jprocter [Tue, 2 May 2006 16:44:33 +0000 (16:44 +0000)]
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
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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
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utils/jalopy/docs/features.html
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utils/jalopy/docs/history.html
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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
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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
amwaterhouse [Tue, 2 May 2006 16:44:32 +0000 (16:44 +0000)]
spelling err
amwaterhouse [Tue, 2 May 2006 12:24:48 +0000 (12:24 +0000)]
2.08.1
amwaterhouse [Tue, 2 May 2006 12:23:48 +0000 (12:23 +0000)]
Make nullFrame only once
amwaterhouse [Tue, 2 May 2006 12:23:28 +0000 (12:23 +0000)]
Remove unnecessary panel, also nullFrame created only once
amwaterhouse [Tue, 2 May 2006 12:23:01 +0000 (12:23 +0000)]
Middle mouse to compress alignment
amwaterhouse [Tue, 2 May 2006 12:22:20 +0000 (12:22 +0000)]
Check that fontsize > 0
amwaterhouse [Tue, 2 May 2006 12:21:57 +0000 (12:21 +0000)]
Toggle Case added
amwaterhouse [Tue, 2 May 2006 09:28:24 +0000 (09:28 +0000)]
Toggle case added to popup menu
amwaterhouse [Mon, 1 May 2006 14:29:21 +0000 (14:29 +0000)]
Remove edit menu if no group defined
amwaterhouse [Mon, 1 May 2006 14:28:51 +0000 (14:28 +0000)]
Maintain original transparency setting
amwaterhouse [Mon, 1 May 2006 14:28:32 +0000 (14:28 +0000)]
Change name to editMenu
amwaterhouse [Mon, 1 May 2006 13:24:10 +0000 (13:24 +0000)]
If Mac, use the fillRoundRect method
amwaterhouse [Mon, 1 May 2006 13:23:46 +0000 (13:23 +0000)]
Forces init of alignPanel if annotations added
amwaterhouse [Mon, 1 May 2006 13:22:58 +0000 (13:22 +0000)]
Fixes redraw top of group bug
amwaterhouse [Mon, 1 May 2006 13:22:38 +0000 (13:22 +0000)]
If no group, hide menu
amwaterhouse [Mon, 1 May 2006 13:22:22 +0000 (13:22 +0000)]
If mac, use the fillRoundRect
amwaterhouse [Mon, 1 May 2006 13:22:02 +0000 (13:22 +0000)]
java 1.1 compatibility
amwaterhouse [Fri, 28 Apr 2006 17:07:13 +0000 (17:07 +0000)]
Helix sizes
amwaterhouse [Fri, 28 Apr 2006 16:38:33 +0000 (16:38 +0000)]
Make sure end is less than sequence width
amwaterhouse [Fri, 28 Apr 2006 16:38:10 +0000 (16:38 +0000)]
Group width -1
amwaterhouse [Fri, 28 Apr 2006 16:37:58 +0000 (16:37 +0000)]
Watch for exceeding width limit
amwaterhouse [Fri, 28 Apr 2006 13:47:24 +0000 (13:47 +0000)]
If autoCalculate selected, recalculate immediately
amwaterhouse [Fri, 28 Apr 2006 13:45:40 +0000 (13:45 +0000)]
Back to gray line
amwaterhouse [Fri, 28 Apr 2006 13:42:04 +0000 (13:42 +0000)]
Back to gray line
amwaterhouse [Fri, 28 Apr 2006 13:38:39 +0000 (13:38 +0000)]
validCharWidth moved to viewport
amwaterhouse [Fri, 28 Apr 2006 13:26:22 +0000 (13:26 +0000)]
Annoying little line at end of wrapped alignment
amwaterhouse [Fri, 28 Apr 2006 12:35:12 +0000 (12:35 +0000)]
validCharWidth checks
amwaterhouse [Fri, 28 Apr 2006 12:34:28 +0000 (12:34 +0000)]
Edit menu added
amwaterhouse [Fri, 28 Apr 2006 12:34:18 +0000 (12:34 +0000)]
Add to palette layer
amwaterhouse [Fri, 28 Apr 2006 12:34:06 +0000 (12:34 +0000)]
Helix glyphs fixed
amwaterhouse [Fri, 28 Apr 2006 12:33:44 +0000 (12:33 +0000)]
Case sensitive
amwaterhouse [Fri, 28 Apr 2006 12:33:24 +0000 (12:33 +0000)]
changeCase
amwaterhouse [Fri, 28 Apr 2006 12:32:58 +0000 (12:32 +0000)]
Helix glyphs drawn correctly
amwaterhouse [Fri, 28 Apr 2006 12:32:36 +0000 (12:32 +0000)]
Dont select groups on ids
amwaterhouse [Fri, 28 Apr 2006 12:32:12 +0000 (12:32 +0000)]
Case shifter
amwaterhouse [Fri, 21 Apr 2006 11:19:13 +0000 (11:19 +0000)]
Alignment compression on middle mouse button
amwaterhouse [Fri, 21 Apr 2006 10:41:29 +0000 (10:41 +0000)]
Modified sequence selection
amwaterhouse [Wed, 19 Apr 2006 15:58:15 +0000 (15:58 +0000)]
Multiple views, alignpanels not being used
amwaterhouse [Wed, 19 Apr 2006 14:32:11 +0000 (14:32 +0000)]
Alignment might not have any annotations
amwaterhouse [Tue, 18 Apr 2006 13:17:20 +0000 (13:17 +0000)]
-1 from east scale, wrapped alignment
amwaterhouse [Thu, 13 Apr 2006 13:28:42 +0000 (13:28 +0000)]
showInternalMessage jdk1.5 bug
amwaterhouse [Mon, 10 Apr 2006 15:54:47 +0000 (15:54 +0000)]
add back in again
amwaterhouse [Mon, 10 Apr 2006 15:30:41 +0000 (15:30 +0000)]
old image
amwaterhouse [Mon, 10 Apr 2006 15:29:56 +0000 (15:29 +0000)]
old images
amwaterhouse [Mon, 10 Apr 2006 15:27:02 +0000 (15:27 +0000)]
New images
amwaterhouse [Mon, 10 Apr 2006 15:16:46 +0000 (15:16 +0000)]
2.08, not 2.07
amwaterhouse [Mon, 10 Apr 2006 14:53:10 +0000 (14:53 +0000)]
To export page
amwaterhouse [Mon, 10 Apr 2006 14:52:56 +0000 (14:52 +0000)]
Links
jprocter [Mon, 10 Apr 2006 14:36:49 +0000 (14:36 +0000)]
load features/annotations typo.
jprocter [Mon, 10 Apr 2006 14:32:54 +0000 (14:32 +0000)]
added note about cursor mode disabling the popup menu.
jprocter [Mon, 10 Apr 2006 14:31:18 +0000 (14:31 +0000)]
typo and explanation for ignore gaps in consensus
jprocter [Mon, 10 Apr 2006 14:29:02 +0000 (14:29 +0000)]
reworded pad gaps
jprocter [Mon, 10 Apr 2006 14:28:53 +0000 (14:28 +0000)]
reworded pad gaps.
amwaterhouse [Mon, 10 Apr 2006 14:17:47 +0000 (14:17 +0000)]
2.08 update
jprocter [Mon, 10 Apr 2006 14:17:16 +0000 (14:17 +0000)]
put modellerpir in correct place!
jprocter [Mon, 10 Apr 2006 14:16:55 +0000 (14:16 +0000)]
updated menus and rearranged seqfeatures (again)
amwaterhouse [Mon, 10 Apr 2006 14:15:00 +0000 (14:15 +0000)]
Displays error line on error
jprocter [Mon, 10 Apr 2006 14:14:58 +0000 (14:14 +0000)]
fix links to complex html (that don't display) by quoting them
verbatim.
amwaterhouse [Mon, 10 Apr 2006 14:14:18 +0000 (14:14 +0000)]
Just removing new line character
jprocter [Mon, 10 Apr 2006 14:01:04 +0000 (14:01 +0000)]
moved Modeller/PIR description to its own home.
jprocter [Mon, 10 Apr 2006 14:00:46 +0000 (14:00 +0000)]
moved modellerpir to io
jprocter [Mon, 10 Apr 2006 13:59:34 +0000 (13:59 +0000)]
describing the Modeller/PIR output.
jprocter [Mon, 10 Apr 2006 13:18:43 +0000 (13:18 +0000)]
Fixed table border and updated restrictions
amwaterhouse [Mon, 10 Apr 2006 13:15:18 +0000 (13:15 +0000)]
Editing tab
jprocter [Mon, 10 Apr 2006 13:10:43 +0000 (13:10 +0000)]
added bit about modeller/pir
jprocter [Mon, 10 Apr 2006 13:06:40 +0000 (13:06 +0000)]
added annotationColouring to whats new and updated IO and cursorMode
(mac os and backspace==delete)
amwaterhouse [Mon, 10 Apr 2006 12:32:58 +0000 (12:32 +0000)]
del and backspace do the same thing
amwaterhouse [Mon, 10 Apr 2006 11:41:39 +0000 (11:41 +0000)]
Release Date width
jprocter [Mon, 10 Apr 2006 11:34:16 +0000 (11:34 +0000)]
extended preamble and added new heading for user defined annotation
instructions.
amwaterhouse [Mon, 10 Apr 2006 11:33:35 +0000 (11:33 +0000)]
tab name is editing
jprocter [Mon, 10 Apr 2006 11:31:10 +0000 (11:31 +0000)]
doco
jprocter [Mon, 10 Apr 2006 11:27:04 +0000 (11:27 +0000)]
doco changes.
jprocter [Mon, 10 Apr 2006 11:21:47 +0000 (11:21 +0000)]
added 2.08 application version dialog box.
jprocter [Mon, 10 Apr 2006 11:19:45 +0000 (11:19 +0000)]
feature settings dialog box for jalview 2.08 application
amwaterhouse [Mon, 10 Apr 2006 11:11:17 +0000 (11:11 +0000)]
Protein desc bug fixed
amwaterhouse [Mon, 10 Apr 2006 11:10:26 +0000 (11:10 +0000)]
dont need to set - to -
amwaterhouse [Mon, 10 Apr 2006 11:10:06 +0000 (11:10 +0000)]
Fixed protein desc bug
jprocter [Sun, 9 Apr 2006 18:02:49 +0000 (18:02 +0000)]
doco writing.
amwaterhouse [Fri, 7 Apr 2006 14:15:40 +0000 (14:15 +0000)]
Takes popup away from mouseevent, prevents immediate copy
amwaterhouse [Fri, 7 Apr 2006 13:58:11 +0000 (13:58 +0000)]
No need for vetoablechange
amwaterhouse [Fri, 7 Apr 2006 13:48:39 +0000 (13:48 +0000)]
Set all gaps to - symbol
amwaterhouse [Fri, 7 Apr 2006 12:57:17 +0000 (12:57 +0000)]
padGaps set in preferences
amwaterhouse [Fri, 7 Apr 2006 12:52:54 +0000 (12:52 +0000)]
Padgaps pref set
amwaterhouse [Fri, 7 Apr 2006 12:52:29 +0000 (12:52 +0000)]
ModellerOutput set in preferences
amwaterhouse [Fri, 7 Apr 2006 11:27:55 +0000 (11:27 +0000)]
Autocalculate consensus set in preferences
amwaterhouse [Fri, 7 Apr 2006 11:27:19 +0000 (11:27 +0000)]
Scroll cursor wrapped alignment
amwaterhouse [Fri, 7 Apr 2006 10:05:51 +0000 (10:05 +0000)]
+1 error in group edit all sequences
amwaterhouse [Fri, 7 Apr 2006 09:36:36 +0000 (09:36 +0000)]
remove new line in alquality
jprocter [Fri, 7 Apr 2006 09:21:14 +0000 (09:21 +0000)]
added full keyset for cursorMode
amwaterhouse [Fri, 7 Apr 2006 08:23:34 +0000 (08:23 +0000)]
Must check consensus length if autocalculate off
jprocter [Thu, 6 Apr 2006 17:02:12 +0000 (17:02 +0000)]
added cursorMode feature page and rearranged keystrokes documentation.
amwaterhouse [Thu, 6 Apr 2006 11:11:34 +0000 (11:11 +0000)]
Hide ref to HiddenRegion
jprocter [Thu, 6 Apr 2006 09:41:17 +0000 (09:41 +0000)]
removed dross, added a safety check to buildextclients and added references to docs/building.html
amwaterhouse [Thu, 6 Apr 2006 09:26:58 +0000 (09:26 +0000)]
Must copy feature settings from one frame to another as they are not attached ot the dataset
amwaterhouse [Thu, 6 Apr 2006 09:24:42 +0000 (09:24 +0000)]
Must copy feature settings from one frame to another as they are not attached ot the dataset
amwaterhouse [Wed, 5 Apr 2006 16:40:20 +0000 (16:40 +0000)]
Maintain feature order
amwaterhouse [Wed, 5 Apr 2006 15:53:09 +0000 (15:53 +0000)]
Save annotationColours
amwaterhouse [Wed, 5 Apr 2006 15:52:56 +0000 (15:52 +0000)]
Public get methods
amwaterhouse [Wed, 5 Apr 2006 15:52:35 +0000 (15:52 +0000)]
public get methods
git://source.jalview.org / jalview.git / log