColourScheme.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/TaylorColourScheme.java
src/jalview/schemes/TurnColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/schemes/ZappoColourScheme.java
src/jalview/structure/AlignmentViewPanelListener.java
src/jalview/structure/SecondaryStructureListener.java
src/jalview/structure/SelectionListener.java
src/jalview/structure/SelectionSource.java
src/jalview/structure/SequenceListener.java
src/jalview/structure/StructureListener.java
src/jalview/structure/StructureMapping.java
src/jalview/structure/StructureMappingcommandSet.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structure/VamsasListener.java
src/jalview/structure/VamsasSource.java
src/jalview/util/AWTConsole.java
src/jalview/util/BrowserLauncher.java
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/GroupUrlLink.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/MessageManager.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/Platform.java
src/jalview/util/QuickSort.java
src/jalview/util/ShiftList.java
src/jalview/util/TableSorter.java
src/jalview/util/UrlLink.java
src/jalview/util/jarInputStreamProvider.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/PCAModel.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignCalcWorker.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/AWsJob.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/EnfinEnvision2OneWay.java
src/jalview/ws/HttpClientUtils.java
src/jalview/ws/JobStateSummary.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/WSClient.java
src/jalview/ws/WSClientI.java
src/jalview/ws/WSMenuEntryProviderI.java
src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
src/jalview/ws/dbsources/EmblCdsSouce.java
src/jalview/ws/dbsources/EmblSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/GeneDbSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Pfam.java
src/jalview/ws/dbsources/PfamFull.java
src/jalview/ws/dbsources/PfamSeed.java
src/jalview/ws/dbsources/Rfam.java
src/jalview/ws/dbsources/RfamFull.java
src/jalview/ws/dbsources/RfamSeed.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/UnprotName.java
src/jalview/ws/dbsources/Xfam.java
src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
src/jalview/ws/dbsources/das/api/jalviewSourceI.java
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/io/mime/HttpContentHandler.java
src/jalview/ws/io/mime/JalviewMimeContentHandler.java
src/jalview/ws/io/mime/MimeTypes.java
src/jalview/ws/jws1/Annotate3D.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/JWS1Thread.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSClient.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws1/WS1Client.java
src/jalview/ws/jws1/WSJob.java
src/jalview/ws/jws2/AAConClient.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AWS2Thread.java
src/jalview/ws/jws2/JWs2Job.java
src/jalview/ws/jws2/JabaParamStore.java
src/jalview/ws/jws2/JabaPreset.java
src/jalview/ws/jws2/JabaWsServerQuery.java
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
src/jalview/ws/jws2/JabawsCalcWorker.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/ParameterUtils.java
src/jalview/ws/jws2/RNAalifoldClient.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/dm/AAConSettings.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/jws2/dm/JabaParameter.java
src/jalview/ws/jws2/dm/JabaValueConstrain.java
src/jalview/ws/jws2/dm/JabaWsParamSet.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
src/jalview/ws/params/ArgumentI.java
src/jalview/ws/params/AutoCalcSetting.java
src/jalview/ws/params/InvalidArgumentException.java
src/jalview/ws/params/OptionI.java
src/jalview/ws/params/ParamDatastoreI.java
src/jalview/ws/params/ParamManager.java
src/jalview/ws/params/ParameterI.java
src/jalview/ws/params/ValueConstrainI.java
src/jalview/ws/params/WsParamSetI.java
src/jalview/ws/params/simple/BooleanOption.java
src/jalview/ws/params/simple/IntegerParameter.java
src/jalview/ws/params/simple/Option.java
src/jalview/ws/params/simple/Parameter.java
src/jalview/ws/params/simple/StringChoiceParameter.java
src/jalview/ws/rest/AlignmentProcessor.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/NoValidInputDataException.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJob.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/rest/RestServiceDescription.java
src/jalview/ws/rest/params/Alignment.java
src/jalview/ws/rest/params/AnnotationFile.java
src/jalview/ws/rest/params/JobConstant.java
src/jalview/ws/rest/params/SeqGroupIndexVector.java
src/jalview/ws/rest/params/SeqIdVector.java
src/jalview/ws/rest/params/SeqVector.java
src/jalview/ws/rest/params/Tree.java
src/jalview/ws/seqfetcher/ASequenceFetcher.java
src/jalview/ws/seqfetcher/DbSourceProxy.java
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
src/jalview/ws/uimodel/AlignAnalysisUIText.java
src/org/jibble/epsgraphics/EpsDocument.java
src/org/jibble/epsgraphics/EpsException.java
src/org/jibble/epsgraphics/EpsGraphics2D.java
src/uk/ac/ebi/picr/model/CrossReference.java
src/uk/ac/ebi/picr/model/CrossReference_Helper.java
src/uk/ac/ebi/picr/model/UPEntry.java
src/uk/ac/ebi/picr/model/UPEntry_Helper.java
src/uk/ac/ebi/www/Data.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/WSFile.java
src/uk/ac/ebi/www/WSWUBlast.java
src/uk/ac/ebi/www/WSWUBlastService.java
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
src/vamsas/IMsaWS.java
src/vamsas/objects/simple/Alignment.java
src/vamsas/objects/simple/Alignment_Helper.java
src/vamsas/objects/simple/JpredResult.java
src/vamsas/objects/simple/JpredResult_Helper.java
src/vamsas/objects/simple/MsaResult.java
src/vamsas/objects/simple/MsaResult_Helper.java
src/vamsas/objects/simple/Msfalignment.java
src/vamsas/objects/simple/Msfalignment_Helper.java
src/vamsas/objects/simple/Object.java
src/vamsas/objects/simple/Object_Helper.java
src/vamsas/objects/simple/Result.java
src/vamsas/objects/simple/Result_Helper.java
src/vamsas/objects/simple/Secstructpred.java
src/vamsas/objects/simple/Secstructpred_Helper.java
src/vamsas/objects/simple/SeqSearchResult.java
src/vamsas/objects/simple/SeqSearchResult_Helper.java
src/vamsas/objects/simple/Sequence.java
src/vamsas/objects/simple/SequenceSet.java
src/vamsas/objects/simple/SequenceSet_Helper.java
src/vamsas/objects/simple/Sequence_Helper.java
src/vamsas/objects/simple/WsJobId.java
src/vamsas/objects/simple/WsJobId_Helper.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/DnaTranslation.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/bin/CommandLineOperations.java
test/jalview/ext/jmol/PDBFileWithJmolTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/gui/JAL1353bugdemo.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/io/TCoffeeScoreFileTest.java
test/jalview/schemes/DnaCodonTests.java
test/jalview/schemes/ScoreMatrixPrinter.java
test/jalview/ws/PDBSequenceFetcherTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
utils/getJavaVersion.java
utils/help2Website.java