README_IA

Change in all repo documentation advising launching Jalview with the

-Djava.ext.dirs=LIB

option to now use

-classpath="LIB/*:..."

instead. Using the -Djava.ext.dirs= option masks the JRE's own ext dir

which contains the sunjce packages. This manifests as cipher problems

when accessing https resources (in particular https://www.ebi.ac.uk/...

when searching for PDB structures, activated when choosing Sequence->"3D

Structure Data...")

Sprout from master 2006-05-02 16:44:32 UTC andrew 'spelling err'

Delete:

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

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

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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

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src/com/stevesoft/pat/BackRefRule.java

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src/com/stevesoft/pat/BasicStringBufferLike.java

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src/com/stevesoft/pat/DirFileRegex.java

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src/com/stevesoft/pat/NoPattern.java

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src/com/stevesoft/pat/Or.java

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src/com/stevesoft/pat/PopRule.java

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src/com/stevesoft/pat/RegexTokenizer.java

src/com/stevesoft/pat/RegexWriter.java

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src/com/stevesoft/pat/SpecialRule.java

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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

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src/ext/vamsas/JpredServiceLocator.java

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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

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utils/jalopy/docs/contact.html

utils/jalopy/docs/contributors.html

utils/jalopy/docs/dedication.html

utils/jalopy/docs/dependencies.html

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utils/jalopy/docs/indentation.html

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utils/jalopy/docs/inspector-naming.html

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utils/jalopy/docs/installation.html

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utils/jalopy/docs/license-antlr.html

utils/jalopy/docs/license-apache.html

utils/jalopy/docs/license-bsd.html

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utils/jalopy/docs/license-gnu-doc.html

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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

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utils/jalopy/docs/plugin-ant-usage.html

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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

Sprout from master 2005-12-12 15:53:10 UTC andrew 'Change dataset name'

Delete:

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/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

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utils/jalopy/docs/part-core.html

utils/jalopy/docs/part-plugins.html

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utils/jalopy/docs/plugin-ant-license.html

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utils/jalopy/docs/plugin-ant.html

utils/jalopy/docs/plugin-console-license.html

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utils/jalopy/docs/plugin-eclipse-integration.html

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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

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utils/jalopy/docs/printer.html

utils/jalopy/docs/project.html

utils/jalopy/docs/separation.html

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utils/jalopy/docs/whitespace.html

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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