source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	jprocter <Jim Procter>
	Mon, 14 Jun 2010 11:05:05 +0000 (11:05 +0000)
committer	jprocter <Jim Procter>
	Mon, 14 Jun 2010 11:05:05 +0000 (11:05 +0000)
commit	93642d621a7f86318a7777b0a70f6113dcd299dc
tree	07395f2ab090ebcc130094bd26b8e8aae7faad41	tree \| snapshot
parent	cdeddbec457461332a4c447d6ac1ffbe94437f7e	commit \| diff

2.5.1 release branding

561 files changed:

RELEASE		diff \| blob \| history
build.xml		diff \| blob \| history
doc/AddingGroovySupport.html		diff \| blob \| history
doc/building.html		diff \| blob \| history
doc/developing.html		diff \| blob \| history
doc/index.html		diff \| blob \| history
doc/newdmobj.html		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/calculations/consensus.html		diff \| blob \| history
help/html/calculations/conservation.html		diff \| blob \| history
help/html/calculations/pairwise.html		diff \| blob \| history
help/html/calculations/pca.html		diff \| blob \| history
help/html/calculations/quality.html		diff \| blob \| history
help/html/calculations/recoverInputdata.html		diff \| blob \| history
help/html/calculations/redundancy.html		diff \| blob \| history
help/html/calculations/sorting.html		diff \| blob \| history
help/html/calculations/tree.html		diff \| blob \| history
help/html/calculations/treeviewer.html		diff \| blob \| history
help/html/colourSchemes/abovePID.html		diff \| blob \| history
help/html/colourSchemes/annotationColouring.html		diff \| blob \| history
help/html/colourSchemes/blosum.html		diff \| blob \| history
help/html/colourSchemes/buried.html		diff \| blob \| history
help/html/colourSchemes/clustal.html		diff \| blob \| history
help/html/colourSchemes/conservation.html		diff \| blob \| history
help/html/colourSchemes/helix.html		diff \| blob \| history
help/html/colourSchemes/hydrophobic.html		diff \| blob \| history
help/html/colourSchemes/index.html		diff \| blob \| history
help/html/colourSchemes/nucleotide.html		diff \| blob \| history
help/html/colourSchemes/pid.html		diff \| blob \| history
help/html/colourSchemes/strand.html		diff \| blob \| history
help/html/colourSchemes/taylor.html		diff \| blob \| history
help/html/colourSchemes/textcolour.html		diff \| blob \| history
help/html/colourSchemes/turn.html		diff \| blob \| history
help/html/colourSchemes/user.html		diff \| blob \| history
help/html/colourSchemes/zappo.html		diff \| blob \| history
help/html/editing/index.html		diff \| blob \| history
help/html/features/annotation.html		diff \| blob \| history
help/html/features/annotationsFormat.html		diff \| blob \| history
help/html/features/clarguments.html		diff \| blob \| history
help/html/features/codingfeatures.html		diff \| blob \| history
help/html/features/commandline.html		diff \| blob \| history
help/html/features/creatinFeatures.html		diff \| blob \| history
help/html/features/cursorMode.html		diff \| blob \| history
help/html/features/dasfeatures.html		diff \| blob \| history
help/html/features/dassettings.html		diff \| blob \| history
help/html/features/editingFeatures.html		diff \| blob \| history
help/html/features/featuresFormat.html		diff \| blob \| history
help/html/features/featureschemes.html		diff \| blob \| history
help/html/features/featuresettings.html		diff \| blob \| history
help/html/features/groovy.html		diff \| blob \| history
help/html/features/hiddenRegions.html		diff \| blob \| history
help/html/features/jalarchive.html		diff \| blob \| history
help/html/features/jmol.html		diff \| blob \| history
help/html/features/multipleViews.html		diff \| blob \| history
help/html/features/newkeystrokes.html		diff \| blob \| history
help/html/features/overview.html		diff \| blob \| history
help/html/features/pdbviewer.html		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/search.html		diff \| blob \| history
help/html/features/seqfeatures.html		diff \| blob \| history
help/html/features/seqfetch.html		diff \| blob \| history
help/html/features/seqmappings.html		diff \| blob \| history
help/html/features/viewingpdbs.html		diff \| blob \| history
help/html/features/wrap.html		diff \| blob \| history
help/html/index.html		diff \| blob \| history
help/html/io/export.html		diff \| blob \| history
help/html/io/fileformats.html		diff \| blob \| history
help/html/io/index.html		diff \| blob \| history
help/html/io/modellerpir.html		diff \| blob \| history
help/html/jalviewjnlp.html		diff \| blob \| history
help/html/keys.html		diff \| blob \| history
help/html/memory.html		diff \| blob \| history
help/html/menus/alignmentMenu.html		diff \| blob \| history
help/html/menus/alwannotations.html		diff \| blob \| history
help/html/menus/alwcalculate.html		diff \| blob \| history
help/html/menus/alwcolour.html		diff \| blob \| history
help/html/menus/alwedit.html		diff \| blob \| history
help/html/menus/alwfile.html		diff \| blob \| history
help/html/menus/alwformat.html		diff \| blob \| history
help/html/menus/alwselect.html		diff \| blob \| history
help/html/menus/alwview.html		diff \| blob \| history
help/html/menus/desktopMenu.html		diff \| blob \| history
help/html/menus/index.html		diff \| blob \| history
help/html/menus/popupMenu.html		diff \| blob \| history
help/html/menus/wsmenu.html		diff \| blob \| history
help/html/misc/aaproperties.html		diff \| blob \| history
help/html/misc/aminoAcids.html		diff \| blob \| history
help/html/misc/geneticCode.html		diff \| blob \| history
help/html/privacy.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/vamsas/index.html		diff \| blob \| history
help/html/webServices/clustalw.html		diff \| blob \| history
help/html/webServices/dbreffetcher.html		diff \| blob \| history
help/html/webServices/index.html		diff \| blob \| history
help/html/webServices/jnet.html		diff \| blob \| history
help/html/webServices/mafft.html		diff \| blob \| history
help/html/webServices/msaclient.html		diff \| blob \| history
help/html/webServices/muscle.html		diff \| blob \| history
help/html/webServices/urllinks.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
resources/embl_mapping.xml		diff \| blob \| history
resources/uniprot_mapping.xml		diff \| blob \| history
schemas/JalviewUserColours.xsd		diff \| blob \| history
schemas/castor-mapping.xsd		diff \| blob \| history
schemas/jalview.xsd		diff \| blob \| history
schemas/jalviewJvV1.xsd		diff \| blob \| history
schemas/vamsas.xsd		diff \| blob \| history
schemas/vamsasJvV1.xsd		diff \| blob \| history
src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/AppletPDBViewer.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/Bond.java		diff \| blob \| history
src/MCview/MCMatrix.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/MCview/Residue.java		diff \| blob \| history
src/MCview/Zsort.java		diff \| blob \| history
src/ext/vamsas/IRegistry.java		diff \| blob \| history
src/ext/vamsas/IRegistryService.java		diff \| blob \| history
src/ext/vamsas/IRegistryServiceLocator.java		diff \| blob \| history
src/ext/vamsas/Jpred.java		diff \| blob \| history
src/ext/vamsas/JpredService.java		diff \| blob \| history
src/ext/vamsas/JpredServiceLocator.java		diff \| blob \| history
src/ext/vamsas/JpredSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/MuscleWS.java		diff \| blob \| history
src/ext/vamsas/MuscleWSService.java		diff \| blob \| history
src/ext/vamsas/MuscleWSServiceLocator.java		diff \| blob \| history
src/ext/vamsas/MuscleWSSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/RegistryServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/SeqSearchI.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceLocator.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceService.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java		diff \| blob \| history
src/ext/vamsas/ServiceHandle.java		diff \| blob \| history
src/ext/vamsas/ServiceHandles.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/Finder.java		diff \| blob \| history
src/jalview/analysis/Grouping.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/ParseProperties.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/SequenceIdMatcher.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/EditNameDialog.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureRenderer.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/Finder.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdCanvas.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/appletgui/JVDialog.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/PaintRefresher.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/RotatableCanvas.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SequenceRenderer.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/Tooltip.java		diff \| blob \| history
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/JalviewLiteURLRetrieve.java		diff \| blob \| history
src/jalview/binding/Alignment.java		diff \| blob \| history
src/jalview/binding/Annotation.java		diff \| blob \| history
src/jalview/binding/AnnotationElement.java		diff \| blob \| history
src/jalview/binding/Colour.java		diff \| blob \| history
src/jalview/binding/Feature.java		diff \| blob \| history
src/jalview/binding/FeatureSettings.java		diff \| blob \| history
src/jalview/binding/Features.java		diff \| blob \| history
src/jalview/binding/JGroup.java		diff \| blob \| history
src/jalview/binding/JSeq.java		diff \| blob \| history
src/jalview/binding/JalviewModel.java		diff \| blob \| history
src/jalview/binding/JalviewModelSequence.java		diff \| blob \| history
src/jalview/binding/JalviewUserColours.java		diff \| blob \| history
src/jalview/binding/Pdbentry.java		diff \| blob \| history
src/jalview/binding/PdbentryItem.java		diff \| blob \| history
src/jalview/binding/Pdbids.java		diff \| blob \| history
src/jalview/binding/Property.java		diff \| blob \| history
src/jalview/binding/Sequence.java		diff \| blob \| history
src/jalview/binding/SequenceSet.java		diff \| blob \| history
src/jalview/binding/SequenceType.java		diff \| blob \| history
src/jalview/binding/Setting.java		diff \| blob \| history
src/jalview/binding/Tree.java		diff \| blob \| history
src/jalview/binding/UserColourScheme.java		diff \| blob \| history
src/jalview/binding/UserColours.java		diff \| blob \| history
src/jalview/binding/VAMSAS.java		diff \| blob \| history
src/jalview/binding/VamsasModel.java		diff \| blob \| history
src/jalview/binding/Viewport.java		diff \| blob \| history
src/jalview/commands/ChangeCaseCommand.java		diff \| blob \| history
src/jalview/commands/CommandI.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/commands/OrderCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapColCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapsCommand.java		diff \| blob \| history
src/jalview/commands/SlideSequencesCommand.java		diff \| blob \| history
src/jalview/commands/TrimRegionCommand.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/BinaryNode.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/CigarArray.java		diff \| blob \| history
src/jalview/datamodel/CigarBase.java		diff \| blob \| history
src/jalview/datamodel/CigarCigar.java		diff \| blob \| history
src/jalview/datamodel/CigarSimple.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/FeatureProperties.java		diff \| blob \| history
src/jalview/datamodel/GraphLine.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/Mapping.java		diff \| blob \| history
src/jalview/datamodel/NodeTransformI.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/Provenance.java		diff \| blob \| history
src/jalview/datamodel/ProvenanceEntry.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/SeqCigar.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceFeature.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/SequenceNode.java		diff \| blob \| history
src/jalview/datamodel/SequencePoint.java		diff \| blob \| history
src/jalview/datamodel/UniprotEntry.java		diff \| blob \| history
src/jalview/datamodel/UniprotFile.java		diff \| blob \| history
src/jalview/datamodel/UniprotProteinName.java		diff \| blob \| history
src/jalview/datamodel/UniprotSequence.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/BasePosition.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblError.java		diff \| blob \| history
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src/jalview/datamodel/xdb/embl/EmblFile.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblSequence.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/Qualifier.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
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src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
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src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/ConservationThread.java		diff \| blob \| history
src/jalview/gui/Console.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/DasSourceBrowser.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/EPSOptions.java		diff \| blob \| history
src/jalview/gui/EditNameDialog.java		diff \| blob \| history
src/jalview/gui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/IProgressIndicator.java		diff \| blob \| history
src/jalview/gui/IProgressIndicatorHandler.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JalviewAppender.java		diff \| blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PaintRefresher.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/ScriptWindow.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/TextColourChooser.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/io/AMSAFile.java		diff \| blob \| history
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src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
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src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/JalviewFileFilter.java		diff \| blob \| history
src/jalview/io/JalviewFileView.java		diff \| blob \| history
src/jalview/io/JnetAnnotationMaker.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/MatrixFile.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
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src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/PileUpfile.java		diff \| blob \| history
src/jalview/io/SimpleBlastFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
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src/jalview/io/vamsas/Dbref.java		diff \| blob \| history
src/jalview/io/vamsas/LocalDocSyncObject.java		diff \| blob \| history
src/jalview/io/vamsas/Rangetype.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencefeature.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencemapping.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
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