From 797df64fa2a0a30773d0f48f5494d4155e5a8be3 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 10 Oct 2011 11:51:25 +0100 Subject: [PATCH] update author list in license for (JAL-826) --- build.xml | 2 +- doc/AddingGroovySupport.html | 2 +- doc/JalviewRNASupport.html | 24 +++++++++++++------- doc/building.html | 2 +- doc/developing.html | 2 +- doc/index.html | 2 +- doc/newdmobj.html | 2 +- help/helpTOC.xml | 2 +- help/html/calculations/consensus.html | 2 +- help/html/calculations/conservation.html | 2 +- help/html/calculations/pairwise.html | 2 +- help/html/calculations/pca.html | 2 +- help/html/calculations/quality.html | 2 +- help/html/calculations/recoverInputdata.html | 2 +- help/html/calculations/redundancy.html | 2 +- help/html/calculations/sorting.html | 2 +- help/html/calculations/structureconsensus.html | 4 ++-- help/html/calculations/tree.html | 2 +- help/html/calculations/treeviewer.html | 2 +- help/html/colourSchemes/abovePID.html | 2 +- help/html/colourSchemes/annotationColouring.html | 2 +- help/html/colourSchemes/blosum.html | 2 +- help/html/colourSchemes/buried.html | 2 +- help/html/colourSchemes/clustal.html | 2 +- help/html/colourSchemes/conservation.html | 2 +- help/html/colourSchemes/helix.html | 2 +- help/html/colourSchemes/hydrophobic.html | 2 +- help/html/colourSchemes/index.html | 2 +- help/html/colourSchemes/nucleotide.html | 2 +- help/html/colourSchemes/pid.html | 2 +- help/html/colourSchemes/purinepyrimidine.html | 4 ++-- help/html/colourSchemes/rnahelicesColouring.html | 4 ++-- help/html/colourSchemes/strand.html | 2 +- help/html/colourSchemes/taylor.html | 2 +- help/html/colourSchemes/textcolour.html | 2 +- help/html/colourSchemes/turn.html | 2 +- help/html/colourSchemes/user.html | 2 +- help/html/colourSchemes/zappo.html | 2 +- help/html/editing/index.html | 2 +- help/html/features/annotation.html | 2 +- help/html/features/annotationsFormat.html | 2 +- help/html/features/clarguments.html | 2 +- help/html/features/codingfeatures.html | 2 +- help/html/features/commandline.html | 2 +- help/html/features/creatinFeatures.html | 2 +- help/html/features/cursorMode.html | 2 +- help/html/features/dasfeatures.html | 2 +- help/html/features/dassettings.html | 2 +- help/html/features/editingFeatures.html | 2 +- help/html/features/featuresFormat.html | 2 +- help/html/features/featureschemes.html | 2 +- help/html/features/featuresettings.html | 2 +- help/html/features/groovy.html | 2 +- help/html/features/hiddenRegions.html | 2 +- help/html/features/jalarchive.html | 2 +- help/html/features/jmol.html | 2 +- help/html/features/multipleViews.html | 2 +- help/html/features/newkeystrokes.html | 2 +- help/html/features/overview.html | 2 +- help/html/features/pdbviewer.html | 2 +- help/html/features/preferences.html | 2 +- help/html/features/search.html | 2 +- help/html/features/seqfeatures.html | 2 +- help/html/features/seqfetch.html | 2 +- help/html/features/seqmappings.html | 2 +- help/html/features/varna.html | 4 ++-- help/html/features/viewingpdbs.html | 2 +- help/html/features/wrap.html | 2 +- help/html/index.html | 2 +- help/html/io/export.html | 2 +- help/html/io/fileformats.html | 2 +- help/html/io/index.html | 2 +- help/html/io/modellerpir.html | 2 +- help/html/jalviewjnlp.html | 2 +- help/html/keys.html | 2 +- help/html/memory.html | 2 +- help/html/menus/alignmentMenu.html | 2 +- help/html/menus/alwannotations.html | 2 +- help/html/menus/alwcalculate.html | 2 +- help/html/menus/alwcolour.html | 2 +- help/html/menus/alwedit.html | 2 +- help/html/menus/alwfile.html | 2 +- help/html/menus/alwformat.html | 2 +- help/html/menus/alwselect.html | 2 +- help/html/menus/alwview.html | 2 +- help/html/menus/desktopMenu.html | 2 +- help/html/menus/index.html | 2 +- help/html/menus/popupMenu.html | 2 +- help/html/menus/wsmenu.html | 2 +- help/html/misc/aaproperties.html | 2 +- help/html/misc/aminoAcids.html | 2 +- help/html/misc/geneticCode.html | 2 +- help/html/na/index.html | 4 ++-- help/html/privacy.html | 2 +- help/html/releases.html | 2 +- help/html/vamsas/index.html | 2 +- help/html/webServices/JABAWS.html | 2 +- help/html/webServices/dbreffetcher.html | 2 +- help/html/webServices/index.html | 2 +- help/html/webServices/jnet.html | 2 +- help/html/webServices/msaclient.html | 2 +- help/html/webServices/shmr.html | 2 +- help/html/webServices/urllinks.html | 2 +- help/html/webServices/webServicesParams.html | 2 +- help/html/webServices/webServicesPrefs.html | 2 +- help/html/whatsNew.html | 2 +- jalview-jalopy.xml | 2 +- nbbuild.xml | 2 +- nbproject/project.xml | 2 +- resources/embl_mapping.xml | 2 +- resources/uniprot_mapping.xml | 2 +- schemas/JalviewUserColours.xsd | 2 +- schemas/JalviewWsParamSet.xsd | 2 +- schemas/castor-mapping.xsd | 2 +- schemas/jalview.xsd | 2 +- schemas/jalviewJvV1.xsd | 2 +- schemas/vamsas.xsd | 2 +- schemas/vamsasJvV1.xsd | 2 +- src/MCview/AppletPDBCanvas.java | 2 +- src/MCview/AppletPDBViewer.java | 2 +- src/MCview/Atom.java | 2 +- src/MCview/Bond.java | 2 +- src/MCview/MCMatrix.java | 2 +- src/MCview/PDBCanvas.java | 2 +- src/MCview/PDBChain.java | 2 +- src/MCview/PDBViewer.java | 2 +- src/MCview/PDBfile.java | 2 +- src/MCview/Residue.java | 2 +- src/MCview/Zsort.java | 2 +- src/ext/vamsas/IRegistry.java | 2 +- src/ext/vamsas/IRegistryService.java | 2 +- src/ext/vamsas/IRegistryServiceLocator.java | 2 +- src/ext/vamsas/Jpred.java | 2 +- src/ext/vamsas/JpredService.java | 2 +- src/ext/vamsas/JpredServiceLocator.java | 2 +- src/ext/vamsas/JpredSoapBindingStub.java | 2 +- src/ext/vamsas/MuscleWS.java | 2 +- src/ext/vamsas/MuscleWSService.java | 2 +- src/ext/vamsas/MuscleWSServiceLocator.java | 2 +- src/ext/vamsas/MuscleWSSoapBindingStub.java | 2 +- src/ext/vamsas/RegistryServiceSoapBindingStub.java | 2 +- src/ext/vamsas/SeqSearchI.java | 2 +- src/ext/vamsas/SeqSearchServiceLocator.java | 2 +- src/ext/vamsas/SeqSearchServiceService.java | 2 +- .../vamsas/SeqSearchServiceSoapBindingStub.java | 2 +- src/ext/vamsas/ServiceHandle.java | 2 +- src/ext/vamsas/ServiceHandles.java | 2 +- src/jalview/analysis/AAFrequency.java | 2 +- src/jalview/analysis/AlignSeq.java | 2 +- src/jalview/analysis/AlignmentSorter.java | 2 +- src/jalview/analysis/Conservation.java | 2 +- src/jalview/analysis/CrossRef.java | 2 +- src/jalview/analysis/Dna.java | 2 +- src/jalview/analysis/Finder.java | 2 +- src/jalview/analysis/Grouping.java | 2 +- src/jalview/analysis/NJTree.java | 2 +- src/jalview/analysis/PCA.java | 2 +- src/jalview/analysis/ParseProperties.java | 2 +- src/jalview/analysis/Rna.java | 5 ++-- src/jalview/analysis/SeqsetUtils.java | 2 +- src/jalview/analysis/SequenceIdMatcher.java | 2 +- src/jalview/analysis/StructureFrequency.java | 5 ++-- src/jalview/api/AlignmentViewPanel.java | 2 +- src/jalview/api/FeatureRenderer.java | 2 +- src/jalview/api/SequenceRenderer.java | 2 +- src/jalview/api/SequenceStructureBinding.java | 2 +- .../api/StructureSelectionManagerProvider.java | 2 +- src/jalview/appletgui/APopupMenu.java | 2 +- src/jalview/appletgui/AlignFrame.java | 2 +- src/jalview/appletgui/AlignViewport.java | 2 +- src/jalview/appletgui/AlignmentPanel.java | 2 +- src/jalview/appletgui/AnnotationColourChooser.java | 2 +- src/jalview/appletgui/AnnotationLabels.java | 2 +- src/jalview/appletgui/AnnotationPanel.java | 2 +- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/appletgui/AppletJmolBinding.java | 2 +- src/jalview/appletgui/CutAndPasteTransfer.java | 2 +- src/jalview/appletgui/EditNameDialog.java | 2 +- src/jalview/appletgui/EmbmenuFrame.java | 2 +- src/jalview/appletgui/ExtJmol.java | 2 +- src/jalview/appletgui/FeatureColourChooser.java | 2 +- src/jalview/appletgui/FeatureRenderer.java | 2 +- src/jalview/appletgui/FeatureSettings.java | 2 +- src/jalview/appletgui/Finder.java | 2 +- src/jalview/appletgui/FontChooser.java | 2 +- src/jalview/appletgui/IdCanvas.java | 2 +- src/jalview/appletgui/IdPanel.java | 2 +- src/jalview/appletgui/IdwidthAdjuster.java | 2 +- src/jalview/appletgui/JVDialog.java | 2 +- src/jalview/appletgui/OverviewPanel.java | 2 +- src/jalview/appletgui/PCAPanel.java | 2 +- src/jalview/appletgui/PaintRefresher.java | 2 +- src/jalview/appletgui/PairwiseAlignPanel.java | 2 +- src/jalview/appletgui/RedundancyPanel.java | 2 +- src/jalview/appletgui/RotatableCanvas.java | 2 +- src/jalview/appletgui/ScalePanel.java | 2 +- src/jalview/appletgui/SeqCanvas.java | 2 +- src/jalview/appletgui/SeqPanel.java | 2 +- src/jalview/appletgui/SequenceRenderer.java | 2 +- src/jalview/appletgui/SliderPanel.java | 2 +- src/jalview/appletgui/Tooltip.java | 2 +- src/jalview/appletgui/TreeCanvas.java | 2 +- src/jalview/appletgui/TreePanel.java | 2 +- src/jalview/appletgui/UserDefinedColours.java | 2 +- src/jalview/bin/Cache.java | 22 +++++++++++++++++- src/jalview/bin/Jalview.java | 2 +- src/jalview/bin/JalviewLite.java | 2 +- src/jalview/bin/JalviewLiteURLRetrieve.java | 2 +- src/jalview/binding/Alignment.java | 2 +- src/jalview/binding/Annotation.java | 2 +- src/jalview/binding/AnnotationElement.java | 2 +- src/jalview/binding/Colour.java | 2 +- src/jalview/binding/Feature.java | 2 +- src/jalview/binding/FeatureSettings.java | 2 +- src/jalview/binding/Features.java | 2 +- src/jalview/binding/JGroup.java | 2 +- src/jalview/binding/JSeq.java | 2 +- src/jalview/binding/JalviewModel.java | 2 +- src/jalview/binding/JalviewModelSequence.java | 2 +- src/jalview/binding/JalviewUserColours.java | 2 +- src/jalview/binding/Pdbentry.java | 2 +- src/jalview/binding/PdbentryItem.java | 2 +- src/jalview/binding/Pdbids.java | 2 +- src/jalview/binding/Property.java | 2 +- src/jalview/binding/Sequence.java | 2 +- src/jalview/binding/SequenceSet.java | 2 +- src/jalview/binding/SequenceType.java | 2 +- src/jalview/binding/Setting.java | 2 +- src/jalview/binding/Tree.java | 2 +- src/jalview/binding/UserColourScheme.java | 2 +- src/jalview/binding/UserColours.java | 2 +- src/jalview/binding/VAMSAS.java | 2 +- src/jalview/binding/VamsasModel.java | 2 +- src/jalview/binding/Viewport.java | 2 +- src/jalview/commands/ChangeCaseCommand.java | 2 +- src/jalview/commands/CommandI.java | 2 +- src/jalview/commands/EditCommand.java | 2 +- src/jalview/commands/OrderCommand.java | 2 +- src/jalview/commands/RemoveGapColCommand.java | 2 +- src/jalview/commands/RemoveGapsCommand.java | 2 +- src/jalview/commands/SlideSequencesCommand.java | 2 +- src/jalview/commands/TrimRegionCommand.java | 2 +- src/jalview/datamodel/AlignedCodonFrame.java | 2 +- src/jalview/datamodel/Alignment.java | 2 +- src/jalview/datamodel/AlignmentAnnotation.java | 2 +- src/jalview/datamodel/AlignmentI.java | 2 +- src/jalview/datamodel/AlignmentOrder.java | 2 +- src/jalview/datamodel/AlignmentView.java | 2 +- src/jalview/datamodel/Annotation.java | 2 +- src/jalview/datamodel/BinaryNode.java | 2 +- src/jalview/datamodel/BinarySequence.java | 2 +- src/jalview/datamodel/CigarArray.java | 2 +- src/jalview/datamodel/CigarBase.java | 2 +- src/jalview/datamodel/CigarCigar.java | 2 +- src/jalview/datamodel/CigarSimple.java | 2 +- src/jalview/datamodel/ColumnSelection.java | 2 +- src/jalview/datamodel/DBRefEntry.java | 2 +- src/jalview/datamodel/DBRefSource.java | 2 +- src/jalview/datamodel/FeatureProperties.java | 2 +- src/jalview/datamodel/GraphLine.java | 2 +- src/jalview/datamodel/HiddenSequences.java | 2 +- src/jalview/datamodel/Mapping.java | 2 +- src/jalview/datamodel/NodeTransformI.java | 2 +- src/jalview/datamodel/PDBEntry.java | 2 +- src/jalview/datamodel/Provenance.java | 2 +- src/jalview/datamodel/ProvenanceEntry.java | 2 +- src/jalview/datamodel/SearchResults.java | 2 +- src/jalview/datamodel/SeqCigar.java | 2 +- src/jalview/datamodel/Sequence.java | 2 +- src/jalview/datamodel/SequenceFeature.java | 2 +- src/jalview/datamodel/SequenceGroup.java | 2 +- src/jalview/datamodel/SequenceI.java | 2 +- src/jalview/datamodel/SequenceNode.java | 2 +- src/jalview/datamodel/SequencePoint.java | 2 +- src/jalview/datamodel/UniprotEntry.java | 2 +- src/jalview/datamodel/UniprotFile.java | 2 +- src/jalview/datamodel/UniprotProteinName.java | 2 +- src/jalview/datamodel/UniprotSequence.java | 2 +- src/jalview/datamodel/xdb/embl/BasePosition.java | 2 +- src/jalview/datamodel/xdb/embl/EmblEntry.java | 2 +- src/jalview/datamodel/xdb/embl/EmblError.java | 2 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 2 +- .../datamodel/xdb/embl/EmblFeatureLocElement.java | 2 +- .../datamodel/xdb/embl/EmblFeatureLocations.java | 2 +- src/jalview/datamodel/xdb/embl/EmblFile.java | 2 +- src/jalview/datamodel/xdb/embl/EmblSequence.java | 2 +- src/jalview/datamodel/xdb/embl/Qualifier.java | 2 +- src/jalview/ext/jmol/JalviewJmolBinding.java | 2 +- src/jalview/ext/jmol/JmolCommands.java | 2 +- src/jalview/ext/varna/JalviewVarnaBinding.java | 4 ++-- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignViewport.java | 2 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/gui/AnnotationColourChooser.java | 2 +- src/jalview/gui/AnnotationExporter.java | 2 +- src/jalview/gui/AnnotationLabels.java | 2 +- src/jalview/gui/AnnotationPanel.java | 2 +- src/jalview/gui/AppJmol.java | 2 +- src/jalview/gui/AppJmolBinding.java | 2 +- src/jalview/gui/AppVarna.java | 4 ++-- src/jalview/gui/AppVarnaBinding.java | 4 ++-- src/jalview/gui/AssociatePdbFileWithSeq.java | 2 +- src/jalview/gui/BlogReader.java | 2 +- src/jalview/gui/ConservationThread.java | 2 +- src/jalview/gui/Console.java | 2 +- src/jalview/gui/CutAndPasteTransfer.java | 2 +- src/jalview/gui/DasSourceBrowser.java | 2 +- src/jalview/gui/Desktop.java | 2 +- src/jalview/gui/EPSOptions.java | 2 +- src/jalview/gui/EditNameDialog.java | 2 +- src/jalview/gui/FeatureColourChooser.java | 2 +- src/jalview/gui/FeatureRenderer.java | 2 +- src/jalview/gui/FeatureSettings.java | 2 +- src/jalview/gui/Finder.java | 2 +- src/jalview/gui/FontChooser.java | 2 +- src/jalview/gui/IProgressIndicator.java | 2 +- src/jalview/gui/IProgressIndicatorHandler.java | 2 +- src/jalview/gui/IdCanvas.java | 2 +- src/jalview/gui/IdPanel.java | 2 +- src/jalview/gui/IdwidthAdjuster.java | 2 +- src/jalview/gui/Jalview2XML.java | 2 +- src/jalview/gui/Jalview2XML_V1.java | 2 +- src/jalview/gui/JalviewAppender.java | 2 +- src/jalview/gui/JalviewChangeSupport.java | 2 +- src/jalview/gui/JalviewDialog.java | 2 +- src/jalview/gui/JvSwingUtils.java | 2 +- src/jalview/gui/OOMWarning.java | 2 +- src/jalview/gui/OptsAndParamsPage.java | 2 +- src/jalview/gui/OptsParametersContainerI.java | 2 +- src/jalview/gui/OverviewPanel.java | 2 +- src/jalview/gui/PCAPanel.java | 2 +- src/jalview/gui/PaintRefresher.java | 2 +- src/jalview/gui/PairwiseAlignPanel.java | 2 +- src/jalview/gui/PopupMenu.java | 2 +- src/jalview/gui/Preferences.java | 2 +- src/jalview/gui/PromptUserConfig.java | 2 +- src/jalview/gui/RNAHelicesColourChooser.java | 4 ++-- src/jalview/gui/RedundancyPanel.java | 2 +- src/jalview/gui/RestInputParamEditDialog.java | 2 +- src/jalview/gui/RestServiceEditorPane.java | 2 +- src/jalview/gui/RotatableCanvas.java | 2 +- src/jalview/gui/ScalePanel.java | 2 +- src/jalview/gui/ScriptWindow.java | 2 +- src/jalview/gui/SeqCanvas.java | 2 +- src/jalview/gui/SeqPanel.java | 2 +- src/jalview/gui/SequenceFetcher.java | 2 +- src/jalview/gui/SequenceRenderer.java | 2 +- src/jalview/gui/SliderPanel.java | 2 +- src/jalview/gui/SplashScreen.java | 2 +- src/jalview/gui/TextColourChooser.java | 2 +- src/jalview/gui/TreeCanvas.java | 2 +- src/jalview/gui/TreePanel.java | 2 +- src/jalview/gui/UserDefinedColours.java | 2 +- src/jalview/gui/UserQuestionnaireCheck.java | 2 +- src/jalview/gui/VamsasApplication.java | 2 +- src/jalview/gui/ViewSelectionMenu.java | 2 +- src/jalview/gui/WebserviceInfo.java | 2 +- src/jalview/gui/WsJobParameters.java | 2 +- src/jalview/gui/WsParamSetManager.java | 2 +- src/jalview/gui/WsPreferences.java | 2 +- src/jalview/io/AMSAFile.java | 2 +- src/jalview/io/AlignFile.java | 2 +- src/jalview/io/AlignmentProperties.java | 2 +- src/jalview/io/AnnotationFile.java | 2 +- src/jalview/io/AppletFormatAdapter.java | 2 +- src/jalview/io/BLCFile.java | 2 +- src/jalview/io/ClansFile.java | 2 +- src/jalview/io/ClustalFile.java | 2 +- src/jalview/io/DBRefFile.java | 2 +- src/jalview/io/FastaFile.java | 2 +- src/jalview/io/FeaturesFile.java | 2 +- src/jalview/io/FileLoader.java | 2 +- src/jalview/io/FileParse.java | 2 +- src/jalview/io/FormatAdapter.java | 2 +- src/jalview/io/HTMLOutput.java | 2 +- src/jalview/io/IdentifyFile.java | 2 +- src/jalview/io/JPredFile.java | 2 +- src/jalview/io/JalviewFileChooser.java | 2 +- src/jalview/io/JalviewFileFilter.java | 2 +- src/jalview/io/JalviewFileView.java | 2 +- src/jalview/io/JnetAnnotationMaker.java | 2 +- src/jalview/io/MSFfile.java | 2 +- src/jalview/io/MatrixFile.java | 2 +- src/jalview/io/ModellerDescription.java | 2 +- src/jalview/io/NewickFile.java | 2 +- src/jalview/io/PIRFile.java | 2 +- src/jalview/io/PfamFile.java | 2 +- src/jalview/io/PileUpfile.java | 2 +- src/jalview/io/SimpleBlastFile.java | 2 +- src/jalview/io/StockholmFile.java | 2 +- src/jalview/io/VamsasAppDatastore.java | 2 +- src/jalview/io/WSWUBlastClient.java | 2 +- src/jalview/io/packed/DataProvider.java | 2 +- src/jalview/io/packed/JalviewDataset.java | 2 +- src/jalview/io/packed/ParsePackedSet.java | 2 +- src/jalview/io/packed/SimpleDataProvider.java | 2 +- src/jalview/io/vamsas/Datasetsequence.java | 2 +- src/jalview/io/vamsas/DatastoreItem.java | 2 +- src/jalview/io/vamsas/DatastoreRegistry.java | 2 +- src/jalview/io/vamsas/Dbref.java | 2 +- src/jalview/io/vamsas/LocalDocSyncObject.java | 2 +- src/jalview/io/vamsas/Rangetype.java | 2 +- src/jalview/io/vamsas/Sequencefeature.java | 2 +- src/jalview/io/vamsas/Sequencemapping.java | 2 +- src/jalview/io/vamsas/Tree.java | 2 +- src/jalview/javascript/JSFunctionExec.java | 2 +- src/jalview/javascript/JalviewLiteJsApi.java | 2 +- src/jalview/javascript/JsCallBack.java | 2 +- src/jalview/javascript/JsSelectionSender.java | 2 +- src/jalview/javascript/MouseOverListener.java | 2 +- .../javascript/MouseOverStructureListener.java | 2 +- src/jalview/jbgui/GAlignFrame.java | 2 +- src/jalview/jbgui/GAlignmentPanel.java | 2 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 2 +- src/jalview/jbgui/GDasSourceBrowser.java | 2 +- src/jalview/jbgui/GDesktop.java | 2 +- src/jalview/jbgui/GFinder.java | 2 +- src/jalview/jbgui/GFontChooser.java | 2 +- src/jalview/jbgui/GPCAPanel.java | 2 +- src/jalview/jbgui/GPairwiseAlignPanel.java | 2 +- src/jalview/jbgui/GPreferences.java | 2 +- src/jalview/jbgui/GRestInputParamEditDialog.java | 2 +- src/jalview/jbgui/GRestServiceEditorPane.java | 2 +- src/jalview/jbgui/GRnaStructureViewer.java | 4 ++-- src/jalview/jbgui/GSequenceLink.java | 2 +- src/jalview/jbgui/GSliderPanel.java | 2 +- src/jalview/jbgui/GStructureViewer.java | 2 +- src/jalview/jbgui/GTreePanel.java | 2 +- src/jalview/jbgui/GUserDefinedColours.java | 2 +- src/jalview/jbgui/GWebserviceInfo.java | 2 +- src/jalview/jbgui/GWsPreferences.java | 2 +- src/jalview/math/Matrix.java | 2 +- src/jalview/math/RotatableMatrix.java | 2 +- src/jalview/schemabinding/version2/AlcodMap.java | 2 +- src/jalview/schemabinding/version2/Alcodon.java | 2 +- .../schemabinding/version2/AlcodonFrame.java | 2 +- src/jalview/schemabinding/version2/Annotation.java | 2 +- .../schemabinding/version2/AnnotationColours.java | 2 +- .../schemabinding/version2/AnnotationElement.java | 2 +- src/jalview/schemabinding/version2/Colour.java | 2 +- src/jalview/schemabinding/version2/DBRef.java | 2 +- src/jalview/schemabinding/version2/Feature.java | 2 +- .../schemabinding/version2/FeatureSettings.java | 2 +- src/jalview/schemabinding/version2/Features.java | 2 +- src/jalview/schemabinding/version2/Group.java | 2 +- .../schemabinding/version2/HiddenColumns.java | 2 +- src/jalview/schemabinding/version2/JGroup.java | 2 +- src/jalview/schemabinding/version2/JSeq.java | 2 +- .../schemabinding/version2/JalviewModel.java | 2 +- .../version2/JalviewModelSequence.java | 2 +- .../schemabinding/version2/JalviewUserColours.java | 2 +- .../schemabinding/version2/MapListFrom.java | 2 +- src/jalview/schemabinding/version2/MapListTo.java | 2 +- .../schemabinding/version2/MapListType.java | 2 +- src/jalview/schemabinding/version2/Mapping.java | 2 +- .../schemabinding/version2/MappingChoice.java | 2 +- src/jalview/schemabinding/version2/OtherData.java | 2 +- src/jalview/schemabinding/version2/Pdbentry.java | 2 +- .../schemabinding/version2/PdbentryItem.java | 2 +- src/jalview/schemabinding/version2/Pdbids.java | 2 +- src/jalview/schemabinding/version2/Property.java | 2 +- src/jalview/schemabinding/version2/Sequence.java | 2 +- .../schemabinding/version2/SequenceSet.java | 2 +- .../version2/SequenceSetProperties.java | 2 +- .../schemabinding/version2/SequenceType.java | 2 +- src/jalview/schemabinding/version2/Setting.java | 2 +- .../schemabinding/version2/StructureState.java | 2 +- .../schemabinding/version2/ThresholdLine.java | 2 +- src/jalview/schemabinding/version2/Tree.java | 2 +- .../schemabinding/version2/UserColourScheme.java | 2 +- .../schemabinding/version2/UserColours.java | 2 +- src/jalview/schemabinding/version2/VAMSAS.java | 2 +- .../schemabinding/version2/VamsasModel.java | 2 +- src/jalview/schemabinding/version2/Viewport.java | 2 +- .../version2/WebServiceParameterSet.java | 2 +- .../version2/descriptors/AlcodMapDescriptor.java | 2 +- .../version2/descriptors/AlcodonDescriptor.java | 2 +- .../descriptors/AlcodonFrameDescriptor.java | 2 +- .../descriptors/AnnotationColoursDescriptor.java | 2 +- .../version2/descriptors/AnnotationDescriptor.java | 2 +- .../descriptors/AnnotationElementDescriptor.java | 2 +- .../version2/descriptors/ColourDescriptor.java | 2 +- .../version2/descriptors/DBRefDescriptor.java | 2 +- .../version2/descriptors/FeatureDescriptor.java | 2 +- .../descriptors/FeatureSettingsDescriptor.java | 2 +- .../version2/descriptors/FeaturesDescriptor.java | 2 +- .../version2/descriptors/GroupDescriptor.java | 2 +- .../descriptors/HiddenColumnsDescriptor.java | 2 +- .../version2/descriptors/JGroupDescriptor.java | 2 +- .../version2/descriptors/JSeqDescriptor.java | 2 +- .../descriptors/JalviewModelDescriptor.java | 2 +- .../JalviewModelSequenceDescriptor.java | 2 +- .../descriptors/JalviewUserColoursDescriptor.java | 2 +- .../descriptors/MapListFromDescriptor.java | 2 +- .../version2/descriptors/MapListToDescriptor.java | 2 +- .../descriptors/MapListTypeDescriptor.java | 2 +- .../descriptors/MappingChoiceDescriptor.java | 2 +- .../version2/descriptors/MappingDescriptor.java | 2 +- .../version2/descriptors/OtherDataDescriptor.java | 2 +- .../version2/descriptors/PdbentryDescriptor.java | 2 +- .../descriptors/PdbentryItemDescriptor.java | 2 +- .../version2/descriptors/PdbidsDescriptor.java | 2 +- .../version2/descriptors/PropertyDescriptor.java | 2 +- .../version2/descriptors/SequenceDescriptor.java | 2 +- .../descriptors/SequenceSetDescriptor.java | 2 +- .../SequenceSetPropertiesDescriptor.java | 2 +- .../descriptors/SequenceTypeDescriptor.java | 2 +- .../version2/descriptors/SettingDescriptor.java | 2 +- .../descriptors/StructureStateDescriptor.java | 2 +- .../descriptors/ThresholdLineDescriptor.java | 2 +- .../version2/descriptors/TreeDescriptor.java | 2 +- .../descriptors/UserColourSchemeDescriptor.java | 2 +- .../descriptors/UserColoursDescriptor.java | 2 +- .../version2/descriptors/VAMSASDescriptor.java | 2 +- .../descriptors/VamsasModelDescriptor.java | 2 +- .../version2/descriptors/ViewportDescriptor.java | 2 +- .../WebServiceParameterSetDescriptor.java | 2 +- src/jalview/schemes/AnnotationColourGradient.java | 2 +- src/jalview/schemes/Blosum62ColourScheme.java | 2 +- src/jalview/schemes/BuriedColourScheme.java | 2 +- src/jalview/schemes/ClustalxColourScheme.java | 2 +- src/jalview/schemes/ColourSchemeI.java | 2 +- src/jalview/schemes/ColourSchemeProperty.java | 2 +- src/jalview/schemes/Consensus.java | 2 +- src/jalview/schemes/CovariationColourScheme.java | 4 ++-- src/jalview/schemes/GraduatedColor.java | 2 +- src/jalview/schemes/HelixColourScheme.java | 2 +- src/jalview/schemes/HydrophobicColourScheme.java | 2 +- src/jalview/schemes/NucleotideColourScheme.java | 2 +- src/jalview/schemes/PIDColourScheme.java | 2 +- .../schemes/PurinePyrimidineColourScheme.java | 4 ++-- src/jalview/schemes/RNAHelicesColour.java | 4 ++-- src/jalview/schemes/ResidueColourScheme.java | 2 +- src/jalview/schemes/ResidueProperties.java | 2 +- src/jalview/schemes/ScoreColourScheme.java | 2 +- src/jalview/schemes/ScoreMatrix.java | 2 +- src/jalview/schemes/StrandColourScheme.java | 2 +- src/jalview/schemes/TaylorColourScheme.java | 2 +- src/jalview/schemes/TurnColourScheme.java | 2 +- src/jalview/schemes/UserColourScheme.java | 2 +- src/jalview/schemes/ZappoColourScheme.java | 2 +- .../structure/AlignmentViewPanelListener.java | 2 +- .../structure/SecondaryStructureListener.java | 4 ++-- src/jalview/structure/SelectionListener.java | 2 +- src/jalview/structure/SelectionSource.java | 2 +- src/jalview/structure/SequenceListener.java | 2 +- src/jalview/structure/StructureListener.java | 2 +- src/jalview/structure/StructureMapping.java | 2 +- .../structure/StructureMappingcommandSet.java | 2 +- .../structure/StructureSelectionManager.java | 2 +- src/jalview/structure/VamsasListener.java | 2 +- src/jalview/structure/VamsasSource.java | 2 +- src/jalview/util/AWTConsole.java | 2 +- src/jalview/util/BrowserLauncher.java | 2 +- src/jalview/util/ColorUtils.java | 4 ++-- src/jalview/util/Comparison.java | 2 +- src/jalview/util/DBRefUtils.java | 2 +- src/jalview/util/Format.java | 2 +- src/jalview/util/GroupUrlLink.java | 2 +- src/jalview/util/ImageMaker.java | 2 +- src/jalview/util/MapList.java | 2 +- src/jalview/util/ParseHtmlBodyAndLinks.java | 2 +- src/jalview/util/Platform.java | 2 +- src/jalview/util/QuickSort.java | 2 +- src/jalview/util/ShiftList.java | 2 +- src/jalview/util/TableSorter.java | 2 +- src/jalview/util/UrlLink.java | 2 +- src/jalview/util/jarInputStreamProvider.java | 2 +- src/jalview/ws/AWSThread.java | 2 +- src/jalview/ws/AWsJob.java | 2 +- src/jalview/ws/DBRefFetcher.java | 2 +- src/jalview/ws/DasSequenceFeatureFetcher.java | 2 +- src/jalview/ws/EnfinEnvision2OneWay.java | 2 +- src/jalview/ws/JobStateSummary.java | 2 +- src/jalview/ws/SequenceFetcher.java | 2 +- src/jalview/ws/WSClient.java | 2 +- src/jalview/ws/WSClientI.java | 2 +- src/jalview/ws/WSMenuEntryProviderI.java | 2 +- src/jalview/ws/dbsources/DasSequenceSource.java | 2 +- .../ws/dbsources/EbiFileRetrievedProxy.java | 2 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 2 +- src/jalview/ws/dbsources/EmblSource.java | 2 +- src/jalview/ws/dbsources/EmblXmlSource.java | 2 +- src/jalview/ws/dbsources/GeneDbSource.java | 2 +- src/jalview/ws/dbsources/Pdb.java | 2 +- src/jalview/ws/dbsources/Pfam.java | 2 +- src/jalview/ws/dbsources/PfamFull.java | 2 +- src/jalview/ws/dbsources/PfamSeed.java | 2 +- src/jalview/ws/dbsources/Rfam.java | 4 ++-- src/jalview/ws/dbsources/RfamFull.java | 4 ++-- src/jalview/ws/dbsources/RfamSeed.java | 4 ++-- src/jalview/ws/dbsources/Uniprot.java | 2 +- src/jalview/ws/dbsources/UnprotName.java | 2 +- src/jalview/ws/dbsources/Xfam.java | 4 ++-- .../dbsources/das/DasSequenceSourceListener.java | 2 +- src/jalview/ws/ebi/EBIFetchClient.java | 2 +- src/jalview/ws/io/mime/HttpContentHandler.java | 2 +- .../ws/io/mime/JalviewMimeContentHandler.java | 2 +- src/jalview/ws/io/mime/MimeTypes.java | 2 +- src/jalview/ws/jws1/Discoverer.java | 2 +- src/jalview/ws/jws1/JPredClient.java | 2 +- src/jalview/ws/jws1/JPredThread.java | 2 +- src/jalview/ws/jws1/JWS1Thread.java | 2 +- src/jalview/ws/jws1/MsaWSClient.java | 2 +- src/jalview/ws/jws1/MsaWSThread.java | 2 +- src/jalview/ws/jws1/SeqSearchWSClient.java | 2 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 2 +- src/jalview/ws/jws1/WS1Client.java | 2 +- src/jalview/ws/jws1/WSJob.java | 2 +- src/jalview/ws/jws2/AWS2Thread.java | 2 +- src/jalview/ws/jws2/JWs2Job.java | 2 +- src/jalview/ws/jws2/JabaParamStore.java | 2 +- src/jalview/ws/jws2/JabaPreset.java | 2 +- src/jalview/ws/jws2/JabaWsServerQuery.java | 2 +- src/jalview/ws/jws2/Jws2Client.java | 2 +- src/jalview/ws/jws2/Jws2Discoverer.java | 2 +- src/jalview/ws/jws2/MsaWSClient.java | 2 +- src/jalview/ws/jws2/MsaWSThread.java | 2 +- src/jalview/ws/jws2/ParameterUtils.java | 2 +- src/jalview/ws/jws2/dm/JabaOption.java | 2 +- src/jalview/ws/jws2/dm/JabaParameter.java | 2 +- src/jalview/ws/jws2/dm/JabaValueConstrain.java | 2 +- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 2 +- src/jalview/ws/params/ArgumentI.java | 2 +- .../ws/params/InvalidArgumentException.java | 2 +- src/jalview/ws/params/OptionI.java | 2 +- src/jalview/ws/params/ParamDatastoreI.java | 2 +- src/jalview/ws/params/ParamManager.java | 2 +- src/jalview/ws/params/ParameterI.java | 2 +- src/jalview/ws/params/ValueConstrainI.java | 2 +- src/jalview/ws/params/WsParamSetI.java | 2 +- src/jalview/ws/params/simple/BooleanOption.java | 2 +- src/jalview/ws/params/simple/IntegerParameter.java | 2 +- src/jalview/ws/params/simple/Option.java | 2 +- src/jalview/ws/params/simple/Parameter.java | 2 +- .../ws/params/simple/StringChoiceParameter.java | 2 +- src/jalview/ws/rest/AlignmentProcessor.java | 2 +- src/jalview/ws/rest/HttpResultSet.java | 2 +- src/jalview/ws/rest/InputType.java | 2 +- src/jalview/ws/rest/NoValidInputDataException.java | 2 +- src/jalview/ws/rest/RestClient.java | 2 +- src/jalview/ws/rest/RestJob.java | 2 +- src/jalview/ws/rest/RestJobThread.java | 2 +- src/jalview/ws/rest/RestServiceDescription.java | 2 +- src/jalview/ws/rest/params/Alignment.java | 2 +- src/jalview/ws/rest/params/AnnotationFile.java | 2 +- src/jalview/ws/rest/params/JobConstant.java | 2 +- .../ws/rest/params/SeqGroupIndexVector.java | 2 +- src/jalview/ws/rest/params/SeqIdVector.java | 2 +- src/jalview/ws/rest/params/SeqVector.java | 2 +- src/jalview/ws/rest/params/Tree.java | 2 +- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 2 +- src/jalview/ws/seqfetcher/DbSourceProxy.java | 2 +- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 2 +- src/uk/ac/ebi/picr/model/CrossReference.java | 2 +- .../ac/ebi/picr/model/CrossReference_Helper.java | 2 +- src/uk/ac/ebi/picr/model/UPEntry.java | 2 +- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 2 +- src/uk/ac/ebi/www/Data.java | 2 +- src/uk/ac/ebi/www/InputParams.java | 2 +- src/uk/ac/ebi/www/WSFile.java | 2 +- src/uk/ac/ebi/www/WSWUBlast.java | 2 +- src/uk/ac/ebi/www/WSWUBlastService.java | 2 +- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 2 +- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 2 +- .../AccessionMapperBindingStub.java | 2 +- .../AccessionMapperInterface.java | 2 +- .../AccessionMapperService.java | 2 +- .../AccessionMapperServiceLocator.java | 2 +- src/vamsas/IMsaWS.java | 2 +- src/vamsas/objects/simple/Alignment.java | 2 +- src/vamsas/objects/simple/Alignment_Helper.java | 2 +- src/vamsas/objects/simple/JpredResult.java | 2 +- src/vamsas/objects/simple/JpredResult_Helper.java | 2 +- src/vamsas/objects/simple/MsaResult.java | 2 +- src/vamsas/objects/simple/MsaResult_Helper.java | 2 +- src/vamsas/objects/simple/Msfalignment.java | 2 +- src/vamsas/objects/simple/Msfalignment_Helper.java | 2 +- src/vamsas/objects/simple/Object.java | 2 +- src/vamsas/objects/simple/Object_Helper.java | 2 +- src/vamsas/objects/simple/Result.java | 2 +- src/vamsas/objects/simple/Result_Helper.java | 2 +- src/vamsas/objects/simple/Secstructpred.java | 2 +- .../objects/simple/Secstructpred_Helper.java | 2 +- src/vamsas/objects/simple/SeqSearchResult.java | 2 +- .../objects/simple/SeqSearchResult_Helper.java | 2 +- src/vamsas/objects/simple/Sequence.java | 2 +- src/vamsas/objects/simple/SequenceSet.java | 2 +- src/vamsas/objects/simple/SequenceSet_Helper.java | 2 +- src/vamsas/objects/simple/Sequence_Helper.java | 2 +- src/vamsas/objects/simple/WsJobId.java | 2 +- src/vamsas/objects/simple/WsJobId_Helper.java | 2 +- utils/InstallAnywhere/jalview_buildinstaller.xml | 2 +- utils/eclipse/JalviewCodeStyle.xml | 2 +- utils/getJavaVersion.java | 2 +- utils/help2Website.java | 2 +- utils/jalopy/docs/acknowledge.html | 2 +- utils/jalopy/docs/bi01.html | 2 +- utils/jalopy/docs/build.html | 2 +- utils/jalopy/docs/comments.html | 2 +- utils/jalopy/docs/contact.html | 2 +- utils/jalopy/docs/contributors.html | 2 +- utils/jalopy/docs/dedication.html | 2 +- utils/jalopy/docs/dependencies.html | 2 +- utils/jalopy/docs/docs.html | 2 +- utils/jalopy/docs/download.html | 2 +- utils/jalopy/docs/environment.html | 2 +- utils/jalopy/docs/faq.html | 2 +- utils/jalopy/docs/features.html | 2 +- utils/jalopy/docs/footer.html | 2 +- utils/jalopy/docs/header.html | 2 +- utils/jalopy/docs/history.html | 2 +- utils/jalopy/docs/imports.html | 2 +- utils/jalopy/docs/indentation.html | 2 +- utils/jalopy/docs/index.html | 2 +- utils/jalopy/docs/inspector-naming.html | 2 +- utils/jalopy/docs/inspector.html | 2 +- utils/jalopy/docs/installation.html | 2 +- utils/jalopy/docs/introduction.html | 2 +- utils/jalopy/docs/ix01.html | 2 +- utils/jalopy/docs/javadoc.html | 2 +- utils/jalopy/docs/license-antlr.html | 2 +- utils/jalopy/docs/license-apache.html | 2 +- utils/jalopy/docs/license-common-public.html | 2 +- utils/jalopy/docs/license-gnu-doc.html | 2 +- utils/jalopy/docs/license-gnu.html | 2 +- utils/jalopy/docs/license-sun-public.html | 2 +- utils/jalopy/docs/links.html | 2 +- utils/jalopy/docs/manual.html | 2 +- utils/jalopy/docs/messages.html | 2 +- utils/jalopy/docs/misc.html | 2 +- utils/jalopy/docs/part-core.html | 2 +- utils/jalopy/docs/part-plugins.html | 2 +- utils/jalopy/docs/plugin-ant-config.html | 2 +- utils/jalopy/docs/plugin-ant-license.html | 2 +- utils/jalopy/docs/plugin-ant-usage.html | 2 +- utils/jalopy/docs/plugin-ant.html | 2 +- utils/jalopy/docs/plugin-console-license.html | 2 +- utils/jalopy/docs/plugin-console-usage.html | 2 +- utils/jalopy/docs/plugin-console.html | 2 +- utils/jalopy/docs/plugin-eclipse-integration.html | 2 +- utils/jalopy/docs/plugin-eclipse-license.html | 2 +- utils/jalopy/docs/plugin-eclipse.html | 2 +- utils/jalopy/docs/plugin-jbuilder-integration.html | 2 +- utils/jalopy/docs/plugin-jbuilder-license.html | 2 +- utils/jalopy/docs/plugin-jbuilder.html | 2 +- utils/jalopy/docs/plugin-jdev-integration.html | 2 +- utils/jalopy/docs/plugin-jdev-license.html | 2 +- utils/jalopy/docs/plugin-jdev.html | 2 +- utils/jalopy/docs/plugin-jedit-integration.html | 2 +- utils/jalopy/docs/plugin-jedit-license.html | 2 +- utils/jalopy/docs/plugin-jedit.html | 2 +- utils/jalopy/docs/plugin-netbeans-integration.html | 2 +- utils/jalopy/docs/plugin-netbeans-license.html | 2 +- utils/jalopy/docs/plugin-netbeans.html | 2 +- utils/jalopy/docs/plugins.html | 2 +- utils/jalopy/docs/printer.html | 2 +- utils/jalopy/docs/project.html | 2 +- utils/jalopy/docs/separation.html | 2 +- utils/jalopy/docs/settings.html | 2 +- utils/jalopy/docs/sorting.html | 2 +- utils/jalopy/docs/usage.html | 2 +- utils/jalopy/docs/whitespace.html | 2 +- utils/jalopy/docs/wrapping.html | 2 +- utils/jalopy/readme.html | 2 +- 765 files changed, 823 insertions(+), 793 deletions(-) diff --git a/build.xml b/build.xml index 736b5e6..d843c00 100755 --- a/build.xml +++ b/build.xml @@ -1,7 +1,7 @@