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
    src/vamsas/objects/simple/Msfalignment_Helper.java
    src/vamsas/objects/simple/Object.java
    src/vamsas/objects/simple/Object_Helper.java
    src/vamsas/objects/simple/Result.java
    src/vamsas/objects/simple/Result_Helper.java
    src/vamsas/objects/simple/Secstructpred.java
    src/vamsas/objects/simple/Secstructpred_Helper.java
    src/vamsas/objects/simple/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
    utils/jalopy/docs/comments.html
    utils/jalopy/docs/contact.html
    utils/jalopy/docs/contributors.html
    utils/jalopy/docs/dedication.html
    utils/jalopy/docs/dependencies.html
    utils/jalopy/docs/docs.html
    utils/jalopy/docs/download.html
    utils/jalopy/docs/environment.html
    utils/jalopy/docs/faq.html
    utils/jalopy/docs/features.html
    utils/jalopy/docs/footer.html
    utils/jalopy/docs/header.html
    utils/jalopy/docs/history.html
    utils/jalopy/docs/imports.html
    utils/jalopy/docs/indentation.html
    utils/jalopy/docs/index.html
    utils/jalopy/docs/inspector-naming.html
    utils/jalopy/docs/inspector.html
    utils/jalopy/docs/installation.html
    utils/jalopy/docs/introduction.html
    utils/jalopy/docs/ix01.html
    utils/jalopy/docs/javadoc.html
    utils/jalopy/docs/license-antlr.html
    utils/jalopy/docs/license-apache.html
    utils/jalopy/docs/license-bsd.html
    utils/jalopy/docs/license-common-public.html
    utils/jalopy/docs/license-gnu-doc.html
    utils/jalopy/docs/license-gnu.html
    utils/jalopy/docs/license-sun-public.html
    utils/jalopy/docs/links.html
    utils/jalopy/docs/manual.html
    utils/jalopy/docs/messages.html
    utils/jalopy/docs/misc.html
    utils/jalopy/docs/part-core.html
    utils/jalopy/docs/part-plugins.html
    utils/jalopy/docs/plugin-ant-config.html
    utils/jalopy/docs/plugin-ant-license.html
    utils/jalopy/docs/plugin-ant-usage.html
    utils/jalopy/docs/plugin-ant.html
    utils/jalopy/docs/plugin-console-license.html
    utils/jalopy/docs/plugin-console-usage.html
    utils/jalopy/docs/plugin-console.html
    utils/jalopy/docs/plugin-eclipse-integration.html
    utils/jalopy/docs/plugin-eclipse-license.html
    utils/jalopy/docs/plugin-eclipse.html
    utils/jalopy/docs/plugin-jbuilder-integration.html
    utils/jalopy/docs/plugin-jbuilder-license.html
    utils/jalopy/docs/plugin-jbuilder.html
    utils/jalopy/docs/plugin-jdev-integration.html
    utils/jalopy/docs/plugin-jdev-license.html
    utils/jalopy/docs/plugin-jdev.html
    utils/jalopy/docs/plugin-jedit-integration.html
    utils/jalopy/docs/plugin-jedit-license.html
    utils/jalopy/docs/plugin-jedit.html
    utils/jalopy/docs/plugin-netbeans-integration.html
    utils/jalopy/docs/plugin-netbeans-license.html
    utils/jalopy/docs/plugin-netbeans.html
    utils/jalopy/docs/plugins.html
    utils/jalopy/docs/printer.html
    utils/jalopy/docs/project.html
    utils/jalopy/docs/separation.html
    utils/jalopy/docs/settings.html
    utils/jalopy/docs/site.css
    utils/jalopy/docs/sorting.html
    utils/jalopy/docs/usage.html
    utils/jalopy/docs/whitespace.html
    utils/jalopy/docs/wrapping.html
    utils/jalopy/lib/aelfred-1.2.jar
    utils/jalopy/lib/jalopy-1.0b11.jar
    utils/jalopy/lib/jalopy-ant-0.6.2.jar
    utils/jalopy/lib/jaxp-1.2.jar
    utils/jalopy/lib/jdom-1.0b8.jar
    utils/jalopy/lib/log4j-1.2.6.jar
    utils/jalopy/lib/oro-2.0.6.jar
    utils/jalopy/lib/sax-2.0.1.jar
    utils/jalopy/readme.html
    utils/jarunsigner.pl
    utils/jhall.jar
    utils/jhindexer
    utils/jhindexer.jar
    utils/proguard.jar
    utils/roxes-ant-tasks-1.2-2004-01-30.jar
    utils/wsdl4j.jar

2.08, not 2.07

To export page

Links

load features/annotations typo.

added note about cursor mode disabling the popup menu.

typo and explanation for ignore gaps in consensus

reworded pad gaps

reworded pad gaps.

2.08 update

put modellerpir in correct place!

updated menus and rearranged seqfeatures (again)

Displays error line on error

fix links to complex html (that don't display) by quoting them
verbatim.

Just removing new line character

moved Modeller/PIR description to its own home.

moved modellerpir to io

describing the Modeller/PIR output.

Fixed table border and updated restrictions

Editing tab

added bit about modeller/pir

added annotationColouring to whats new and updated IO and cursorMode
(mac os and backspace==delete)

del and backspace do the same thing

Release Date width

extended preamble and added new heading for user defined annotation
instructions.

tab name is editing

doco

doco changes.

added 2.08 application version dialog box.

feature settings dialog box for jalview 2.08 application

Protein desc bug fixed

dont need to set - to -

Fixed protein desc bug

doco writing.

Takes popup away from mouseevent, prevents immediate copy

No need for vetoablechange

Set all gaps to - symbol

padGaps set in preferences

Padgaps pref set

ModellerOutput set in preferences

Autocalculate consensus set in preferences

Scroll cursor wrapped alignment

+1 error in group edit all sequences

remove new line in alquality

added full keyset for cursorMode

Must check consensus length if autocalculate off

added cursorMode feature page and rearranged keystrokes documentation.

Hide ref to HiddenRegion

removed dross, added a safety check to buildextclients and added references to docs/building.html

Must copy feature settings from one frame to another as they are not attached ot the dataset

Must copy feature settings from one frame to another as they are not attached ot the dataset

Maintain feature order

Save annotationColours

Public get methods

public get methods

Save graph threshold and annotation colours

2.08 updates

Order of menuitems

Turn off validation for speed

No need for minorSpacing

Shift also for group editing

Padgap history

Note on build target being usage

Default raget is :usage

2.08 update

2.08 updates

Modified for 2.08

New files

Draw threshold over graph

loadDataFile is public

Add annoations from the command line

Overview follows cursor movement

Set keyboard numbers to null if esc pressed

Keyboard editing added to applet

set current tree once the tree is prepared

Jalview2XML does not use static load

Pad gaps removes excess gaps

Specify com.stevesoft.pat.Regex

Autocalculate consensus

More keys for editing

Get hiddenBoundaryLeft and right

Jalview2XML does not use static load anymore

Disable hide regions

Scrolls if dragged off the screen

Keyboard editing

Cursor colour

Set current tree when ready

Allows loading of archive XML

For archive only

Uses descriptors

Binding with descriptors

Namespace changes

Feature settings

Has its own featureRenderer

Group colours not used

Associated Data menu item

Cursor added

Typo

fr.transferSettings

FeatureSettings bug fixed