This commit was manufactured by cvs2svn to create tag 'Release_2_08'.

This commit was manufactured by cvs2svn to create tag 'Release_2_08'.

Sprout from master 2006-04-10 15:16:46 UTC andrew '2.08, not 2.07'
Delete:
    help/html/misc/properties.gif
    lib/activation.jar
    lib/axis.jar
    lib/castor-0.9.6-xml.jar
    lib/commons-discovery.jar
    lib/commons-logging.jar
    lib/jaxrpc.jar
    lib/jhall.jar
    lib/log4j-1.2.8.jar
    lib/mail.jar
    lib/regex.jar
    lib/saaj.jar
    lib/wsdl4j.jar
    lib/xercesImpl.jar
    lib/xml-apis.jar
    resources/images/dna.gif
    resources/images/dna1.gif
    resources/images/dna2.gif
    resources/images/dna3.gif
    resources/images/dna4.gif
    resources/images/dna5.gif
    resources/images/dna6.gif
    resources/images/dna7.gif
    resources/images/dna8.gif
    resources/images/dna9.gif
    resources/images/file.png
    resources/images/idwidth.gif
    resources/images/logo.gif
    resources/images/logo_big.gif
    resources/uniprot_mapping.xml
    schemas/JalviewUserColours.xsd
    schemas/jalview.xsd
    schemas/vamsas.xsd
    src/MCview/AppletPDBCanvas.java
    src/MCview/AppletPDBViewer.java
    src/MCview/Atom.java
    src/MCview/Bond.java
    src/MCview/MCMatrix.java
    src/MCview/PDBCanvas.java
    src/MCview/PDBChain.java
    src/MCview/PDBViewer.java
    src/MCview/PDBfile.java
    src/MCview/Residue.java
    src/MCview/Zsort.java
    src/com/stevesoft/pat/AmpersandRule.java
    src/com/stevesoft/pat/Any.java
    src/com/stevesoft/pat/BackG.java
    src/com/stevesoft/pat/BackMatch.java
    src/com/stevesoft/pat/BackRefRule.java
    src/com/stevesoft/pat/Backup.java
    src/com/stevesoft/pat/BasicStringBufferLike.java
    src/com/stevesoft/pat/Bits.java
    src/com/stevesoft/pat/Boundary.java
    src/com/stevesoft/pat/Bracket.java
    src/com/stevesoft/pat/CaseMgr.java
    src/com/stevesoft/pat/ChangeRule.java
    src/com/stevesoft/pat/CodeRule.java
    src/com/stevesoft/pat/Ctrl.java
    src/com/stevesoft/pat/Custom.java
    src/com/stevesoft/pat/CustomEndpoint.java
    src/com/stevesoft/pat/DirFileRegex.java
    src/com/stevesoft/pat/DotMulti.java
    src/com/stevesoft/pat/End.java
    src/com/stevesoft/pat/FastBracket.java
    src/com/stevesoft/pat/FastMulti.java
    src/com/stevesoft/pat/FileRegex.java
    src/com/stevesoft/pat/Group.java
    src/com/stevesoft/pat/LeftRule.java
    src/com/stevesoft/pat/Multi.java
    src/com/stevesoft/pat/MultiMin.java
    src/com/stevesoft/pat/Multi_stage2.java
    src/com/stevesoft/pat/NoPattern.java
    src/com/stevesoft/pat/NonDirFileRegex.java
    src/com/stevesoft/pat/NotImplementedError.java
    src/com/stevesoft/pat/NullPattern.java
    src/com/stevesoft/pat/NullRule.java
    src/com/stevesoft/pat/Or.java
    src/com/stevesoft/pat/OrMark.java
    src/com/stevesoft/pat/PartialBuffer.java
    src/com/stevesoft/pat/Pattern.java
    src/com/stevesoft/pat/PatternSub.java
    src/com/stevesoft/pat/PopRule.java
    src/com/stevesoft/pat/Prop.java
    src/com/stevesoft/pat/Pthings.java
    src/com/stevesoft/pat/PushRule.java
    src/com/stevesoft/pat/RBuffer.java
    src/com/stevesoft/pat/Range.java
    src/com/stevesoft/pat/RegOpt.java
    src/com/stevesoft/pat/RegRes.java
    src/com/stevesoft/pat/RegSyntax.java
    src/com/stevesoft/pat/RegSyntaxError.java
    src/com/stevesoft/pat/Regex.java
    src/com/stevesoft/pat/RegexReader.java
    src/com/stevesoft/pat/RegexTokenizer.java
    src/com/stevesoft/pat/RegexWriter.java
    src/com/stevesoft/pat/ReplaceRule.java
    src/com/stevesoft/pat/Replacer.java
    src/com/stevesoft/pat/RightRule.java
    src/com/stevesoft/pat/Rthings.java
    src/com/stevesoft/pat/RuleHolder.java
    src/com/stevesoft/pat/Skip.java
    src/com/stevesoft/pat/Skip2.java
    src/com/stevesoft/pat/SkipBMH.java
    src/com/stevesoft/pat/Skipped.java
    src/com/stevesoft/pat/SpecialRule.java
    src/com/stevesoft/pat/Start.java
    src/com/stevesoft/pat/StrPos.java
    src/com/stevesoft/pat/StringBufferLike.java
    src/com/stevesoft/pat/StringLike.java
    src/com/stevesoft/pat/StringRule.java
    src/com/stevesoft/pat/SubMark.java
    src/com/stevesoft/pat/TransPat.java
    src/com/stevesoft/pat/Transformer.java
    src/com/stevesoft/pat/UniValidator.java
    src/com/stevesoft/pat/Validator.java
    src/com/stevesoft/pat/WantMoreTextReplaceRule.java
    src/com/stevesoft/pat/lookAhead.java
    src/com/stevesoft/pat/oneChar.java
    src/com/stevesoft/pat/parsePerl.java
    src/com/stevesoft/pat/patInf.java
    src/com/stevesoft/pat/patInt.java
    src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
    src/com/stevesoft/pat/wrap/CharArrayWrap.java
    src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
    src/com/stevesoft/pat/wrap/StringBufferWrap.java
    src/com/stevesoft/pat/wrap/StringWrap.java
    src/com/stevesoft/pat/wrap/WriterWrap.java
    src/ext/vamsas/IRegistry.java
    src/ext/vamsas/IRegistryService.java
    src/ext/vamsas/IRegistryServiceLocator.java
    src/ext/vamsas/Jpred.java
    src/ext/vamsas/JpredService.java
    src/ext/vamsas/JpredServiceLocator.java
    src/ext/vamsas/JpredSoapBindingStub.java
    src/ext/vamsas/MuscleWS.java
    src/ext/vamsas/MuscleWSService.java
    src/ext/vamsas/MuscleWSServiceLocator.java
    src/ext/vamsas/MuscleWSSoapBindingStub.java
    src/ext/vamsas/RegistryServiceSoapBindingStub.java
    src/ext/vamsas/ServiceHandle.java
    src/ext/vamsas/ServiceHandles.java
    src/jalview/analysis/AAFrequency.java
    src/jalview/analysis/AlignSeq.java
    src/jalview/analysis/AlignmentSorter.java
    src/jalview/analysis/Conservation.java
    src/jalview/analysis/NJTree.java
    src/jalview/analysis/PCA.java
    src/jalview/analysis/SeqsetUtils.java
    src/jalview/analysis/SequenceIdMatcher.java
    src/jalview/appletgui/APopupMenu.java
    src/jalview/appletgui/AlignFrame.java
    src/jalview/appletgui/AlignViewport.java
    src/jalview/appletgui/AlignmentPanel.java
    src/jalview/appletgui/AnnotationColourChooser.java
    src/jalview/appletgui/AnnotationLabels.java
    src/jalview/appletgui/AnnotationPanel.java
    src/jalview/appletgui/ColumnSelection.java
    src/jalview/appletgui/CutAndPasteTransfer.java
    src/jalview/appletgui/FeatureRenderer.java
    src/jalview/appletgui/FeatureSettings.java
    src/jalview/appletgui/Finder.java
    src/jalview/appletgui/FontChooser.java
    src/jalview/appletgui/IdCanvas.java
    src/jalview/appletgui/IdPanel.java
    src/jalview/appletgui/IdwidthAdjuster.java
    src/jalview/appletgui/OverviewPanel.java
    src/jalview/appletgui/PCAPanel.java
    src/jalview/appletgui/PaintRefresher.java
    src/jalview/appletgui/PairwiseAlignPanel.java
    src/jalview/appletgui/RedundancyPanel.java
    src/jalview/appletgui/RotatableCanvas.java
    src/jalview/appletgui/ScalePanel.java
    src/jalview/appletgui/SeqCanvas.java
    src/jalview/appletgui/SeqPanel.java
    src/jalview/appletgui/SequenceRenderer.java
    src/jalview/appletgui/SliderPanel.java
    src/jalview/appletgui/TreeCanvas.java
    src/jalview/appletgui/TreePanel.java
    src/jalview/appletgui/UserDefinedColours.java
    src/jalview/bin/Cache.java
    src/jalview/bin/Jalview.java
    src/jalview/bin/JalviewLite.java
    src/jalview/binding/Alignment.java
    src/jalview/binding/Annotation.java
    src/jalview/binding/AnnotationElement.java
    src/jalview/binding/Colour.java
    src/jalview/binding/Feature.java
    src/jalview/binding/FeatureSettings.java
    src/jalview/binding/Features.java
    src/jalview/binding/JGroup.java
    src/jalview/binding/JSeq.java
    src/jalview/binding/JalviewModel.java
    src/jalview/binding/JalviewModelSequence.java
    src/jalview/binding/JalviewUserColours.java
    src/jalview/binding/JalviewUserColoursItem.java
    src/jalview/binding/Pdbentry.java
    src/jalview/binding/PdbentryItem.java
    src/jalview/binding/Pdbids.java
    src/jalview/binding/Property.java
    src/jalview/binding/Residue.java
    src/jalview/binding/Sequence.java
    src/jalview/binding/SequenceSet.java
    src/jalview/binding/SequenceType.java
    src/jalview/binding/Setting.java
    src/jalview/binding/Tree.java
    src/jalview/binding/UserColour.java
    src/jalview/binding/UserColourScheme.java
    src/jalview/binding/UserColours.java
    src/jalview/binding/VAMSAS.java
    src/jalview/binding/VamsasModel.java
    src/jalview/binding/Viewport.java
    src/jalview/datamodel/Alignment.java
    src/jalview/datamodel/AlignmentAnnotation.java
    src/jalview/datamodel/AlignmentI.java
    src/jalview/datamodel/AlignmentOrder.java
    src/jalview/datamodel/Annotation.java
    src/jalview/datamodel/BinaryNode.java
    src/jalview/datamodel/BinarySequence.java
    src/jalview/datamodel/DBRefEntry.java
    src/jalview/datamodel/GraphLine.java
    src/jalview/datamodel/HiddenSequences.java
    src/jalview/datamodel/HistoryItem.java
    src/jalview/datamodel/PDBEntry.java
    src/jalview/datamodel/Provenance.java
    src/jalview/datamodel/ProvenanceEntry.java
    src/jalview/datamodel/SearchResults.java
    src/jalview/datamodel/Sequence.java
    src/jalview/datamodel/SequenceFeature.java
    src/jalview/datamodel/SequenceGroup.java
    src/jalview/datamodel/SequenceI.java
    src/jalview/datamodel/SequenceNode.java
    src/jalview/datamodel/SequencePoint.java
    src/jalview/datamodel/UniprotEntry.java
    src/jalview/datamodel/UniprotFile.java
    src/jalview/datamodel/UniprotProteinName.java
    src/jalview/datamodel/UniprotSequence.java
    src/jalview/gui/AlignFrame.java
    src/jalview/gui/AlignViewport.java
    src/jalview/gui/AlignmentPanel.java
    src/jalview/gui/AnnotationColourChooser.java
    src/jalview/gui/AnnotationLabels.java
    src/jalview/gui/AnnotationPanel.java
    src/jalview/gui/ColumnSelection.java
    src/jalview/gui/CutAndPasteTransfer.java
    src/jalview/gui/Desktop.java
    src/jalview/gui/EPSOptions.java
    src/jalview/gui/FeatureRenderer.java
    src/jalview/gui/FeatureSettings.java
    src/jalview/gui/Finder.java
    src/jalview/gui/FontChooser.java
    src/jalview/gui/IdCanvas.java
    src/jalview/gui/IdPanel.java
    src/jalview/gui/IdwidthAdjuster.java
    src/jalview/gui/Jalview2XML.java
    src/jalview/gui/Jalview2XML_V1.java
    src/jalview/gui/OverviewPanel.java
    src/jalview/gui/PCAPanel.java
    src/jalview/gui/PaintRefresher.java
    src/jalview/gui/PairwiseAlignPanel.java
    src/jalview/gui/PopupMenu.java
    src/jalview/gui/Preferences.java
    src/jalview/gui/RedundancyPanel.java
    src/jalview/gui/RotatableCanvas.java
    src/jalview/gui/ScalePanel.java
    src/jalview/gui/SeqCanvas.java
    src/jalview/gui/SeqPanel.java
    src/jalview/gui/SequenceFetcher.java
    src/jalview/gui/SequenceRenderer.java
    src/jalview/gui/SliderPanel.java
    src/jalview/gui/SplashScreen.java
    src/jalview/gui/TreeCanvas.java
    src/jalview/gui/TreePanel.java
    src/jalview/gui/UserDefinedColours.java
    src/jalview/gui/WebserviceInfo.java
    src/jalview/io/AlignFile.java
    src/jalview/io/AnnotationReader.java
    src/jalview/io/AppletFormatAdapter.java
    src/jalview/io/BLCFile.java
    src/jalview/io/ClustalFile.java
    src/jalview/io/EBIFetchClient.java
    src/jalview/io/FastaFile.java
    src/jalview/io/FileLoader.java
    src/jalview/io/FileParse.java
    src/jalview/io/FormatAdapter.java
    src/jalview/io/HTMLOutput.java
    src/jalview/io/IdentifyFile.java
    src/jalview/io/JPredFile.java
    src/jalview/io/JalviewFileChooser.java
    src/jalview/io/JalviewFileFilter.java
    src/jalview/io/JalviewFileView.java
    src/jalview/io/MSFfile.java
    src/jalview/io/ModellerDescription.java
    src/jalview/io/NewickFile.java
    src/jalview/io/PIRFile.java
    src/jalview/io/PfamFile.java
    src/jalview/io/PileUpfile.java
    src/jalview/io/SequenceFeatureFetcher.java
    src/jalview/io/WSWUBlastClient.java
    src/jalview/jbgui/GAlignFrame.java
    src/jalview/jbgui/GAlignmentPanel.java
    src/jalview/jbgui/GCutAndPasteTransfer.java
    src/jalview/jbgui/GDesktop.java
    src/jalview/jbgui/GFinder.java
    src/jalview/jbgui/GFontChooser.java
    src/jalview/jbgui/GPCAPanel.java
    src/jalview/jbgui/GPairwiseAlignPanel.java
    src/jalview/jbgui/GPreferences.java
    src/jalview/jbgui/GSequenceLink.java
    src/jalview/jbgui/GSliderPanel.java
    src/jalview/jbgui/GTreePanel.java
    src/jalview/jbgui/GUserDefinedColours.java
    src/jalview/jbgui/GWebserviceInfo.java
    src/jalview/math/Matrix.java
    src/jalview/math/RotatableMatrix.java
    src/jalview/schemabinding/version2/Alignment.java
    src/jalview/schemabinding/version2/AlignmentDescriptor.java
    src/jalview/schemabinding/version2/Annotation.java
    src/jalview/schemabinding/version2/AnnotationColours.java
    src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
    src/jalview/schemabinding/version2/AnnotationDescriptor.java
    src/jalview/schemabinding/version2/AnnotationElement.java
    src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
    src/jalview/schemabinding/version2/Colour.java
    src/jalview/schemabinding/version2/ColourDescriptor.java
    src/jalview/schemabinding/version2/Feature.java
    src/jalview/schemabinding/version2/FeatureDescriptor.java
    src/jalview/schemabinding/version2/FeatureSettings.java
    src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
    src/jalview/schemabinding/version2/Features.java
    src/jalview/schemabinding/version2/FeaturesDescriptor.java
    src/jalview/schemabinding/version2/JGroup.java
    src/jalview/schemabinding/version2/JGroupDescriptor.java
    src/jalview/schemabinding/version2/JSeq.java
    src/jalview/schemabinding/version2/JSeqDescriptor.java
    src/jalview/schemabinding/version2/JalviewModel.java
    src/jalview/schemabinding/version2/JalviewModelDescriptor.java
    src/jalview/schemabinding/version2/JalviewModelSequence.java
    src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
    src/jalview/schemabinding/version2/JalviewUserColours.java
    src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
    src/jalview/schemabinding/version2/Pdbentry.java
    src/jalview/schemabinding/version2/PdbentryDescriptor.java
    src/jalview/schemabinding/version2/PdbentryItem.java
    src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
    src/jalview/schemabinding/version2/Pdbids.java
    src/jalview/schemabinding/version2/PdbidsDescriptor.java
    src/jalview/schemabinding/version2/Property.java
    src/jalview/schemabinding/version2/PropertyDescriptor.java
    src/jalview/schemabinding/version2/Sequence.java
    src/jalview/schemabinding/version2/SequenceDescriptor.java
    src/jalview/schemabinding/version2/SequenceSet.java
    src/jalview/schemabinding/version2/SequenceSetDescriptor.java
    src/jalview/schemabinding/version2/SequenceType.java
    src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
    src/jalview/schemabinding/version2/Setting.java
    src/jalview/schemabinding/version2/SettingDescriptor.java
    src/jalview/schemabinding/version2/ThresholdLine.java
    src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
    src/jalview/schemabinding/version2/Tree.java
    src/jalview/schemabinding/version2/TreeDescriptor.java
    src/jalview/schemabinding/version2/UserColourScheme.java
    src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
    src/jalview/schemabinding/version2/UserColours.java
    src/jalview/schemabinding/version2/UserColoursDescriptor.java
    src/jalview/schemabinding/version2/VAMSAS.java
    src/jalview/schemabinding/version2/VAMSASDescriptor.java
    src/jalview/schemabinding/version2/VamsasModel.java
    src/jalview/schemabinding/version2/VamsasModelDescriptor.java
    src/jalview/schemabinding/version2/Viewport.java
    src/jalview/schemabinding/version2/ViewportDescriptor.java
    src/jalview/schemes/AnnotationColourGradient.java
    src/jalview/schemes/Blosum62ColourScheme.java
    src/jalview/schemes/BuriedColourScheme.java
    src/jalview/schemes/ClustalxColourScheme.java
    src/jalview/schemes/ColourSchemeI.java
    src/jalview/schemes/ColourSchemeProperty.java
    src/jalview/schemes/Consensus.java
    src/jalview/schemes/HelixColourScheme.java
    src/jalview/schemes/HydrophobicColourScheme.java
    src/jalview/schemes/NucleotideColourScheme.java
    src/jalview/schemes/PIDColourScheme.java
    src/jalview/schemes/ResidueColourScheme.java
    src/jalview/schemes/ResidueProperties.java
    src/jalview/schemes/ScoreColourScheme.java
    src/jalview/schemes/StrandColourScheme.java
    src/jalview/schemes/TaylorColourScheme.java
    src/jalview/schemes/TurnColourScheme.java
    src/jalview/schemes/UserColourScheme.java
    src/jalview/schemes/ZappoColourScheme.java
    src/jalview/util/BrowserLauncher.java
    src/jalview/util/Comparison.java
    src/jalview/util/DBRefUtils.java
    src/jalview/util/Format.java
    src/jalview/util/ImageMaker.java
    src/jalview/util/QuickSort.java
    src/jalview/ws/Discoverer.java
    src/jalview/ws/JPredClient.java
    src/jalview/ws/MsaWSClient.java
    src/jalview/ws/WSClient.java
    src/jalview/ws/WSClientI.java
    src/org/jibble/epsgraphics/EpsDocument.java
    src/org/jibble/epsgraphics/EpsException.java
    src/org/jibble/epsgraphics/EpsGraphics2D.java
    src/uk/ac/ebi/www/Data.java
    src/uk/ac/ebi/www/InputParams.java
    src/uk/ac/ebi/www/WSFile.java
    src/uk/ac/ebi/www/WSWUBlast.java
    src/uk/ac/ebi/www/WSWUBlastService.java
    src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
    src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
    src/vamsas/IMsaWS.java
    src/vamsas/objects/simple/Alignment.java
    src/vamsas/objects/simple/Alignment_Helper.java
    src/vamsas/objects/simple/JpredResult.java
    src/vamsas/objects/simple/JpredResult_Helper.java
    src/vamsas/objects/simple/MsaResult.java
    src/vamsas/objects/simple/MsaResult_Helper.java
    src/vamsas/objects/simple/Msfalignment.java
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    src/vamsas/objects/simple/Object.java
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    src/vamsas/objects/simple/Secstructpred.java
    src/vamsas/objects/simple/Secstructpred_Helper.java
    src/vamsas/objects/simple/Sequence.java
    src/vamsas/objects/simple/SequenceSet.java
    src/vamsas/objects/simple/SequenceSet_Helper.java
    src/vamsas/objects/simple/Sequence_Helper.java
    src/vamsas/objects/simple/WsJobId.java
    src/vamsas/objects/simple/WsJobId_Helper.java
    utils/InstallAnywhere/Jalview.iap_xml
    utils/InstallAnywhere/README_IA
    utils/InstallAnywhere/align.gif
    utils/InstallAnywhere/bartonGroup.gif
    utils/InstallAnywhere/jalview.gif
    utils/InstallAnywhere/mac_logo.icns
    utils/axis-ant.jar
    utils/help2Website.java
    utils/jalopy/bin/lcp.bat
    utils/jalopy/bin/preferences.bat
    utils/jalopy/bin/preferences.sh
    utils/jalopy/docs/acknowledge.html
    utils/jalopy/docs/bi01.html
    utils/jalopy/docs/build.html
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