10:20 pm
- … 1990 more files in changeset.
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Tuesday 27 Aug 2019
10:20 pm
Ben Soares
JAL-3210 Barebones gradle/buildship/eclipse. See README
Wednesday 12 Sep 2018
12:13 pm
Wednesday 05 Sep 2018
9:01 am
Jim Procter
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.
Tuesday 04 Sep 2018
4:17 pm
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.
Thursday 26 Jul 2018
11:36 am
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
11:00 am
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
10:31 am
Tuesday 17 Jul 2018
12:17 pm
Ben Soares
JAL-3065Change in all repo documentation advising launching Jalview with the-Djava.ext.dirs=LIBoption to now use-classpath="LIB/*:..."instead. Using the -Djava.ext.dirs= option masks the JRE's own ext dirwhich contains the sunjce packages. This manifests as cipher problemswhen accessing https resources (in particular https://www.ebi.ac.uk/...when searching for PDB structures, activated when choosing Sequence->"3DStructure Data...")
Wednesday 11 Nov 2009
9:05 am
additional instructions and use of -jar for launching
9:05 am
additional instructions and use of -jar for launching
Tuesday 02 May 2006
5:44 pm
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
Monday 10 Apr 2006
4:16 pm
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
Monday 12 Dec 2005
3:53 pm
This commit was manufactured by cvs2svn to create tag 'Release_2_07'.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 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
Tuesday 09 Aug 2005
6:06 pm
InstallAnywhere readme
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