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JAL-3210 Barebones gradle/buildship/eclipse. See README

  1. … 1990 more files in changeset.
JAL-3065 - amended commit 4906697ab6e5a79fbce3baae89f7f64178c9a739 to exclude .settings/..groovy Added notes to the instructions, also adjusted the jalviewDesktopRunner test to lookup OS and use ';' or ':' accordingly. All the CommandLineOperations tests failed on my (hastily set up) linux box, so I'm committing and will test on MacOS too.

  1. … 3 more files in changeset.
Added notes to the instructions, also adjusted the jalviewDesktopRunner test to lookup OS and use ';' or ':' accordingly. All the CommandLineOperations tests failed on my (hastily set up) linux box, so I'm committing and will test on MacOS too.

  1. … 4 more files in changeset.
should really explain what path to classes is as well as path to lib here

should really explain what path to classes is as well as path to lib here

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

JAL-3065

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...")

  1. … 4 more files in changeset.
additional instructions and use of -jar for launching

additional instructions and use of -jar for launching

This commit was manufactured by cvs2svn to create tag 'Release_2_08_1'.

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

  1. … 526 more files in changeset.
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

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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

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Delete:

src/uk/ac/ebi/www/Data.java

src/uk/ac/ebi/www/InputParams.java

src/uk/ac/ebi/www/WSFile.java

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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

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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

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utils/jalopy/lib/oro-2.0.6.jar

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utils/jalopy/readme.html

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InstallAnywhere readme