From 2de8acfae59aced665e4c37ad0f7dcc2ed68818e Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 8 Jun 2009 10:58:52 +0000 Subject: [PATCH] apply gpl development license --- help/helpTOC.xml | 18 ++++++ resources/embl_mapping.xml | 58 +++++++++++++------- resources/uniprot_mapping.xml | 18 ++++++ schemas/JalviewUserColours.xsd | 49 ++++++++++++----- schemas/castor-mapping.xsd | 19 +++++++ schemas/jalview.xsd | 19 +++++++ schemas/jalviewJvV1.xsd | 19 +++++++ schemas/vamsas.xsd | 19 +++++++ schemas/vamsasJvV1.xsd | 19 +++++++ src/MCview/AppletPDBCanvas.java | 4 +- src/MCview/AppletPDBViewer.java | 4 +- src/MCview/Atom.java | 4 +- src/MCview/Bond.java | 4 +- src/MCview/MCMatrix.java | 4 +- src/MCview/PDBCanvas.java | 4 +- src/MCview/PDBChain.java | 9 ++- src/MCview/PDBViewer.java | 4 +- src/MCview/Residue.java | 4 +- src/MCview/Zsort.java | 4 +- src/ext/vamsas/IRegistry.java | 4 +- src/ext/vamsas/IRegistryService.java | 4 +- src/ext/vamsas/IRegistryServiceLocator.java | 4 +- src/ext/vamsas/Jpred.java | 4 +- src/ext/vamsas/JpredService.java | 4 +- src/ext/vamsas/JpredServiceLocator.java | 4 +- src/ext/vamsas/JpredSoapBindingStub.java | 4 +- src/ext/vamsas/MuscleWS.java | 4 +- src/ext/vamsas/MuscleWSService.java | 4 +- src/ext/vamsas/MuscleWSServiceLocator.java | 4 +- src/ext/vamsas/MuscleWSSoapBindingStub.java | 4 +- src/ext/vamsas/RegistryServiceSoapBindingStub.java | 4 +- src/ext/vamsas/SeqSearchI.java | 4 +- src/ext/vamsas/SeqSearchServiceLocator.java | 4 +- src/ext/vamsas/SeqSearchServiceService.java | 4 +- .../vamsas/SeqSearchServiceSoapBindingStub.java | 4 +- src/ext/vamsas/ServiceHandle.java | 4 +- src/ext/vamsas/ServiceHandles.java | 4 +- src/jalview/analysis/AAFrequency.java | 4 +- src/jalview/analysis/AlignSeq.java | 4 +- src/jalview/analysis/AlignmentSorter.java | 4 +- src/jalview/analysis/Conservation.java | 4 +- src/jalview/analysis/CrossRef.java | 4 +- src/jalview/analysis/Dna.java | 4 +- src/jalview/analysis/Finder.java | 4 +- src/jalview/analysis/NJTree.java | 4 +- src/jalview/analysis/PCA.java | 4 +- src/jalview/analysis/ParseProperties.java | 4 +- src/jalview/analysis/SeqsetUtils.java | 4 +- src/jalview/analysis/SequenceIdMatcher.java | 4 +- src/jalview/appletgui/APopupMenu.java | 4 +- src/jalview/appletgui/AlignFrame.java | 4 +- src/jalview/appletgui/AlignViewport.java | 4 +- src/jalview/appletgui/AlignmentPanel.java | 4 +- src/jalview/appletgui/AnnotationColourChooser.java | 4 +- src/jalview/appletgui/AnnotationLabels.java | 4 +- src/jalview/appletgui/AnnotationPanel.java | 4 +- src/jalview/appletgui/AppletJmol.java | 4 +- src/jalview/appletgui/CutAndPasteTransfer.java | 4 +- src/jalview/appletgui/EditNameDialog.java | 4 +- src/jalview/appletgui/EmbmenuFrame.java | 4 +- src/jalview/appletgui/FeatureColourChooser.java | 4 +- src/jalview/appletgui/FeatureRenderer.java | 4 +- src/jalview/appletgui/FeatureSettings.java | 4 +- src/jalview/appletgui/Finder.java | 4 +- src/jalview/appletgui/FontChooser.java | 4 +- src/jalview/appletgui/IdCanvas.java | 4 +- src/jalview/appletgui/IdPanel.java | 4 +- src/jalview/appletgui/IdwidthAdjuster.java | 4 +- src/jalview/appletgui/JVDialog.java | 4 +- src/jalview/appletgui/OverviewPanel.java | 4 +- src/jalview/appletgui/PCAPanel.java | 4 +- src/jalview/appletgui/PaintRefresher.java | 4 +- src/jalview/appletgui/PairwiseAlignPanel.java | 4 +- src/jalview/appletgui/RedundancyPanel.java | 4 +- src/jalview/appletgui/RotatableCanvas.java | 4 +- src/jalview/appletgui/ScalePanel.java | 4 +- src/jalview/appletgui/SeqCanvas.java | 4 +- src/jalview/appletgui/SeqPanel.java | 4 +- src/jalview/appletgui/SequenceRenderer.java | 4 +- src/jalview/appletgui/SliderPanel.java | 4 +- src/jalview/appletgui/Tooltip.java | 4 +- src/jalview/appletgui/TreeCanvas.java | 4 +- src/jalview/appletgui/TreePanel.java | 4 +- src/jalview/appletgui/UserDefinedColours.java | 4 +- src/jalview/bin/JalviewLite.java | 4 +- src/jalview/binding/Alignment.java | 21 +++++-- src/jalview/binding/Annotation.java | 21 +++++-- src/jalview/binding/AnnotationElement.java | 21 +++++-- src/jalview/binding/Colour.java | 21 +++++-- src/jalview/binding/Feature.java | 21 +++++-- src/jalview/binding/FeatureSettings.java | 21 +++++-- src/jalview/binding/Features.java | 21 +++++-- src/jalview/binding/JGroup.java | 21 +++++-- src/jalview/binding/JSeq.java | 21 +++++-- src/jalview/binding/JalviewModel.java | 21 +++++-- src/jalview/binding/JalviewModelSequence.java | 21 +++++-- src/jalview/binding/JalviewUserColours.java | 21 +++++-- src/jalview/binding/Pdbentry.java | 21 +++++-- src/jalview/binding/PdbentryItem.java | 21 +++++-- src/jalview/binding/Pdbids.java | 21 +++++-- src/jalview/binding/Property.java | 21 +++++-- src/jalview/binding/Sequence.java | 21 +++++-- src/jalview/binding/SequenceSet.java | 21 +++++-- src/jalview/binding/SequenceType.java | 21 +++++-- src/jalview/binding/Setting.java | 21 +++++-- src/jalview/binding/Tree.java | 21 +++++-- src/jalview/binding/UserColourScheme.java | 21 +++++-- src/jalview/binding/UserColours.java | 21 +++++-- src/jalview/binding/VAMSAS.java | 21 +++++-- src/jalview/binding/VamsasModel.java | 21 +++++-- src/jalview/binding/Viewport.java | 21 +++++-- src/jalview/commands/ChangeCaseCommand.java | 4 +- src/jalview/commands/CommandI.java | 4 +- src/jalview/commands/EditCommand.java | 4 +- src/jalview/commands/OrderCommand.java | 4 +- src/jalview/commands/RemoveGapColCommand.java | 4 +- src/jalview/commands/RemoveGapsCommand.java | 4 +- src/jalview/commands/SlideSequencesCommand.java | 4 +- src/jalview/commands/TrimRegionCommand.java | 4 +- src/jalview/datamodel/AlignedCodonFrame.java | 4 +- src/jalview/datamodel/Alignment.java | 4 +- src/jalview/datamodel/AlignmentAnnotation.java | 4 +- src/jalview/datamodel/AlignmentI.java | 4 +- src/jalview/datamodel/AlignmentOrder.java | 4 +- src/jalview/datamodel/AlignmentView.java | 4 +- src/jalview/datamodel/Annotation.java | 4 +- src/jalview/datamodel/BinaryNode.java | 4 +- src/jalview/datamodel/BinarySequence.java | 4 +- src/jalview/datamodel/CigarArray.java | 4 +- src/jalview/datamodel/CigarBase.java | 4 +- src/jalview/datamodel/CigarCigar.java | 4 +- src/jalview/datamodel/CigarSimple.java | 4 +- src/jalview/datamodel/ColumnSelection.java | 4 +- src/jalview/datamodel/DBRefEntry.java | 4 +- src/jalview/datamodel/DBRefSource.java | 4 +- src/jalview/datamodel/FeatureProperties.java | 4 +- src/jalview/datamodel/GraphLine.java | 4 +- src/jalview/datamodel/HiddenSequences.java | 4 +- src/jalview/datamodel/Mapping.java | 4 +- src/jalview/datamodel/NodeTransformI.java | 17 +++++- src/jalview/datamodel/PDBEntry.java | 4 +- src/jalview/datamodel/Provenance.java | 4 +- src/jalview/datamodel/ProvenanceEntry.java | 4 +- src/jalview/datamodel/SearchResults.java | 4 +- src/jalview/datamodel/SeqCigar.java | 4 +- src/jalview/datamodel/Sequence.java | 4 +- src/jalview/datamodel/SequenceFeature.java | 4 +- src/jalview/datamodel/SequenceGroup.java | 4 +- src/jalview/datamodel/SequenceI.java | 4 +- src/jalview/datamodel/SequenceNode.java | 4 +- src/jalview/datamodel/SequencePoint.java | 4 +- src/jalview/datamodel/UniprotEntry.java | 4 +- src/jalview/datamodel/UniprotFile.java | 4 +- src/jalview/datamodel/UniprotProteinName.java | 4 +- src/jalview/datamodel/UniprotSequence.java | 4 +- src/jalview/datamodel/xdb/embl/BasePosition.java | 4 +- src/jalview/datamodel/xdb/embl/EmblEntry.java | 4 +- src/jalview/datamodel/xdb/embl/EmblError.java | 4 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 4 +- .../datamodel/xdb/embl/EmblFeatureLocElement.java | 4 +- .../datamodel/xdb/embl/EmblFeatureLocations.java | 4 +- src/jalview/datamodel/xdb/embl/EmblFile.java | 4 +- src/jalview/datamodel/xdb/embl/EmblSequence.java | 4 +- src/jalview/datamodel/xdb/embl/Qualifier.java | 4 +- src/jalview/gui/AlignViewport.java | 4 +- src/jalview/gui/AnnotationColourChooser.java | 4 +- src/jalview/gui/AnnotationExporter.java | 4 +- src/jalview/gui/AnnotationLabels.java | 4 +- src/jalview/gui/AnnotationPanel.java | 4 +- src/jalview/gui/AppJmol.java | 4 +- src/jalview/gui/CutAndPasteTransfer.java | 4 +- src/jalview/gui/DasSourceBrowser.java | 4 +- src/jalview/gui/EPSOptions.java | 4 +- src/jalview/gui/EditNameDialog.java | 4 +- src/jalview/gui/FeatureColourChooser.java | 4 +- src/jalview/gui/FeatureRenderer.java | 4 +- src/jalview/gui/FeatureSettings.java | 4 +- src/jalview/gui/Finder.java | 4 +- src/jalview/gui/FontChooser.java | 4 +- src/jalview/gui/IProgressIndicator.java | 4 +- src/jalview/gui/IProgressIndicatorHandler.java | 18 ++++++ src/jalview/gui/IdCanvas.java | 4 +- src/jalview/gui/IdwidthAdjuster.java | 4 +- src/jalview/gui/Jalview2XML_V1.java | 4 +- src/jalview/gui/OOMWarning.java | 4 +- src/jalview/gui/OverviewPanel.java | 4 +- src/jalview/gui/PCAPanel.java | 4 +- src/jalview/gui/PaintRefresher.java | 4 +- src/jalview/gui/PairwiseAlignPanel.java | 4 +- src/jalview/gui/PopupMenu.java | 4 +- src/jalview/gui/Preferences.java | 4 +- src/jalview/gui/RedundancyPanel.java | 4 +- src/jalview/gui/RotatableCanvas.java | 4 +- src/jalview/gui/ScalePanel.java | 4 +- src/jalview/gui/ScriptWindow.java | 4 +- src/jalview/gui/SeqCanvas.java | 4 +- src/jalview/gui/SequenceFetcher.java | 4 +- src/jalview/gui/SequenceRenderer.java | 4 +- src/jalview/gui/SliderPanel.java | 4 +- src/jalview/gui/SplashScreen.java | 4 +- src/jalview/gui/TextColourChooser.java | 4 +- src/jalview/gui/TreeCanvas.java | 4 +- src/jalview/gui/TreePanel.java | 6 +- src/jalview/gui/UserDefinedColours.java | 4 +- src/jalview/gui/UserQuestionnaireCheck.java | 4 +- src/jalview/gui/WebserviceInfo.java | 4 +- src/jalview/io/AMSAFile.java | 4 +- src/jalview/io/AlignFile.java | 4 +- src/jalview/io/AnnotationFile.java | 4 +- src/jalview/io/AppletFormatAdapter.java | 4 +- src/jalview/io/BLCFile.java | 4 +- src/jalview/io/ClansFile.java | 4 +- src/jalview/io/ClustalFile.java | 4 +- src/jalview/io/DBRefFile.java | 4 +- src/jalview/io/FastaFile.java | 4 +- src/jalview/io/FeaturesFile.java | 4 +- src/jalview/io/FileLoader.java | 4 +- src/jalview/io/FileParse.java | 4 +- src/jalview/io/FormatAdapter.java | 4 +- src/jalview/io/HTMLOutput.java | 4 +- src/jalview/io/IdentifyFile.java | 4 +- src/jalview/io/JPredFile.java | 4 +- src/jalview/io/JalviewFileChooser.java | 4 +- src/jalview/io/JalviewFileFilter.java | 4 +- src/jalview/io/JalviewFileView.java | 4 +- src/jalview/io/JnetAnnotationMaker.java | 4 +- src/jalview/io/MSFfile.java | 4 +- src/jalview/io/MatrixFile.java | 4 +- src/jalview/io/ModellerDescription.java | 4 +- src/jalview/io/NewickFile.java | 4 +- src/jalview/io/PIRFile.java | 4 +- src/jalview/io/PfamFile.java | 4 +- src/jalview/io/PileUpfile.java | 4 +- src/jalview/io/StockholmFile.java | 4 +- src/jalview/io/WSWUBlastClient.java | 4 +- src/jalview/io/vamsas/Datasetsequence.java | 18 ++++++ src/jalview/io/vamsas/DatastoreItem.java | 4 +- src/jalview/io/vamsas/Dbref.java | 4 +- src/jalview/io/vamsas/LocalDocSyncObject.java | 4 +- src/jalview/io/vamsas/Rangetype.java | 4 +- src/jalview/io/vamsas/Sequencefeature.java | 17 +++++- src/jalview/io/vamsas/Sequencemapping.java | 4 +- src/jalview/io/vamsas/Tree.java | 4 +- src/jalview/jbgui/GAlignFrame.java | 4 +- src/jalview/jbgui/GAlignmentPanel.java | 4 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 4 +- src/jalview/jbgui/GDasSourceBrowser.java | 4 +- src/jalview/jbgui/GDesktop.java | 4 +- src/jalview/jbgui/GFinder.java | 4 +- src/jalview/jbgui/GFontChooser.java | 4 +- src/jalview/jbgui/GPCAPanel.java | 4 +- src/jalview/jbgui/GPairwiseAlignPanel.java | 4 +- src/jalview/jbgui/GPreferences.java | 4 +- src/jalview/jbgui/GSequenceLink.java | 4 +- src/jalview/jbgui/GSliderPanel.java | 4 +- src/jalview/jbgui/GStructureViewer.java | 4 +- src/jalview/jbgui/GTreePanel.java | 4 +- src/jalview/jbgui/GUserDefinedColours.java | 4 +- src/jalview/jbgui/GWebserviceInfo.java | 4 +- src/jalview/math/Matrix.java | 4 +- src/jalview/math/RotatableMatrix.java | 4 +- src/jalview/schemabinding/version2/AlcodMap.java | 21 +++++-- src/jalview/schemabinding/version2/Alcodon.java | 21 +++++-- .../schemabinding/version2/AlcodonFrame.java | 21 +++++-- src/jalview/schemabinding/version2/Annotation.java | 21 +++++-- .../schemabinding/version2/AnnotationColours.java | 21 +++++-- .../schemabinding/version2/AnnotationElement.java | 21 +++++-- src/jalview/schemabinding/version2/Colour.java | 21 +++++-- src/jalview/schemabinding/version2/DBRef.java | 21 +++++-- src/jalview/schemabinding/version2/Feature.java | 21 +++++-- .../schemabinding/version2/FeatureSettings.java | 21 +++++-- src/jalview/schemabinding/version2/Features.java | 21 +++++-- src/jalview/schemabinding/version2/Group.java | 21 +++++-- .../schemabinding/version2/HiddenColumns.java | 21 +++++-- src/jalview/schemabinding/version2/JGroup.java | 21 +++++-- src/jalview/schemabinding/version2/JSeq.java | 21 +++++-- .../schemabinding/version2/JalviewModel.java | 21 +++++-- .../version2/JalviewModelSequence.java | 21 +++++-- .../schemabinding/version2/JalviewUserColours.java | 21 +++++-- .../schemabinding/version2/MapListFrom.java | 21 +++++-- src/jalview/schemabinding/version2/MapListTo.java | 21 +++++-- .../schemabinding/version2/MapListType.java | 21 +++++-- src/jalview/schemabinding/version2/Mapping.java | 21 +++++-- .../schemabinding/version2/MappingChoice.java | 21 +++++-- src/jalview/schemabinding/version2/OtherData.java | 21 +++++-- src/jalview/schemabinding/version2/Pdbentry.java | 21 +++++-- .../schemabinding/version2/PdbentryItem.java | 21 +++++-- src/jalview/schemabinding/version2/Pdbids.java | 21 +++++-- src/jalview/schemabinding/version2/Property.java | 21 +++++-- src/jalview/schemabinding/version2/Sequence.java | 21 +++++-- .../schemabinding/version2/SequenceSet.java | 21 +++++-- .../version2/SequenceSetProperties.java | 21 +++++-- .../schemabinding/version2/SequenceType.java | 21 +++++-- src/jalview/schemabinding/version2/Setting.java | 21 +++++-- .../schemabinding/version2/StructureState.java | 21 +++++-- .../schemabinding/version2/ThresholdLine.java | 21 +++++-- src/jalview/schemabinding/version2/Tree.java | 21 +++++-- .../schemabinding/version2/UserColourScheme.java | 21 +++++-- .../schemabinding/version2/UserColours.java | 21 +++++-- src/jalview/schemabinding/version2/VAMSAS.java | 21 +++++-- .../schemabinding/version2/VamsasModel.java | 21 +++++-- src/jalview/schemabinding/version2/Viewport.java | 21 +++++-- .../version2/descriptors/AlcodMapDescriptor.java | 21 +++++-- .../version2/descriptors/AlcodonDescriptor.java | 21 +++++-- .../descriptors/AlcodonFrameDescriptor.java | 21 +++++-- .../descriptors/AnnotationColoursDescriptor.java | 21 +++++-- .../version2/descriptors/AnnotationDescriptor.java | 21 +++++-- .../descriptors/AnnotationElementDescriptor.java | 21 +++++-- .../version2/descriptors/ColourDescriptor.java | 21 +++++-- .../version2/descriptors/DBRefDescriptor.java | 21 +++++-- .../version2/descriptors/FeatureDescriptor.java | 21 +++++-- .../descriptors/FeatureSettingsDescriptor.java | 21 +++++-- .../version2/descriptors/FeaturesDescriptor.java | 21 +++++-- .../version2/descriptors/GroupDescriptor.java | 21 +++++-- .../descriptors/HiddenColumnsDescriptor.java | 21 +++++-- .../version2/descriptors/JGroupDescriptor.java | 21 +++++-- .../version2/descriptors/JSeqDescriptor.java | 21 +++++-- .../descriptors/JalviewModelDescriptor.java | 21 +++++-- .../JalviewModelSequenceDescriptor.java | 21 +++++-- .../descriptors/JalviewUserColoursDescriptor.java | 21 +++++-- .../descriptors/MapListFromDescriptor.java | 21 +++++-- .../version2/descriptors/MapListToDescriptor.java | 21 +++++-- .../descriptors/MapListTypeDescriptor.java | 21 +++++-- .../descriptors/MappingChoiceDescriptor.java | 21 +++++-- .../version2/descriptors/MappingDescriptor.java | 21 +++++-- .../version2/descriptors/OtherDataDescriptor.java | 21 +++++-- .../version2/descriptors/PdbentryDescriptor.java | 21 +++++-- .../descriptors/PdbentryItemDescriptor.java | 21 +++++-- .../version2/descriptors/PdbidsDescriptor.java | 21 +++++-- .../version2/descriptors/PropertyDescriptor.java | 21 +++++-- .../version2/descriptors/SequenceDescriptor.java | 21 +++++-- .../descriptors/SequenceSetDescriptor.java | 21 +++++-- .../SequenceSetPropertiesDescriptor.java | 21 +++++-- .../descriptors/SequenceTypeDescriptor.java | 21 +++++-- .../version2/descriptors/SettingDescriptor.java | 21 +++++-- .../descriptors/StructureStateDescriptor.java | 21 +++++-- .../descriptors/ThresholdLineDescriptor.java | 21 +++++-- .../version2/descriptors/TreeDescriptor.java | 21 +++++-- .../descriptors/UserColourSchemeDescriptor.java | 21 +++++-- .../descriptors/UserColoursDescriptor.java | 21 +++++-- .../version2/descriptors/VAMSASDescriptor.java | 21 +++++-- .../descriptors/VamsasModelDescriptor.java | 21 +++++-- .../version2/descriptors/ViewportDescriptor.java | 21 +++++-- src/jalview/schemes/AnnotationColourGradient.java | 4 +- src/jalview/schemes/Blosum62ColourScheme.java | 4 +- src/jalview/schemes/BuriedColourScheme.java | 4 +- src/jalview/schemes/ClustalxColourScheme.java | 4 +- src/jalview/schemes/ColourSchemeI.java | 4 +- src/jalview/schemes/ColourSchemeProperty.java | 4 +- src/jalview/schemes/Consensus.java | 4 +- src/jalview/schemes/GraduatedColor.java | 17 +++++- src/jalview/schemes/HelixColourScheme.java | 4 +- src/jalview/schemes/HydrophobicColourScheme.java | 4 +- src/jalview/schemes/NucleotideColourScheme.java | 4 +- src/jalview/schemes/PIDColourScheme.java | 4 +- src/jalview/schemes/ResidueColourScheme.java | 4 +- src/jalview/schemes/ResidueProperties.java | 4 +- src/jalview/schemes/ScoreColourScheme.java | 4 +- src/jalview/schemes/ScoreMatrix.java | 4 +- src/jalview/schemes/StrandColourScheme.java | 4 +- src/jalview/schemes/TaylorColourScheme.java | 4 +- src/jalview/schemes/TurnColourScheme.java | 4 +- src/jalview/schemes/UserColourScheme.java | 4 +- src/jalview/schemes/ZappoColourScheme.java | 4 +- src/jalview/structure/SelectionListener.java | 17 +++++- src/jalview/structure/SelectionSource.java | 18 ++++++ src/jalview/structure/SequenceListener.java | 4 +- src/jalview/structure/StructureListener.java | 4 +- src/jalview/structure/StructureMapping.java | 4 +- .../structure/StructureSelectionManager.java | 4 +- src/jalview/structure/VamsasListener.java | 4 +- src/jalview/util/BrowserLauncher.java | 4 +- src/jalview/util/Comparison.java | 4 +- src/jalview/util/DBRefUtils.java | 4 +- src/jalview/util/Format.java | 4 +- src/jalview/util/ImageMaker.java | 4 +- src/jalview/util/MapList.java | 4 +- src/jalview/util/Platform.java | 4 +- src/jalview/util/QuickSort.java | 4 +- src/jalview/util/ShiftList.java | 4 +- src/jalview/util/TableSorter.java | 4 +- src/jalview/util/UrlLink.java | 4 +- src/jalview/util/jarInputStreamProvider.java | 20 ++++++- src/jalview/ws/DasSequenceFeatureFetcher.java | 4 +- src/jalview/ws/Discoverer.java | 4 +- src/jalview/ws/JPredClient.java | 4 +- src/jalview/ws/JPredThread.java | 4 +- src/jalview/ws/MsaWSClient.java | 4 +- src/jalview/ws/MsaWSThread.java | 4 +- src/jalview/ws/SeqSearchWSClient.java | 4 +- src/jalview/ws/SeqSearchWSThread.java | 4 +- src/jalview/ws/SequenceFetcher.java | 4 +- src/jalview/ws/WSClient.java | 4 +- src/jalview/ws/WSClientI.java | 4 +- src/jalview/ws/WSThread.java | 4 +- src/jalview/ws/dbsources/DasSequenceSource.java | 4 +- .../ws/dbsources/EbiFileRetrievedProxy.java | 4 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 4 +- src/jalview/ws/dbsources/EmblSource.java | 4 +- src/jalview/ws/dbsources/EmblXmlSource.java | 4 +- src/jalview/ws/dbsources/GeneDbSource.java | 4 +- src/jalview/ws/dbsources/Pdb.java | 4 +- src/jalview/ws/dbsources/Pfam.java | 4 +- src/jalview/ws/dbsources/PfamFull.java | 4 +- src/jalview/ws/dbsources/PfamSeed.java | 4 +- src/jalview/ws/dbsources/Uniprot.java | 4 +- src/jalview/ws/dbsources/UnprotName.java | 4 +- .../dbsources/das/DasSequenceSourceListener.java | 4 +- src/jalview/ws/ebi/EBIFetchClient.java | 4 +- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 4 +- src/jalview/ws/seqfetcher/DbSourceProxy.java | 4 +- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 4 +- src/uk/ac/ebi/picr/model/CrossReference.java | 23 ++++++-- .../ac/ebi/picr/model/CrossReference_Helper.java | 23 ++++++-- src/uk/ac/ebi/picr/model/UPEntry.java | 23 ++++++-- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 23 ++++++-- src/uk/ac/ebi/www/Data.java | 23 ++++++-- src/uk/ac/ebi/www/InputParams.java | 23 ++++++-- src/uk/ac/ebi/www/WSFile.java | 23 ++++++-- src/uk/ac/ebi/www/WSWUBlast.java | 23 ++++++-- src/uk/ac/ebi/www/WSWUBlastService.java | 23 ++++++-- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 23 ++++++-- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 23 ++++++-- .../AccessionMapperBindingStub.java | 23 ++++++-- .../AccessionMapperInterface.java | 23 ++++++-- .../AccessionMapperService.java | 23 ++++++-- .../AccessionMapperServiceLocator.java | 23 ++++++-- src/vamsas/IMsaWS.java | 4 +- src/vamsas/objects/simple/Alignment.java | 4 +- src/vamsas/objects/simple/Alignment_Helper.java | 4 +- src/vamsas/objects/simple/JpredResult.java | 4 +- src/vamsas/objects/simple/JpredResult_Helper.java | 4 +- src/vamsas/objects/simple/MsaResult.java | 4 +- src/vamsas/objects/simple/MsaResult_Helper.java | 4 +- src/vamsas/objects/simple/Msfalignment.java | 4 +- src/vamsas/objects/simple/Msfalignment_Helper.java | 4 +- src/vamsas/objects/simple/Object.java | 4 +- src/vamsas/objects/simple/Object_Helper.java | 4 +- src/vamsas/objects/simple/Result.java | 4 +- src/vamsas/objects/simple/Result_Helper.java | 4 +- src/vamsas/objects/simple/Secstructpred.java | 4 +- .../objects/simple/Secstructpred_Helper.java | 4 +- src/vamsas/objects/simple/SeqSearchResult.java | 4 +- .../objects/simple/SeqSearchResult_Helper.java | 4 +- src/vamsas/objects/simple/Sequence.java | 4 +- src/vamsas/objects/simple/SequenceSet.java | 4 +- src/vamsas/objects/simple/SequenceSet_Helper.java | 4 +- src/vamsas/objects/simple/Sequence_Helper.java | 4 +- src/vamsas/objects/simple/WsJobId.java | 4 +- src/vamsas/objects/simple/WsJobId_Helper.java | 4 +- utils/InstallAnywhere/jalview_buildinstaller.xml | 18 ++++++ utils/help2Website.java | 4 +- 452 files changed, 2967 insertions(+), 1295 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 9ad08fa..bd5a9d5 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,4 +1,22 @@ + diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml index 2f3f046..c203c71 100644 --- a/resources/embl_mapping.xml +++ b/resources/embl_mapping.xml @@ -1,12 +1,28 @@ - + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +--> - + @@ -19,8 +35,8 @@ - - + + @@ -35,14 +51,14 @@ - - + + - + @@ -51,7 +67,7 @@ - + @@ -61,15 +77,15 @@ - + - - + + - - + + @@ -89,7 +105,7 @@ - + @@ -131,12 +147,12 @@ - + - - + + - + diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml index 0f7ffd5..5664440 100755 --- a/resources/uniprot_mapping.xml +++ b/resources/uniprot_mapping.xml @@ -1,4 +1,22 @@ + diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd index 84220c2..27f57da 100755 --- a/schemas/JalviewUserColours.xsd +++ b/schemas/JalviewUserColours.xsd @@ -1,15 +1,34 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + diff --git a/schemas/castor-mapping.xsd b/schemas/castor-mapping.xsd index 0955245..2f68870 100644 --- a/schemas/castor-mapping.xsd +++ b/schemas/castor-mapping.xsd @@ -1,4 +1,23 @@ + + + diff --git a/schemas/jalviewJvV1.xsd b/schemas/jalviewJvV1.xsd index 2022ce2..30cdf21 100644 --- a/schemas/jalviewJvV1.xsd +++ b/schemas/jalviewJvV1.xsd @@ -1,4 +1,23 @@ + + + + diff --git a/schemas/vamsasJvV1.xsd b/schemas/vamsasJvV1.xsd index b830c94..69477b0 100644 --- a/schemas/vamsasJvV1.xsd +++ b/schemas/vamsasJvV1.xsd @@ -1,4 +1,23 @@ + + diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index 390e20f..fa33c6c 100755 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java index 8299abc..8be34b7 100755 --- a/src/MCview/AppletPDBViewer.java +++ b/src/MCview/AppletPDBViewer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java index e69e1ce..08b237b 100755 --- a/src/MCview/Atom.java +++ b/src/MCview/Atom.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java index cc5e67c..32727f3 100755 --- a/src/MCview/Bond.java +++ b/src/MCview/Bond.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java index 1b9a2d8..252e8f1 100755 --- a/src/MCview/MCMatrix.java +++ b/src/MCview/MCMatrix.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index ccc359b..016cd66 100755 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index c1c586a..61ad26a 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -250,7 +250,6 @@ public class PDBChain SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset + count, offset + count, pdbid); - // MCview.PDBChain.PDBFILEFEATURE); resFeatures.addElement(sf); resAnnotation.addElement(new Annotation(tmpat.tfactor)); @@ -279,6 +278,10 @@ public class PDBChain // resNumber-offset // ~= // seq.size() + // Add normalised feature scores to RESNUM indicating start/end of sequence + // sf.setScore(offset+count); + + // System.out.println("PDB Sequence is :\nSequence = " + seq); // System.out.println("No of residues = " + residues.size()); for (i = 0, iSize = resFeatures.size(); i < iSize; i++) diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index dda04a8..7ce8882 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java index 4516b96..6e95c89 100755 --- a/src/MCview/Residue.java +++ b/src/MCview/Residue.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java index 05a1fc9..ce24fce 100755 --- a/src/MCview/Zsort.java +++ b/src/MCview/Zsort.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/IRegistry.java b/src/ext/vamsas/IRegistry.java index 9b91b5d..949e7fc 100755 --- a/src/ext/vamsas/IRegistry.java +++ b/src/ext/vamsas/IRegistry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/IRegistryService.java b/src/ext/vamsas/IRegistryService.java index c99414d..f8869b9 100755 --- a/src/ext/vamsas/IRegistryService.java +++ b/src/ext/vamsas/IRegistryService.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java index b83a9ee..0e65f45 100755 --- a/src/ext/vamsas/IRegistryServiceLocator.java +++ b/src/ext/vamsas/IRegistryServiceLocator.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/Jpred.java b/src/ext/vamsas/Jpred.java index 2805a1d..d0d7e7f 100755 --- a/src/ext/vamsas/Jpred.java +++ b/src/ext/vamsas/Jpred.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/JpredService.java b/src/ext/vamsas/JpredService.java index 61ef50b..81cdc00 100755 --- a/src/ext/vamsas/JpredService.java +++ b/src/ext/vamsas/JpredService.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java index ec70fe6..8ed095b 100755 --- a/src/ext/vamsas/JpredServiceLocator.java +++ b/src/ext/vamsas/JpredServiceLocator.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java index 5915dca..47a39dc 100755 --- a/src/ext/vamsas/JpredSoapBindingStub.java +++ b/src/ext/vamsas/JpredSoapBindingStub.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java index c4e1f77..97fe420 100755 --- a/src/ext/vamsas/MuscleWS.java +++ b/src/ext/vamsas/MuscleWS.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/MuscleWSService.java b/src/ext/vamsas/MuscleWSService.java index 76a5995..2f4bf33 100755 --- a/src/ext/vamsas/MuscleWSService.java +++ b/src/ext/vamsas/MuscleWSService.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java index 0f08435..56c6f84 100755 --- a/src/ext/vamsas/MuscleWSServiceLocator.java +++ b/src/ext/vamsas/MuscleWSServiceLocator.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java index 958a4c2..3741a2d 100755 --- a/src/ext/vamsas/MuscleWSSoapBindingStub.java +++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java index c361e8d..02c0042 100755 --- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java +++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/SeqSearchI.java b/src/ext/vamsas/SeqSearchI.java index f8b0fb7..fd36b53 100644 --- a/src/ext/vamsas/SeqSearchI.java +++ b/src/ext/vamsas/SeqSearchI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java index 598e1ad..d8e26a2 100644 --- a/src/ext/vamsas/SeqSearchServiceLocator.java +++ b/src/ext/vamsas/SeqSearchServiceLocator.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/SeqSearchServiceService.java b/src/ext/vamsas/SeqSearchServiceService.java index 1775b9d..e2bffb5 100644 --- a/src/ext/vamsas/SeqSearchServiceService.java +++ b/src/ext/vamsas/SeqSearchServiceService.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java index 11e307b..7f6a4f8 100644 --- a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java +++ b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java index 8b15688..34eb879 100755 --- a/src/ext/vamsas/ServiceHandle.java +++ b/src/ext/vamsas/ServiceHandle.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java index 60e4ffd..a0fd4f5 100755 --- a/src/ext/vamsas/ServiceHandles.java +++ b/src/ext/vamsas/ServiceHandles.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 36534a3..922a7b5 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index c9a8077..02776f9 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 9353aab..e16e2ab 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 31a4b66..1f7913b 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index ffda7f2..7002f07 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java index 30bc378..ce13665 100644 --- a/src/jalview/analysis/Dna.java +++ b/src/jalview/analysis/Dna.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java index 4e068c5..1fa15e3 100644 --- a/src/jalview/analysis/Finder.java +++ b/src/jalview/analysis/Finder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java index 13ba909..915f161 100755 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index f9a0343..a14be50 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java index 211f4e2..c79d53b 100644 --- a/src/jalview/analysis/ParseProperties.java +++ b/src/jalview/analysis/ParseProperties.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java index a86775d..ca00532 100755 --- a/src/jalview/analysis/SeqsetUtils.java +++ b/src/jalview/analysis/SeqsetUtils.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index 1de93f2..56b760a 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index eab52f2..5f2a977 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 648b642..2159de5 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 9244166..ceb30d7 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 7e42d34..874b552 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 4416ec3..fb2db99 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 28270c9..d498ca5 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 13db915..aef6511 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 7939d9b..c7be8fb 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index 6f5498d..f4b0a1d 100755 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java index b1cd40e..f5a385d 100644 --- a/src/jalview/appletgui/EditNameDialog.java +++ b/src/jalview/appletgui/EditNameDialog.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java index df59ef4..6ef30ef 100644 --- a/src/jalview/appletgui/EmbmenuFrame.java +++ b/src/jalview/appletgui/EmbmenuFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java index d389b9a..f4ad1d5 100644 --- a/src/jalview/appletgui/FeatureColourChooser.java +++ b/src/jalview/appletgui/FeatureColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index ab4b55e..08b0970 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index f71159d..2eb203c 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index 6d205b6..f9962a6 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java index 514b059..9a3fb6b 100755 --- a/src/jalview/appletgui/FontChooser.java +++ b/src/jalview/appletgui/FontChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index d530fd8..96318b4 100755 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/IdCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index b973913..3153301 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java index 4a9f9ef..c779fee 100755 --- a/src/jalview/appletgui/IdwidthAdjuster.java +++ b/src/jalview/appletgui/IdwidthAdjuster.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/JVDialog.java b/src/jalview/appletgui/JVDialog.java index b85424c..8bef740 100644 --- a/src/jalview/appletgui/JVDialog.java +++ b/src/jalview/appletgui/JVDialog.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index ef7c16d..06df9f4 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java index 922941b..46b41f2 100755 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java index 20edeeb..e5e9e89 100755 --- a/src/jalview/appletgui/PaintRefresher.java +++ b/src/jalview/appletgui/PaintRefresher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java index c122b3f..cf82ea0 100755 --- a/src/jalview/appletgui/PairwiseAlignPanel.java +++ b/src/jalview/appletgui/PairwiseAlignPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 9682000..c9fc0b7 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index 4f54670..5e90f06 100755 --- a/src/jalview/appletgui/RotatableCanvas.java +++ b/src/jalview/appletgui/RotatableCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java index 431bc66..e6c9855 100755 --- a/src/jalview/appletgui/ScalePanel.java +++ b/src/jalview/appletgui/ScalePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 68b8501..f0031a8 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index c5352f5..28fe5a8 100755 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index 531b4d0..cf4c359 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java index a05bbf0..0e4a379 100755 --- a/src/jalview/appletgui/SliderPanel.java +++ b/src/jalview/appletgui/SliderPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java index 0bbe98b..7168cf3 100755 --- a/src/jalview/appletgui/Tooltip.java +++ b/src/jalview/appletgui/Tooltip.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 8c445f0..4e15fd3 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java index d6c0069..735a11b 100755 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index e8e0e57..825cfd3 100755 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 5d2aa04..7329a6f 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index 5b107b5..fd118ef 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 108d3ad..9a1dcd2 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index d133fe0..ec026ff 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java index 488ff98..4dff29e 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java index d429df3..ba8103a 100755 --- a/src/jalview/binding/Feature.java +++ b/src/jalview/binding/Feature.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java index f3d06be..c43114c 100755 --- a/src/jalview/binding/FeatureSettings.java +++ b/src/jalview/binding/FeatureSettings.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java index e50ae7c..a8e2b91 100755 --- a/src/jalview/binding/Features.java +++ b/src/jalview/binding/Features.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 862eebd..329c526 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 14b1f2f..45a516b 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java index 21f8be9..530a69d 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index 5ebcee6..6ea1f67 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index b5d0335..ac6cf6f 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java index cac4cf6..71e2eb6 100755 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java index 83bc40a..a4ba524 100755 --- a/src/jalview/binding/PdbentryItem.java +++ b/src/jalview/binding/PdbentryItem.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; /** diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java index b4745a2..6666b22 100755 --- a/src/jalview/binding/Pdbids.java +++ b/src/jalview/binding/Pdbids.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java index f1114f7..833e859 100755 --- a/src/jalview/binding/Property.java +++ b/src/jalview/binding/Property.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java index 9c8cbc2..903e569 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 13a9020..8942009 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java index 1bb2a62..0929aa0 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java index 9cd84b4..32d5d05 100755 --- a/src/jalview/binding/Setting.java +++ b/src/jalview/binding/Setting.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java index 5f138d0..4126fac 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java index 24c97ff..4e362b7 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java index bdefe05..0b29053 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index 1c92bd3..349fc6e 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java index 5fda35e..9763d79 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java index 643c323..045bb38 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; //---------------------------------/ diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java index 7a74e08..a1dc3ba 100644 --- a/src/jalview/commands/ChangeCaseCommand.java +++ b/src/jalview/commands/ChangeCaseCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java index 9fe508b..43d61cf 100644 --- a/src/jalview/commands/CommandI.java +++ b/src/jalview/commands/CommandI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 85e6ad5..019e11e 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java index 6ea28ee..ccb0dc6 100644 --- a/src/jalview/commands/OrderCommand.java +++ b/src/jalview/commands/OrderCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java index c5e12f5..b9b2648 100644 --- a/src/jalview/commands/RemoveGapColCommand.java +++ b/src/jalview/commands/RemoveGapColCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java index d2bd486..7d5f39e 100644 --- a/src/jalview/commands/RemoveGapsCommand.java +++ b/src/jalview/commands/RemoveGapsCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java index c8a5533..88e5129 100644 --- a/src/jalview/commands/SlideSequencesCommand.java +++ b/src/jalview/commands/SlideSequencesCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java index 30f813f..a61d491 100644 --- a/src/jalview/commands/TrimRegionCommand.java +++ b/src/jalview/commands/TrimRegionCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 3b59249..0e9444f 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 64b79b7..7fcbda2 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 381a054..adc25c2 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index d9791f1..f0a9ef4 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java index f807890..28ec445 100755 --- a/src/jalview/datamodel/AlignmentOrder.java +++ b/src/jalview/datamodel/AlignmentOrder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index 0884ea4..db95c71 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index 348c9a4..a73ea7a 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java index 0a22419..bfe8c04 100755 --- a/src/jalview/datamodel/BinaryNode.java +++ b/src/jalview/datamodel/BinaryNode.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java index 52b0ece..ce96959 100755 --- a/src/jalview/datamodel/BinarySequence.java +++ b/src/jalview/datamodel/BinarySequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java index 6842f4a..aeaa374 100644 --- a/src/jalview/datamodel/CigarArray.java +++ b/src/jalview/datamodel/CigarArray.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java index b0efe6c..2f20c00 100644 --- a/src/jalview/datamodel/CigarBase.java +++ b/src/jalview/datamodel/CigarBase.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java index f5619cf..f453e2c 100644 --- a/src/jalview/datamodel/CigarCigar.java +++ b/src/jalview/datamodel/CigarCigar.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java index 4013f93..e0327ee 100644 --- a/src/jalview/datamodel/CigarSimple.java +++ b/src/jalview/datamodel/CigarSimple.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 9dbaced..6bba5d2 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java index c9d59ec..887a751 100755 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index 6dca74f..575ba68 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java index d736a49..e6f2cb8 100644 --- a/src/jalview/datamodel/FeatureProperties.java +++ b/src/jalview/datamodel/FeatureProperties.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/GraphLine.java b/src/jalview/datamodel/GraphLine.java index 7a4aa56..a484546 100755 --- a/src/jalview/datamodel/GraphLine.java +++ b/src/jalview/datamodel/GraphLine.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java index 22fe523..e841648 100755 --- a/src/jalview/datamodel/HiddenSequences.java +++ b/src/jalview/datamodel/HiddenSequences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java index c7e359b..d45abca 100644 --- a/src/jalview/datamodel/Mapping.java +++ b/src/jalview/datamodel/Mapping.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/NodeTransformI.java b/src/jalview/datamodel/NodeTransformI.java index f78188a..b740115 100644 --- a/src/jalview/datamodel/NodeTransformI.java +++ b/src/jalview/datamodel/NodeTransformI.java @@ -1,5 +1,20 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.datamodel; diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java index 446d719..cbc9bb6 100755 --- a/src/jalview/datamodel/PDBEntry.java +++ b/src/jalview/datamodel/PDBEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java index bed8004..2c2c2d8 100755 --- a/src/jalview/datamodel/Provenance.java +++ b/src/jalview/datamodel/Provenance.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/ProvenanceEntry.java b/src/jalview/datamodel/ProvenanceEntry.java index a33f203..36263c3 100755 --- a/src/jalview/datamodel/ProvenanceEntry.java +++ b/src/jalview/datamodel/ProvenanceEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java index 329f447..2400524 100755 --- a/src/jalview/datamodel/SearchResults.java +++ b/src/jalview/datamodel/SearchResults.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java index cc9eaa7..1092bcd 100644 --- a/src/jalview/datamodel/SeqCigar.java +++ b/src/jalview/datamodel/SeqCigar.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index eda5684..7670452 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 0686419..302f3cd 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 49f270d..abc6d45 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 3e9c4c7..10bee55 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java index ea3e515..c96db97 100755 --- a/src/jalview/datamodel/SequenceNode.java +++ b/src/jalview/datamodel/SequenceNode.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java index a8b0503..9a881bc 100755 --- a/src/jalview/datamodel/SequencePoint.java +++ b/src/jalview/datamodel/SequencePoint.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java index bd2c37c..f2a605f 100755 --- a/src/jalview/datamodel/UniprotEntry.java +++ b/src/jalview/datamodel/UniprotEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/UniprotFile.java b/src/jalview/datamodel/UniprotFile.java index 6df0bad..3c4ce8f 100755 --- a/src/jalview/datamodel/UniprotFile.java +++ b/src/jalview/datamodel/UniprotFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java index ebdf7d7..c999483 100755 --- a/src/jalview/datamodel/UniprotProteinName.java +++ b/src/jalview/datamodel/UniprotProteinName.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/UniprotSequence.java b/src/jalview/datamodel/UniprotSequence.java index 410f7b8..7f5dd28 100755 --- a/src/jalview/datamodel/UniprotSequence.java +++ b/src/jalview/datamodel/UniprotSequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/BasePosition.java b/src/jalview/datamodel/xdb/embl/BasePosition.java index a3dffd1..f835097 100644 --- a/src/jalview/datamodel/xdb/embl/BasePosition.java +++ b/src/jalview/datamodel/xdb/embl/BasePosition.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 0cee0b4..770bf7c 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblError.java b/src/jalview/datamodel/xdb/embl/EmblError.java index ee76978..0bc4764 100644 --- a/src/jalview/datamodel/xdb/embl/EmblError.java +++ b/src/jalview/datamodel/xdb/embl/EmblError.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java index 091846e..f9b551a 100644 --- a/src/jalview/datamodel/xdb/embl/EmblFeature.java +++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java index 4df9f67..bf70788 100644 --- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java +++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java index 2444592..92fa4e3 100644 --- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java +++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java index 8421aad..6219ca8 100644 --- a/src/jalview/datamodel/xdb/embl/EmblFile.java +++ b/src/jalview/datamodel/xdb/embl/EmblFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java index 5bdae54..d1820b9 100644 --- a/src/jalview/datamodel/xdb/embl/EmblSequence.java +++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/datamodel/xdb/embl/Qualifier.java b/src/jalview/datamodel/xdb/embl/Qualifier.java index 27806ff..0ef5274 100644 --- a/src/jalview/datamodel/xdb/embl/Qualifier.java +++ b/src/jalview/datamodel/xdb/embl/Qualifier.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 19ec9e0..8c23e4d 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 4c7bc0c..1ed9461 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index a058c87..2a3da7b 100755 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 8050490..bed71d3 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index af1ff7a..743e1fa 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 32fc85f..2137a80 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 6459de4..e18a562 100755 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index 9074105..afcecc0 100755 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java index 193cfcc..d442c0e 100755 --- a/src/jalview/gui/EPSOptions.java +++ b/src/jalview/gui/EPSOptions.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java index cf11803..3181e19 100644 --- a/src/jalview/gui/EditNameDialog.java +++ b/src/jalview/gui/EditNameDialog.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 55865db..3c618e7 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 8d09d10..75ce63a 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index f5580b9..22800ea 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index cad734b..c2c02d1 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 6e99d91..afd2d62 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/IProgressIndicator.java b/src/jalview/gui/IProgressIndicator.java index 0345107..30953fe 100644 --- a/src/jalview/gui/IProgressIndicator.java +++ b/src/jalview/gui/IProgressIndicator.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/IProgressIndicatorHandler.java b/src/jalview/gui/IProgressIndicatorHandler.java index f8012d3..7d03225 100644 --- a/src/jalview/gui/IProgressIndicatorHandler.java +++ b/src/jalview/gui/IProgressIndicatorHandler.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; public interface IProgressIndicatorHandler diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index b1fbe08..7ccc379 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java index c257900..725a0f1 100755 --- a/src/jalview/gui/IdwidthAdjuster.java +++ b/src/jalview/gui/IdwidthAdjuster.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 7bcea33..f5f37c4 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java index 9b69825..a2d1ede 100644 --- a/src/jalview/gui/OOMWarning.java +++ b/src/jalview/gui/OOMWarning.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 6bc630c..360bcbf 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index b397cf5..1a9f466 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java index 19fe4c9..f505453 100755 --- a/src/jalview/gui/PaintRefresher.java +++ b/src/jalview/gui/PaintRefresher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 15c8c70..2d93d33 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e2865a8..1fb4a3b 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index aa4d193..26d7260 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 2355b47..cb4c595 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index 4611533..a9e2ebf 100755 --- a/src/jalview/gui/RotatableCanvas.java +++ b/src/jalview/gui/RotatableCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java index 8e9d829..045471a 100755 --- a/src/jalview/gui/ScalePanel.java +++ b/src/jalview/gui/ScalePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java index 9b13847..00b724e 100644 --- a/src/jalview/gui/ScriptWindow.java +++ b/src/jalview/gui/ScriptWindow.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 052932b..a7ba035 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 64d88af..2201167 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 98329b4..c390041 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index a200699..8c290b5 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java index f4c5e8e..30503b1 100755 --- a/src/jalview/gui/SplashScreen.java +++ b/src/jalview/gui/SplashScreen.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index c0f3916..771d9c7 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 29626fe..7644673 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index eef07fa..c6d87d7 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -748,4 +748,4 @@ public class TreePanel extends GTreePanel } }); } -} \ No newline at end of file +} diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 83f9d0c..17682c9 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java index 8a596ad..0fdea6c 100644 --- a/src/jalview/gui/UserQuestionnaireCheck.java +++ b/src/jalview/gui/UserQuestionnaireCheck.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index a0eeedf..ea2e166 100755 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java index 569d351..20cf745 100644 --- a/src/jalview/io/AMSAFile.java +++ b/src/jalview/io/AMSAFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 3ca2563..7a469dd 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 101fe2e..641894a 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index e5fc584..d2dc8f3 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 9b5b3e5..46cf02a 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/ClansFile.java b/src/jalview/io/ClansFile.java index 696ccb2..cbe2d73 100644 --- a/src/jalview/io/ClansFile.java +++ b/src/jalview/io/ClansFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index f46e3ad..702715f 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java index 9ebc661..18e56cb 100644 --- a/src/jalview/io/DBRefFile.java +++ b/src/jalview/io/DBRefFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index 2ee715d..b3fb3a1 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 01cbd8a..1afe4c4 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 6cb1212..f53cd88 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index cca8ace..1e67579 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 6514e60..25e2fea 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index 3d2a148..87fce94 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index f1f51b1..071b6f2 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index a038cac..185674b 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index b381d62..8a68113 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java index 7178aae..9430dcc 100755 --- a/src/jalview/io/JalviewFileFilter.java +++ b/src/jalview/io/JalviewFileFilter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java index d09b200..7194a27 100755 --- a/src/jalview/io/JalviewFileView.java +++ b/src/jalview/io/JalviewFileView.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index 993737b..8c841a8 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 73d0f0f..1192f28 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java index 011eda3..2918aa7 100644 --- a/src/jalview/io/MatrixFile.java +++ b/src/jalview/io/MatrixFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java index e4483a5..5652a25 100755 --- a/src/jalview/io/ModellerDescription.java +++ b/src/jalview/io/ModellerDescription.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 8dc2389..3726909 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 4c10abe..7a46d21 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 223e7a4..7e0a976 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index 947d982..ce67cc0 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 2183f2d..7c58022 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index ad291db..b822bf8 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java index 85a228e..39ff94d 100644 --- a/src/jalview/io/vamsas/Datasetsequence.java +++ b/src/jalview/io/vamsas/Datasetsequence.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.io.vamsas; import jalview.datamodel.AlignmentI; diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java index ce5acd3..0815055 100644 --- a/src/jalview/io/vamsas/DatastoreItem.java +++ b/src/jalview/io/vamsas/DatastoreItem.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java index c27bc9a..11c62b5 100644 --- a/src/jalview/io/vamsas/Dbref.java +++ b/src/jalview/io/vamsas/Dbref.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/LocalDocSyncObject.java b/src/jalview/io/vamsas/LocalDocSyncObject.java index 50b0cdb..d1a7ff0 100644 --- a/src/jalview/io/vamsas/LocalDocSyncObject.java +++ b/src/jalview/io/vamsas/LocalDocSyncObject.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java index 8c8b7d7..169eae1 100644 --- a/src/jalview/io/vamsas/Rangetype.java +++ b/src/jalview/io/vamsas/Rangetype.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java index 0ddfc6f..1348227 100644 --- a/src/jalview/io/vamsas/Sequencefeature.java +++ b/src/jalview/io/vamsas/Sequencefeature.java @@ -1,5 +1,20 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.io.vamsas; diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java index 2e8d31b..b0a3dd4 100644 --- a/src/jalview/io/vamsas/Sequencemapping.java +++ b/src/jalview/io/vamsas/Sequencemapping.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index 1866336..9992da1 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 0249e76..49ab7c1 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java index cc3d68f..76da389 100755 --- a/src/jalview/jbgui/GAlignmentPanel.java +++ b/src/jalview/jbgui/GAlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java index 2697e1c..122e100 100755 --- a/src/jalview/jbgui/GCutAndPasteTransfer.java +++ b/src/jalview/jbgui/GCutAndPasteTransfer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java index 625e2c4..3f9f490 100755 --- a/src/jalview/jbgui/GDasSourceBrowser.java +++ b/src/jalview/jbgui/GDasSourceBrowser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index a8e2ef5..5ff13af 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java index 6444582..1d26615 100755 --- a/src/jalview/jbgui/GFinder.java +++ b/src/jalview/jbgui/GFinder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java index a30293a..8b7c585 100755 --- a/src/jalview/jbgui/GFontChooser.java +++ b/src/jalview/jbgui/GFontChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java index 6ad36e8..08a2f3a 100755 --- a/src/jalview/jbgui/GPCAPanel.java +++ b/src/jalview/jbgui/GPCAPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java index b4e6321..8892283 100755 --- a/src/jalview/jbgui/GPairwiseAlignPanel.java +++ b/src/jalview/jbgui/GPairwiseAlignPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 22a4737..7ff1757 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java index b412f6c..8fbc2d6 100755 --- a/src/jalview/jbgui/GSequenceLink.java +++ b/src/jalview/jbgui/GSequenceLink.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java index e8df12d..dc7f2e5 100755 --- a/src/jalview/jbgui/GSliderPanel.java +++ b/src/jalview/jbgui/GSliderPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java index d2bebc3..a03ec76 100644 --- a/src/jalview/jbgui/GStructureViewer.java +++ b/src/jalview/jbgui/GStructureViewer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java index d6677f4..8e5a152 100755 --- a/src/jalview/jbgui/GTreePanel.java +++ b/src/jalview/jbgui/GTreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java index 70a75e4..f79359c 100755 --- a/src/jalview/jbgui/GUserDefinedColours.java +++ b/src/jalview/jbgui/GUserDefinedColours.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java index 89c5bf2..8664a80 100755 --- a/src/jalview/jbgui/GWebserviceInfo.java +++ b/src/jalview/jbgui/GWebserviceInfo.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index 5baf47c..b7f8705 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java index 3487c6d..babaeeb 100755 --- a/src/jalview/math/RotatableMatrix.java +++ b/src/jalview/math/RotatableMatrix.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java index f43acd6..91dff9c 100644 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ b/src/jalview/schemabinding/version2/AlcodMap.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java index cffbd9a..b07051b 100644 --- a/src/jalview/schemabinding/version2/Alcodon.java +++ b/src/jalview/schemabinding/version2/Alcodon.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index b8b2a41..683e421 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 9ee76e3..884f159 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java index 36f9f93..7b8bdb7 100755 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java index eca3e6a..9c18d02 100755 --- a/src/jalview/schemabinding/version2/AnnotationElement.java +++ b/src/jalview/schemabinding/version2/AnnotationElement.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java index 54d64ff..689718b 100755 --- a/src/jalview/schemabinding/version2/Colour.java +++ b/src/jalview/schemabinding/version2/Colour.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java index 4d67250..298ae8f 100644 --- a/src/jalview/schemabinding/version2/DBRef.java +++ b/src/jalview/schemabinding/version2/DBRef.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index 109ec6e..9c27bd1 100755 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java index 5ce4054..1050270 100755 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java index 47b28a3..57699f3 100755 --- a/src/jalview/schemabinding/version2/Features.java +++ b/src/jalview/schemabinding/version2/Features.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java index 826667e..0b4499c 100644 --- a/src/jalview/schemabinding/version2/Group.java +++ b/src/jalview/schemabinding/version2/Group.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java index 716bfbc..8c8f4c6 100644 --- a/src/jalview/schemabinding/version2/HiddenColumns.java +++ b/src/jalview/schemabinding/version2/HiddenColumns.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index 3563186..79a4229 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java index a5dc2f7..060ea0d 100755 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java index f7e049a..584f6e4 100755 --- a/src/jalview/schemabinding/version2/JalviewModel.java +++ b/src/jalview/schemabinding/version2/JalviewModel.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index cb66b37..691c7e5 100755 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java index 7c059da..a0cf9d9 100755 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ b/src/jalview/schemabinding/version2/JalviewUserColours.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java index acfe18e..7604f51 100644 --- a/src/jalview/schemabinding/version2/MapListFrom.java +++ b/src/jalview/schemabinding/version2/MapListFrom.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java index 8c3a7e0..8530f78 100644 --- a/src/jalview/schemabinding/version2/MapListTo.java +++ b/src/jalview/schemabinding/version2/MapListTo.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index 21d56e7..eca79ba 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java index 8dbc12f..b0add53 100644 --- a/src/jalview/schemabinding/version2/Mapping.java +++ b/src/jalview/schemabinding/version2/Mapping.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java index 5f1930d..079e85a 100644 --- a/src/jalview/schemabinding/version2/MappingChoice.java +++ b/src/jalview/schemabinding/version2/MappingChoice.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java index 94a5566..3311b79 100644 --- a/src/jalview/schemabinding/version2/OtherData.java +++ b/src/jalview/schemabinding/version2/OtherData.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 6ff1819..50d7896 100755 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java index 3dbc99c..02818a0 100755 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ b/src/jalview/schemabinding/version2/PdbentryItem.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; /** diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index 04685b9..fb8665f 100755 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java index bfc4dde..1faa76d 100755 --- a/src/jalview/schemabinding/version2/Property.java +++ b/src/jalview/schemabinding/version2/Property.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index e606eeb..568233d 100755 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java index 481c37f..7a738fa 100755 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java index a078c78..b001952 100644 --- a/src/jalview/schemabinding/version2/SequenceSetProperties.java +++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java index 0d07812..3da6017 100755 --- a/src/jalview/schemabinding/version2/SequenceType.java +++ b/src/jalview/schemabinding/version2/SequenceType.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index e6f824f..c15ae2e 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 24eed77..fa22401 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java index 4e3f124..26df339 100755 --- a/src/jalview/schemabinding/version2/ThresholdLine.java +++ b/src/jalview/schemabinding/version2/ThresholdLine.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java index c73cb12..7cba5b2 100755 --- a/src/jalview/schemabinding/version2/Tree.java +++ b/src/jalview/schemabinding/version2/Tree.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java index 3cb65e0..30bb7a2 100755 --- a/src/jalview/schemabinding/version2/UserColourScheme.java +++ b/src/jalview/schemabinding/version2/UserColourScheme.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java index 062024f..ee5e800 100755 --- a/src/jalview/schemabinding/version2/UserColours.java +++ b/src/jalview/schemabinding/version2/UserColours.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index ae8e17f..4ff836d 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java index 26814dc..9e52cda 100755 --- a/src/jalview/schemabinding/version2/VamsasModel.java +++ b/src/jalview/schemabinding/version2/VamsasModel.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index d212e84..6ef4c7e 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java index fbc56a3..97ddee7 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java index cd87309..55ccb7d 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java index 5341376..c6206ba 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 3d32ff6..43c709c 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java index 44576ee..50871c2 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java index 61221a1..4429896 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java index bdd9739..92cf058 100644 --- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java index 1a55978..ae17890 100644 --- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java index 92c919e..940402f 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java index 930aac9..4225cc1 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java index 380d46e..70f43a9 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java index 417dbbb..89756a8 100644 --- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java index f307ee4..1260958 100644 --- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index e6ebec7..55ddef5 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java index 427702d..d13bf7c 100644 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java index 9aad95c..fcc1157 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java index d6fd0ba..42a122b 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java index dd155dd..78d08bd 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java index f39b18f..df350bb 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java index 4de1738..d839ed9 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java index 7dc7bc5..ecc8a41 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java index 63543d7..52ad67f 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java index 95e1a87..046d48f 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java index 46f6682..400774d 100644 --- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java index dbf0c3a..bb6fed8 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java index 693ad61..1851876 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java index 2547f1d..6fcd30e 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java index 15f2e37..57f8f1f 100644 --- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java index 4dfd168..0aede27 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java index aa0c798..bbb40f3 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java index 9c3c578..0f8d406 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java index fa73621..967759e 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java index 8122411..e4841c9 100644 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java index a904165..fac5631 100644 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java index 951e7ca..b01ea88 100644 --- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java index f4741a2..2c421a5 100644 --- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java index be7012a..c2beb48 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java index bda1c5e..6e9f4d7 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java index 375f435..bc48f19 100644 --- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java index bc14cfd..eda5f5a 100644 --- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index e9b93d4..0780d44 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1,10 +1,21 @@ /* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.schemabinding.version2.descriptors; //---------------------------------/ diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 57cd1fa..7233b9e 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index 57b1664..898b674 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java index 476e9f7..201c437 100755 --- a/src/jalview/schemes/BuriedColourScheme.java +++ b/src/jalview/schemes/BuriedColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index 5f9f8f0..2c3f2c0 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java index 8deb556..f48f679 100755 --- a/src/jalview/schemes/ColourSchemeI.java +++ b/src/jalview/schemes/ColourSchemeI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index dd4eb53..3333a82 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java index c60b0b6..af2be8d 100755 --- a/src/jalview/schemes/Consensus.java +++ b/src/jalview/schemes/Consensus.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java index b134968..3d3f321 100644 --- a/src/jalview/schemes/GraduatedColor.java +++ b/src/jalview/schemes/GraduatedColor.java @@ -1,5 +1,20 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.schemes; diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java index 4ab0431..95855d9 100755 --- a/src/jalview/schemes/HelixColourScheme.java +++ b/src/jalview/schemes/HelixColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java index b934714..0539f51 100755 --- a/src/jalview/schemes/HydrophobicColourScheme.java +++ b/src/jalview/schemes/HydrophobicColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index 39a0d6c..7906ed1 100755 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index 18fc6e4..ae148a6 100755 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 4990791..cde457d 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index ff73050..69b43a2 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java index 743df65..9514ac5 100755 --- a/src/jalview/schemes/ScoreColourScheme.java +++ b/src/jalview/schemes/ScoreColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java index a5a5ed3..345e206 100644 --- a/src/jalview/schemes/ScoreMatrix.java +++ b/src/jalview/schemes/ScoreMatrix.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java index 8c69fcc..04c7d16 100755 --- a/src/jalview/schemes/StrandColourScheme.java +++ b/src/jalview/schemes/StrandColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java index 590191b..d03c04d 100755 --- a/src/jalview/schemes/TaylorColourScheme.java +++ b/src/jalview/schemes/TaylorColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java index e461586..0dafddc 100755 --- a/src/jalview/schemes/TurnColourScheme.java +++ b/src/jalview/schemes/TurnColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index e42fd29..9a781cb 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java index 27f1f33..204228d 100755 --- a/src/jalview/schemes/ZappoColourScheme.java +++ b/src/jalview/schemes/ZappoColourScheme.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/structure/SelectionListener.java b/src/jalview/structure/SelectionListener.java index 40c44f4..696d860 100644 --- a/src/jalview/structure/SelectionListener.java +++ b/src/jalview/structure/SelectionListener.java @@ -1,5 +1,20 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.structure; diff --git a/src/jalview/structure/SelectionSource.java b/src/jalview/structure/SelectionSource.java index df383b5..25ffa73 100644 --- a/src/jalview/structure/SelectionSource.java +++ b/src/jalview/structure/SelectionSource.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.structure; /** diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java index 7021f95..bf6ceb9 100644 --- a/src/jalview/structure/SequenceListener.java +++ b/src/jalview/structure/SequenceListener.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java index 0f7bf30..7468d0a 100644 --- a/src/jalview/structure/StructureListener.java +++ b/src/jalview/structure/StructureListener.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java index b119e73..20c491c 100644 --- a/src/jalview/structure/StructureMapping.java +++ b/src/jalview/structure/StructureMapping.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 88d9f24..47973d0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/structure/VamsasListener.java b/src/jalview/structure/VamsasListener.java index 962c928..6f0110f 100644 --- a/src/jalview/structure/VamsasListener.java +++ b/src/jalview/structure/VamsasListener.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java index f3c8cfd..5ea4588 100755 --- a/src/jalview/util/BrowserLauncher.java +++ b/src/jalview/util/BrowserLauncher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java index 9cb2430..316cf5b 100755 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 9704170..0129f6e 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java index 46abdb9..49e4027 100755 --- a/src/jalview/util/Format.java +++ b/src/jalview/util/Format.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java index 511212a..d95feb1 100755 --- a/src/jalview/util/ImageMaker.java +++ b/src/jalview/util/ImageMaker.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index 6405f98..943705a 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java index e225857..c353bc2 100644 --- a/src/jalview/util/Platform.java +++ b/src/jalview/util/Platform.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java index 8f7e116..a482fef 100755 --- a/src/jalview/util/QuickSort.java +++ b/src/jalview/util/QuickSort.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java index be416dc..15f4552 100644 --- a/src/jalview/util/ShiftList.java +++ b/src/jalview/util/ShiftList.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java index a6ead15..5f3b2a4 100755 --- a/src/jalview/util/TableSorter.java +++ b/src/jalview/util/TableSorter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java index e332614..24ea605 100644 --- a/src/jalview/util/UrlLink.java +++ b/src/jalview/util/UrlLink.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/util/jarInputStreamProvider.java b/src/jalview/util/jarInputStreamProvider.java index 6012cfd..0f3ec36 100644 --- a/src/jalview/util/jarInputStreamProvider.java +++ b/src/jalview/util/jarInputStreamProvider.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.util; import java.io.IOException; @@ -20,4 +38,4 @@ public interface jarInputStreamProvider { * @return human readable name for datasource used when reporting any problems with it */ String getFilename(); -} \ No newline at end of file +} diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index 8fc49b1..d3c20ba 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java index 7e822aa..87e8bb8 100755 --- a/src/jalview/ws/Discoverer.java +++ b/src/jalview/ws/Discoverer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 3add58d..0e33e02 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java index 68360d6..272b147 100644 --- a/src/jalview/ws/JPredThread.java +++ b/src/jalview/ws/JPredThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java index 089b243..ddd00c3 100755 --- a/src/jalview/ws/MsaWSClient.java +++ b/src/jalview/ws/MsaWSClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java index 3f05213..5189b91 100644 --- a/src/jalview/ws/MsaWSThread.java +++ b/src/jalview/ws/MsaWSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/SeqSearchWSClient.java b/src/jalview/ws/SeqSearchWSClient.java index 9b6023c..31fbe85 100644 --- a/src/jalview/ws/SeqSearchWSClient.java +++ b/src/jalview/ws/SeqSearchWSClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java index 0c34518..d96131d 100644 --- a/src/jalview/ws/SeqSearchWSThread.java +++ b/src/jalview/ws/SeqSearchWSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index 2be142a..adf386c 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java index e883ea4..fdeb01b 100755 --- a/src/jalview/ws/WSClient.java +++ b/src/jalview/ws/WSClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java index 8e78ba5..8832443 100755 --- a/src/jalview/ws/WSClientI.java +++ b/src/jalview/ws/WSClientI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java index 72d1e4f..03cfba7 100644 --- a/src/jalview/ws/WSThread.java +++ b/src/jalview/ws/WSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java index 9283c66..c0b288f 100644 --- a/src/jalview/ws/dbsources/DasSequenceSource.java +++ b/src/jalview/ws/dbsources/DasSequenceSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java index de2a034..7cfa7ac 100644 --- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java +++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java index b3242ad..41db106 100644 --- a/src/jalview/ws/dbsources/EmblCdsSouce.java +++ b/src/jalview/ws/dbsources/EmblCdsSouce.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java index 344182f..ac4a988 100644 --- a/src/jalview/ws/dbsources/EmblSource.java +++ b/src/jalview/ws/dbsources/EmblSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java index 61f2d8b..01f502b 100644 --- a/src/jalview/ws/dbsources/EmblXmlSource.java +++ b/src/jalview/ws/dbsources/EmblXmlSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java index ab779f6..57baf52 100644 --- a/src/jalview/ws/dbsources/GeneDbSource.java +++ b/src/jalview/ws/dbsources/GeneDbSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index 754176c..48ea306 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java index 91ffbca..7a99213 100644 --- a/src/jalview/ws/dbsources/Pfam.java +++ b/src/jalview/ws/dbsources/Pfam.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java index 25e08fc..0a2a4a4 100644 --- a/src/jalview/ws/dbsources/PfamFull.java +++ b/src/jalview/ws/dbsources/PfamFull.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java index 5cde798..6589b20 100644 --- a/src/jalview/ws/dbsources/PfamSeed.java +++ b/src/jalview/ws/dbsources/PfamSeed.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 814c534..4c984d4 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/UnprotName.java b/src/jalview/ws/dbsources/UnprotName.java index c827b03..93eb32d 100644 --- a/src/jalview/ws/dbsources/UnprotName.java +++ b/src/jalview/ws/dbsources/UnprotName.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java index e036404..3a19875 100644 --- a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java +++ b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java index 2a13baa..bf1c4fb 100644 --- a/src/jalview/ws/ebi/EBIFetchClient.java +++ b/src/jalview/ws/ebi/EBIFetchClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java index 013fb15..7d2097a 100644 --- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java +++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java index 25fbcbf..895c03e 100644 --- a/src/jalview/ws/seqfetcher/DbSourceProxy.java +++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java index e3f5664..6c61282 100644 --- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java +++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/uk/ac/ebi/picr/model/CrossReference.java b/src/uk/ac/ebi/picr/model/CrossReference.java index 58f8a8b..b79d525 100644 --- a/src/uk/ac/ebi/picr/model/CrossReference.java +++ b/src/uk/ac/ebi/picr/model/CrossReference.java @@ -1,10 +1,21 @@ -/** - * CrossReference.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.picr.model; public class CrossReference implements java.io.Serializable diff --git a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java index e07e14e..a8eb30b 100644 --- a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java +++ b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java @@ -1,10 +1,21 @@ -/** - * CrossReference_Helper.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.picr.model; public class CrossReference_Helper diff --git a/src/uk/ac/ebi/picr/model/UPEntry.java b/src/uk/ac/ebi/picr/model/UPEntry.java index b7ad7a6..166fce1 100644 --- a/src/uk/ac/ebi/picr/model/UPEntry.java +++ b/src/uk/ac/ebi/picr/model/UPEntry.java @@ -1,10 +1,21 @@ -/** - * UPEntry.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.picr.model; public class UPEntry implements java.io.Serializable diff --git a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java index 579a1b1..9ce6bc9 100644 --- a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java +++ b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java @@ -1,10 +1,21 @@ -/** - * UPEntry_Helper.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.picr.model; public class UPEntry_Helper diff --git a/src/uk/ac/ebi/www/Data.java b/src/uk/ac/ebi/www/Data.java index d9e1037..7f006fa 100755 --- a/src/uk/ac/ebi/www/Data.java +++ b/src/uk/ac/ebi/www/Data.java @@ -1,10 +1,21 @@ -/** - * Data.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public class Data implements java.io.Serializable diff --git a/src/uk/ac/ebi/www/InputParams.java b/src/uk/ac/ebi/www/InputParams.java index 0284103..a74a9ff 100755 --- a/src/uk/ac/ebi/www/InputParams.java +++ b/src/uk/ac/ebi/www/InputParams.java @@ -1,10 +1,21 @@ -/** - * InputParams.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public class InputParams implements java.io.Serializable diff --git a/src/uk/ac/ebi/www/WSFile.java b/src/uk/ac/ebi/www/WSFile.java index 0dd62b1..e38525a 100755 --- a/src/uk/ac/ebi/www/WSFile.java +++ b/src/uk/ac/ebi/www/WSFile.java @@ -1,10 +1,21 @@ -/** - * WSFile.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public class WSFile implements java.io.Serializable diff --git a/src/uk/ac/ebi/www/WSWUBlast.java b/src/uk/ac/ebi/www/WSWUBlast.java index 09d59a4..ba47dd4 100755 --- a/src/uk/ac/ebi/www/WSWUBlast.java +++ b/src/uk/ac/ebi/www/WSWUBlast.java @@ -1,10 +1,21 @@ -/** - * WSWUBlast.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public interface WSWUBlast extends java.rmi.Remote diff --git a/src/uk/ac/ebi/www/WSWUBlastService.java b/src/uk/ac/ebi/www/WSWUBlastService.java index ececb65..87c0d30 100755 --- a/src/uk/ac/ebi/www/WSWUBlastService.java +++ b/src/uk/ac/ebi/www/WSWUBlastService.java @@ -1,10 +1,21 @@ -/** - * WSWUBlastService.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public interface WSWUBlastService extends javax.xml.rpc.Service diff --git a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java index 6e8fca9..f89d382 100755 --- a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java +++ b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java @@ -1,10 +1,21 @@ -/** - * WSWUBlastServiceLocator.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public class WSWUBlastServiceLocator extends org.apache.axis.client.Service diff --git a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java index a8157b8..c9f493f 100755 --- a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java +++ b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java @@ -1,10 +1,21 @@ -/** - * WSWUBlastSoapBindingStub.java - * - * This file was auto-generated from WSDL - * by the Apache Axis WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www; public class WSWUBlastSoapBindingStub extends org.apache.axis.client.Stub diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java index ed401ad..5c18d77 100644 --- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java +++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java @@ -1,10 +1,21 @@ -/** - * AccessionMapperBindingStub.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www.picr.AccessionMappingService; public class AccessionMapperBindingStub extends org.apache.axis.client.Stub diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java index faf327b..212b8e2 100644 --- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java +++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java @@ -1,10 +1,21 @@ -/** - * AccessionMapperInterface.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www.picr.AccessionMappingService; public interface AccessionMapperInterface extends java.rmi.Remote diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java index a234689..2316ccf 100644 --- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java +++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java @@ -1,10 +1,21 @@ -/** - * AccessionMapperService.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www.picr.AccessionMappingService; public interface AccessionMapperService extends javax.xml.rpc.Service diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java index debb3c9..68388e2 100644 --- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java +++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java @@ -1,10 +1,21 @@ -/** - * AccessionMapperServiceLocator.java - * - * This file was auto-generated from WSDL - * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter. +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package uk.ac.ebi.www.picr.AccessionMappingService; public class AccessionMapperServiceLocator extends diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java index 93d6289..5035a86 100755 --- a/src/vamsas/IMsaWS.java +++ b/src/vamsas/IMsaWS.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java index 0eb9256..9072c41 100755 --- a/src/vamsas/objects/simple/Alignment.java +++ b/src/vamsas/objects/simple/Alignment.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java index 7bd91d0..b686925 100755 --- a/src/vamsas/objects/simple/Alignment_Helper.java +++ b/src/vamsas/objects/simple/Alignment_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/JpredResult.java b/src/vamsas/objects/simple/JpredResult.java index f294d51..4c3ad52 100755 --- a/src/vamsas/objects/simple/JpredResult.java +++ b/src/vamsas/objects/simple/JpredResult.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/JpredResult_Helper.java b/src/vamsas/objects/simple/JpredResult_Helper.java index edc1fc3..c3fe1a2 100755 --- a/src/vamsas/objects/simple/JpredResult_Helper.java +++ b/src/vamsas/objects/simple/JpredResult_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java index 3b9bb2a..8edad6a 100755 --- a/src/vamsas/objects/simple/MsaResult.java +++ b/src/vamsas/objects/simple/MsaResult.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java index 3065aeb..bff7127 100755 --- a/src/vamsas/objects/simple/MsaResult_Helper.java +++ b/src/vamsas/objects/simple/MsaResult_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java index a2b179e..2b3275c 100755 --- a/src/vamsas/objects/simple/Msfalignment.java +++ b/src/vamsas/objects/simple/Msfalignment.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Msfalignment_Helper.java b/src/vamsas/objects/simple/Msfalignment_Helper.java index 96fbca0..14d8a05 100755 --- a/src/vamsas/objects/simple/Msfalignment_Helper.java +++ b/src/vamsas/objects/simple/Msfalignment_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java index 81d954a..240c4a3 100755 --- a/src/vamsas/objects/simple/Object.java +++ b/src/vamsas/objects/simple/Object.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java index 6ea63e7..dd44b00 100755 --- a/src/vamsas/objects/simple/Object_Helper.java +++ b/src/vamsas/objects/simple/Object_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java index 84df25d..50397a6 100755 --- a/src/vamsas/objects/simple/Result.java +++ b/src/vamsas/objects/simple/Result.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java index 011ebf9..299384e 100755 --- a/src/vamsas/objects/simple/Result_Helper.java +++ b/src/vamsas/objects/simple/Result_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Secstructpred.java b/src/vamsas/objects/simple/Secstructpred.java index 93c8467..722a9f8 100755 --- a/src/vamsas/objects/simple/Secstructpred.java +++ b/src/vamsas/objects/simple/Secstructpred.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Secstructpred_Helper.java b/src/vamsas/objects/simple/Secstructpred_Helper.java index 1052f69..2e362a7 100755 --- a/src/vamsas/objects/simple/Secstructpred_Helper.java +++ b/src/vamsas/objects/simple/Secstructpred_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/SeqSearchResult.java b/src/vamsas/objects/simple/SeqSearchResult.java index c902117..978e095 100644 --- a/src/vamsas/objects/simple/SeqSearchResult.java +++ b/src/vamsas/objects/simple/SeqSearchResult.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/SeqSearchResult_Helper.java b/src/vamsas/objects/simple/SeqSearchResult_Helper.java index 3e10bab..30d84a0 100644 --- a/src/vamsas/objects/simple/SeqSearchResult_Helper.java +++ b/src/vamsas/objects/simple/SeqSearchResult_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java index 40c8ea0..1328877 100755 --- a/src/vamsas/objects/simple/Sequence.java +++ b/src/vamsas/objects/simple/Sequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java index d8416b8..e041436 100755 --- a/src/vamsas/objects/simple/SequenceSet.java +++ b/src/vamsas/objects/simple/SequenceSet.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java index 5ad832f..b0a61fd 100755 --- a/src/vamsas/objects/simple/SequenceSet_Helper.java +++ b/src/vamsas/objects/simple/SequenceSet_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java index f45ff0c..1d98093 100755 --- a/src/vamsas/objects/simple/Sequence_Helper.java +++ b/src/vamsas/objects/simple/Sequence_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java index cce5388..3381ef0 100755 --- a/src/vamsas/objects/simple/WsJobId.java +++ b/src/vamsas/objects/simple/WsJobId.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java index 77272d7..cf8b861 100755 --- a/src/vamsas/objects/simple/WsJobId_Helper.java +++ b/src/vamsas/objects/simple/WsJobId_Helper.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License diff --git a/utils/InstallAnywhere/jalview_buildinstaller.xml b/utils/InstallAnywhere/jalview_buildinstaller.xml index ac65ad2..86effb6 100644 --- a/utils/InstallAnywhere/jalview_buildinstaller.xml +++ b/utils/InstallAnywhere/jalview_buildinstaller.xml @@ -1,4 +1,22 @@ + diff --git a/utils/help2Website.java b/utils/help2Website.java index 25435f4..3de49e5 100755 --- a/utils/help2Website.java +++ b/utils/help2Website.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License -- 1.7.10.2