From ab43013b7e357b84b4abade0dba949668dfb2a0e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 15 Dec 2014 06:34:15 +0000 Subject: [PATCH] JAL-1620 version bump and release notes --- README | 2 +- RELEASE | 4 ++-- build.xml | 2 +- doc/AddingGroovySupport.html | 2 +- doc/JalviewRNASupport.html | 2 +- doc/building.html | 2 +- doc/developing.html | 2 +- doc/index.html | 2 +- doc/newdmobj.html | 2 +- examples-jbake/assets/css/ie6.css | 2 +- examples-jbake/assets/css/ie7.css | 2 +- examples-jbake/assets/css/reset.css | 2 +- examples-jbake/assets/css/style.css | 2 +- examples-jbake/assets/exampleFeatures.txt | 2 +- examples-jbake/assets/javascript/jalview.js | 2 +- examples-jbake/templates/header.ftl | 2 +- examples/appletParameters.html | 2 +- examples/applets.html | 2 +- examples/css/ie6.css | 2 +- examples/css/ie7.css | 2 +- examples/css/reset.css | 2 +- examples/css/style.css | 2 +- examples/embedded.html | 2 +- examples/embeddedWJmol.html | 2 +- examples/exampleFeatures.txt | 2 +- examples/formComplete.html | 2 +- examples/jalviewLiteJs.html | 2 +- examples/javascript/jalview.js | 2 +- examples/javascriptLaunch.html | 2 +- examples/linkedapplets_ng.html | 2 +- examples/u_applets.html | 2 +- examples/u_embedded.html | 2 +- examples/u_embeddedWJmol.html | 2 +- examples/u_formComplete.html | 2 +- examples/u_javascriptLaunch.html | 2 +- examples/u_linkedapplets_ng.html | 2 +- help/help.hs | 2 +- help/help.jhm | 2 +- help/helpTOC.xml | 2 +- help/html/calculations/consensus.html | 2 +- help/html/calculations/conservation.html | 2 +- help/html/calculations/pairwise.html | 2 +- help/html/calculations/pca.html | 2 +- help/html/calculations/quality.html | 2 +- help/html/calculations/recoverInputdata.html | 2 +- help/html/calculations/redundancy.html | 2 +- help/html/calculations/scorematrices.html | 2 +- help/html/calculations/sorting.html | 2 +- help/html/calculations/structureconsensus.html | 2 +- help/html/calculations/tree.html | 2 +- help/html/calculations/treeviewer.html | 2 +- help/html/colourSchemes/abovePID.html | 2 +- help/html/colourSchemes/annotationColouring.html | 2 +- help/html/colourSchemes/blosum.html | 2 +- help/html/colourSchemes/buried.html | 2 +- help/html/colourSchemes/clustal.html | 2 +- help/html/colourSchemes/conservation.html | 2 +- help/html/colourSchemes/helix.html | 2 +- help/html/colourSchemes/hydrophobic.html | 2 +- help/html/colourSchemes/index.html | 2 +- help/html/colourSchemes/nucleotide.html | 2 +- help/html/colourSchemes/pid.html | 2 +- help/html/colourSchemes/purinepyrimidine.html | 2 +- help/html/colourSchemes/rnahelicesColouring.html | 2 +- help/html/colourSchemes/strand.html | 2 +- help/html/colourSchemes/taylor.html | 2 +- help/html/colourSchemes/textcolour.html | 2 +- help/html/colourSchemes/turn.html | 2 +- help/html/colourSchemes/user.html | 2 +- help/html/colourSchemes/zappo.html | 2 +- help/html/editing/index.html | 2 +- help/html/features/annotation.html | 2 +- help/html/features/annotationsFormat.html | 2 +- help/html/features/chimera.html | 2 +- help/html/features/clarguments.html | 2 +- help/html/features/codingfeatures.html | 2 +- help/html/features/commandline.html | 2 +- help/html/features/creatinFeatures.html | 2 +- help/html/features/cursorMode.html | 2 +- help/html/features/dasfeatures.html | 2 +- help/html/features/dassettings.html | 2 +- help/html/features/editingFeatures.html | 2 +- help/html/features/featuresFormat.html | 2 +- help/html/features/featureschemes.html | 2 +- help/html/features/featuresettings.html | 2 +- help/html/features/groovy.html | 2 +- help/html/features/hiddenRegions.html | 2 +- help/html/features/jalarchive.html | 2 +- help/html/features/jmol.html | 2 +- help/html/features/multipleViews.html | 2 +- help/html/features/newkeystrokes.html | 2 +- help/html/features/overview.html | 2 +- help/html/features/pdbviewer.html | 2 +- help/html/features/preferences.html | 2 +- help/html/features/search.html | 2 +- help/html/features/seqfeatures.html | 2 +- help/html/features/seqfetch.html | 2 +- help/html/features/seqmappings.html | 2 +- help/html/features/varna.html | 2 +- help/html/features/viewingpdbs.html | 2 +- help/html/features/wrap.html | 2 +- help/html/features/xsspannotation.html | 2 +- help/html/index.html | 2 +- help/html/io/export.html | 2 +- help/html/io/exportseqreport.html | 2 +- help/html/io/fileformats.html | 2 +- help/html/io/index.html | 2 +- help/html/io/modellerpir.html | 2 +- help/html/io/tcoffeescores.html | 2 +- help/html/keys.html | 2 +- help/html/memory.html | 2 +- help/html/menus/alignmentMenu.html | 2 +- help/html/menus/alwannotation.html | 2 +- help/html/menus/alwannotationpanel.html | 2 +- help/html/menus/alwcalculate.html | 2 +- help/html/menus/alwcolour.html | 2 +- help/html/menus/alwedit.html | 2 +- help/html/menus/alwfile.html | 2 +- help/html/menus/alwformat.html | 2 +- help/html/menus/alwselect.html | 2 +- help/html/menus/alwview.html | 2 +- help/html/menus/desktopMenu.html | 2 +- help/html/menus/index.html | 2 +- help/html/menus/popupMenu.html | 2 +- help/html/menus/wsmenu.html | 2 +- help/html/misc/aaproperties.html | 2 +- help/html/misc/aminoAcids.html | 2 +- help/html/misc/geneticCode.html | 2 +- help/html/na/index.html | 2 +- help/html/privacy.html | 2 +- help/html/releases.html | 20 +++++++++++++++++++- help/html/vamsas/index.html | 2 +- help/html/webServices/AACon.html | 2 +- help/html/webServices/JABAWS.html | 2 +- help/html/webServices/RNAalifold.html | 2 +- help/html/webServices/dbreffetcher.html | 2 +- help/html/webServices/index.html | 2 +- help/html/webServices/jnet.html | 2 +- help/html/webServices/msaclient.html | 2 +- help/html/webServices/newsreader.html | 2 +- help/html/webServices/proteinDisorder.html | 2 +- help/html/webServices/shmr.html | 2 +- help/html/webServices/urllinks.html | 2 +- help/html/webServices/webServicesParams.html | 2 +- help/html/webServices/webServicesPrefs.html | 2 +- help/html/whatsNew.html | 2 +- jalview-jalopy.xml | 2 +- nbbuild.xml | 2 +- nbproject/project.xml | 2 +- resources/embl_mapping.xml | 2 +- resources/uniprot_mapping.xml | 2 +- schemas/JalviewWsParamSet.xsd | 2 +- schemas/castor-mapping.xsd | 2 +- schemas/jalview.nodesc.properties | 2 +- schemas/jalview.properties | 2 +- schemas/jalview.xsd | 2 +- schemas/jalviewJvV1.xsd | 2 +- schemas/vamsas.xsd | 2 +- schemas/vamsasJvV1.xsd | 2 +- src/MCview/AppletPDBCanvas.java | 2 +- src/MCview/AppletPDBViewer.java | 2 +- src/MCview/Atom.java | 2 +- src/MCview/Bond.java | 2 +- src/MCview/MCMatrix.java | 2 +- src/MCview/PDBCanvas.java | 2 +- src/MCview/PDBChain.java | 2 +- src/MCview/PDBViewer.java | 2 +- src/MCview/PDBfile.java | 2 +- src/MCview/Residue.java | 2 +- src/MCview/Zsort.java | 2 +- src/castor.properties | 2 +- src/ext/vamsas/IRegistry.java | 2 +- src/ext/vamsas/IRegistryService.java | 2 +- src/ext/vamsas/IRegistryServiceLocator.java | 2 +- src/ext/vamsas/Jpred.java | 2 +- src/ext/vamsas/JpredService.java | 2 +- src/ext/vamsas/JpredServiceLocator.java | 2 +- src/ext/vamsas/JpredSoapBindingStub.java | 2 +- src/ext/vamsas/MuscleWS.java | 2 +- src/ext/vamsas/MuscleWSService.java | 2 +- src/ext/vamsas/MuscleWSServiceLocator.java | 2 +- src/ext/vamsas/MuscleWSSoapBindingStub.java | 2 +- src/ext/vamsas/RegistryServiceSoapBindingStub.java | 2 +- src/ext/vamsas/SeqSearchI.java | 2 +- src/ext/vamsas/SeqSearchServiceLocator.java | 2 +- src/ext/vamsas/SeqSearchServiceService.java | 2 +- .../vamsas/SeqSearchServiceSoapBindingStub.java | 2 +- src/ext/vamsas/ServiceHandle.java | 2 +- src/ext/vamsas/ServiceHandles.java | 2 +- src/jalview/analysis/AAFrequency.java | 2 +- src/jalview/analysis/AlignSeq.java | 2 +- src/jalview/analysis/AlignmentSorter.java | 2 +- src/jalview/analysis/AlignmentUtils.java | 2 +- src/jalview/analysis/Conservation.java | 2 +- src/jalview/analysis/CrossRef.java | 2 +- src/jalview/analysis/Dna.java | 2 +- src/jalview/analysis/Finder.java | 2 +- src/jalview/analysis/Grouping.java | 2 +- src/jalview/analysis/NJTree.java | 2 +- src/jalview/analysis/PCA.java | 2 +- src/jalview/analysis/ParseProperties.java | 2 +- src/jalview/analysis/Rna.java | 2 +- src/jalview/analysis/SecStrConsensus.java | 2 +- src/jalview/analysis/SeqsetUtils.java | 2 +- src/jalview/analysis/SequenceIdMatcher.java | 2 +- src/jalview/analysis/StructureFrequency.java | 2 +- src/jalview/analysis/WUSSParseException.java | 2 +- .../analysis/scoremodels/PIDScoreModel.java | 2 +- .../scoremodels/PairwiseSeqScoreModel.java | 2 +- src/jalview/analysis/scoremodels/SWScoreModel.java | 2 +- src/jalview/api/AlignCalcManagerI.java | 2 +- src/jalview/api/AlignCalcWorkerI.java | 2 +- src/jalview/api/AlignViewControllerGuiI.java | 2 +- src/jalview/api/AlignViewControllerI.java | 2 +- src/jalview/api/AlignViewportI.java | 2 +- src/jalview/api/AlignmentViewPanel.java | 2 +- src/jalview/api/FeatureRenderer.java | 2 +- src/jalview/api/OOMHandlerI.java | 2 +- src/jalview/api/RotatableCanvasI.java | 2 +- src/jalview/api/SequenceRenderer.java | 2 +- src/jalview/api/SequenceStructureBinding.java | 2 +- .../api/StructureSelectionManagerProvider.java | 2 +- src/jalview/api/analysis/ScoreModelI.java | 2 +- .../api/structures/JalviewStructureDisplayI.java | 2 +- src/jalview/appletgui/APopupMenu.java | 2 +- src/jalview/appletgui/AlignFrame.java | 2 +- src/jalview/appletgui/AlignViewport.java | 2 +- src/jalview/appletgui/AlignmentPanel.java | 2 +- src/jalview/appletgui/AnnotationColourChooser.java | 2 +- src/jalview/appletgui/AnnotationLabels.java | 2 +- src/jalview/appletgui/AnnotationPanel.java | 2 +- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/appletgui/AppletJmolBinding.java | 2 +- src/jalview/appletgui/CutAndPasteTransfer.java | 2 +- src/jalview/appletgui/EditNameDialog.java | 2 +- src/jalview/appletgui/EmbmenuFrame.java | 2 +- src/jalview/appletgui/ExtJmol.java | 2 +- src/jalview/appletgui/FeatureColourChooser.java | 2 +- src/jalview/appletgui/FeatureRenderer.java | 2 +- src/jalview/appletgui/FeatureSettings.java | 2 +- src/jalview/appletgui/Finder.java | 2 +- src/jalview/appletgui/FontChooser.java | 2 +- src/jalview/appletgui/IdCanvas.java | 2 +- src/jalview/appletgui/IdPanel.java | 2 +- src/jalview/appletgui/IdwidthAdjuster.java | 2 +- src/jalview/appletgui/JVDialog.java | 2 +- src/jalview/appletgui/OverviewPanel.java | 2 +- src/jalview/appletgui/PCAPanel.java | 2 +- src/jalview/appletgui/PaintRefresher.java | 2 +- src/jalview/appletgui/PairwiseAlignPanel.java | 2 +- src/jalview/appletgui/RedundancyPanel.java | 2 +- src/jalview/appletgui/RotatableCanvas.java | 2 +- src/jalview/appletgui/ScalePanel.java | 2 +- src/jalview/appletgui/SeqCanvas.java | 2 +- src/jalview/appletgui/SeqPanel.java | 2 +- src/jalview/appletgui/SequenceRenderer.java | 2 +- src/jalview/appletgui/SliderPanel.java | 2 +- src/jalview/appletgui/Tooltip.java | 2 +- src/jalview/appletgui/TreeCanvas.java | 2 +- src/jalview/appletgui/TreePanel.java | 2 +- src/jalview/appletgui/UserDefinedColours.java | 2 +- src/jalview/bin/Cache.java | 2 +- src/jalview/bin/Jalview.java | 2 +- src/jalview/bin/JalviewLite.java | 2 +- src/jalview/bin/JalviewLiteURLRetrieve.java | 2 +- src/jalview/binding/Alignment.java | 2 +- src/jalview/binding/Annotation.java | 2 +- src/jalview/binding/AnnotationElement.java | 2 +- src/jalview/binding/Colour.java | 2 +- src/jalview/binding/Feature.java | 2 +- src/jalview/binding/FeatureSettings.java | 2 +- src/jalview/binding/Features.java | 2 +- src/jalview/binding/JGroup.java | 2 +- src/jalview/binding/JSeq.java | 2 +- src/jalview/binding/JalviewModel.java | 2 +- src/jalview/binding/JalviewModelSequence.java | 2 +- src/jalview/binding/JalviewUserColours.java | 2 +- src/jalview/binding/Pdbentry.java | 2 +- src/jalview/binding/PdbentryItem.java | 2 +- src/jalview/binding/Pdbids.java | 2 +- src/jalview/binding/Property.java | 2 +- src/jalview/binding/Sequence.java | 2 +- src/jalview/binding/SequenceSet.java | 2 +- src/jalview/binding/SequenceType.java | 2 +- src/jalview/binding/Setting.java | 2 +- src/jalview/binding/Tree.java | 2 +- src/jalview/binding/UserColourScheme.java | 2 +- src/jalview/binding/UserColours.java | 2 +- src/jalview/binding/VAMSAS.java | 2 +- src/jalview/binding/VamsasModel.java | 2 +- src/jalview/binding/Viewport.java | 2 +- src/jalview/commands/ChangeCaseCommand.java | 2 +- src/jalview/commands/CommandI.java | 2 +- src/jalview/commands/EditCommand.java | 2 +- src/jalview/commands/OrderCommand.java | 2 +- src/jalview/commands/RemoveGapColCommand.java | 2 +- src/jalview/commands/RemoveGapsCommand.java | 2 +- src/jalview/commands/SlideSequencesCommand.java | 2 +- src/jalview/commands/TrimRegionCommand.java | 2 +- src/jalview/controller/AlignViewController.java | 2 +- src/jalview/datamodel/AlignedCodonFrame.java | 2 +- src/jalview/datamodel/Alignment.java | 2 +- src/jalview/datamodel/AlignmentAnnotation.java | 2 +- src/jalview/datamodel/AlignmentI.java | 2 +- src/jalview/datamodel/AlignmentOrder.java | 2 +- src/jalview/datamodel/AlignmentView.java | 2 +- src/jalview/datamodel/AnnotatedCollectionI.java | 2 +- src/jalview/datamodel/Annotation.java | 2 +- src/jalview/datamodel/BinaryNode.java | 2 +- src/jalview/datamodel/BinarySequence.java | 2 +- src/jalview/datamodel/CigarArray.java | 2 +- src/jalview/datamodel/CigarBase.java | 2 +- src/jalview/datamodel/CigarCigar.java | 2 +- src/jalview/datamodel/CigarSimple.java | 2 +- src/jalview/datamodel/ColumnSelection.java | 2 +- src/jalview/datamodel/DBRefEntry.java | 2 +- src/jalview/datamodel/DBRefSource.java | 2 +- src/jalview/datamodel/FeatureProperties.java | 2 +- src/jalview/datamodel/GraphLine.java | 2 +- src/jalview/datamodel/HiddenSequences.java | 2 +- src/jalview/datamodel/Mapping.java | 2 +- src/jalview/datamodel/NodeTransformI.java | 2 +- src/jalview/datamodel/PDBEntry.java | 2 +- src/jalview/datamodel/Provenance.java | 2 +- src/jalview/datamodel/ProvenanceEntry.java | 2 +- src/jalview/datamodel/SearchResults.java | 2 +- .../datamodel/SecondaryStructureAnnotation.java | 2 +- src/jalview/datamodel/SeqCigar.java | 2 +- src/jalview/datamodel/Sequence.java | 2 +- src/jalview/datamodel/SequenceCollectionI.java | 2 +- src/jalview/datamodel/SequenceFeature.java | 2 +- src/jalview/datamodel/SequenceGroup.java | 2 +- src/jalview/datamodel/SequenceI.java | 2 +- src/jalview/datamodel/SequenceNode.java | 2 +- src/jalview/datamodel/SequencePoint.java | 2 +- src/jalview/datamodel/UniprotEntry.java | 2 +- src/jalview/datamodel/UniprotFile.java | 2 +- src/jalview/datamodel/UniprotProteinName.java | 2 +- src/jalview/datamodel/UniprotSequence.java | 2 +- src/jalview/datamodel/xdb/embl/BasePosition.java | 2 +- src/jalview/datamodel/xdb/embl/EmblEntry.java | 2 +- src/jalview/datamodel/xdb/embl/EmblError.java | 2 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 2 +- .../datamodel/xdb/embl/EmblFeatureLocElement.java | 2 +- .../datamodel/xdb/embl/EmblFeatureLocations.java | 2 +- src/jalview/datamodel/xdb/embl/EmblFile.java | 2 +- src/jalview/datamodel/xdb/embl/EmblSequence.java | 2 +- src/jalview/datamodel/xdb/embl/Qualifier.java | 2 +- src/jalview/ext/jmol/JalviewJmolBinding.java | 2 +- src/jalview/ext/jmol/JmolCommands.java | 2 +- src/jalview/ext/jmol/PDBFileWithJmol.java | 2 +- src/jalview/ext/paradise/Annotate3D.java | 2 +- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 2 +- .../ext/rbvi/chimera/JalviewChimeraBinding.java | 2 +- src/jalview/ext/varna/JalviewVarnaBinding.java | 2 +- src/jalview/ext/varna/VarnaCommands.java | 2 +- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignViewport.java | 2 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/gui/AnnotationColourChooser.java | 2 +- src/jalview/gui/AnnotationExporter.java | 2 +- src/jalview/gui/AnnotationLabels.java | 2 +- src/jalview/gui/AnnotationPanel.java | 2 +- src/jalview/gui/AppJmol.java | 2 +- src/jalview/gui/AppJmolBinding.java | 2 +- src/jalview/gui/AppVarna.java | 2 +- src/jalview/gui/AppVarnaBinding.java | 2 +- src/jalview/gui/AssociatePdbFileWithSeq.java | 2 +- src/jalview/gui/BlogReader.java | 2 +- src/jalview/gui/ChimeraViewFrame.java | 2 +- src/jalview/gui/Console.java | 2 +- src/jalview/gui/CutAndPasteHtmlTransfer.java | 2 +- src/jalview/gui/CutAndPasteTransfer.java | 2 +- src/jalview/gui/DasSourceBrowser.java | 2 +- src/jalview/gui/Desktop.java | 2 +- src/jalview/gui/EPSOptions.java | 2 +- src/jalview/gui/EditNameDialog.java | 2 +- src/jalview/gui/FeatureColourChooser.java | 2 +- src/jalview/gui/FeatureRenderer.java | 2 +- src/jalview/gui/FeatureSettings.java | 2 +- src/jalview/gui/Finder.java | 2 +- src/jalview/gui/FontChooser.java | 2 +- src/jalview/gui/IProgressIndicator.java | 2 +- src/jalview/gui/IProgressIndicatorHandler.java | 2 +- src/jalview/gui/IdCanvas.java | 2 +- src/jalview/gui/IdPanel.java | 2 +- src/jalview/gui/IdwidthAdjuster.java | 2 +- src/jalview/gui/JDatabaseTree.java | 2 +- src/jalview/gui/Jalview2XML.java | 2 +- src/jalview/gui/Jalview2XML_V1.java | 2 +- src/jalview/gui/JalviewAppender.java | 2 +- src/jalview/gui/JalviewChangeSupport.java | 2 +- src/jalview/gui/JalviewDialog.java | 2 +- src/jalview/gui/JvSwingUtils.java | 2 +- src/jalview/gui/MenuChooser.java | 2 +- src/jalview/gui/OOMWarning.java | 2 +- src/jalview/gui/OptsAndParamsPage.java | 2 +- src/jalview/gui/OptsParametersContainerI.java | 2 +- src/jalview/gui/OverviewPanel.java | 2 +- src/jalview/gui/PCAPanel.java | 2 +- src/jalview/gui/PaintRefresher.java | 2 +- src/jalview/gui/PairwiseAlignPanel.java | 2 +- src/jalview/gui/PopupMenu.java | 2 +- src/jalview/gui/Preferences.java | 2 +- src/jalview/gui/PromptUserConfig.java | 2 +- src/jalview/gui/RedundancyPanel.java | 2 +- src/jalview/gui/RestInputParamEditDialog.java | 2 +- src/jalview/gui/RestServiceEditorPane.java | 2 +- src/jalview/gui/RotatableCanvas.java | 2 +- src/jalview/gui/SVGOptions.java | 2 +- src/jalview/gui/ScalePanel.java | 2 +- src/jalview/gui/ScriptWindow.java | 2 +- src/jalview/gui/SeqCanvas.java | 2 +- src/jalview/gui/SeqPanel.java | 2 +- src/jalview/gui/SequenceFetcher.java | 2 +- src/jalview/gui/SequenceRenderer.java | 2 +- src/jalview/gui/SliderPanel.java | 2 +- src/jalview/gui/SplashScreen.java | 2 +- src/jalview/gui/StructureViewer.java | 2 +- src/jalview/gui/TextColourChooser.java | 2 +- src/jalview/gui/TreeCanvas.java | 2 +- src/jalview/gui/TreePanel.java | 2 +- src/jalview/gui/UserDefinedColours.java | 2 +- src/jalview/gui/UserQuestionnaireCheck.java | 2 +- src/jalview/gui/VamsasApplication.java | 2 +- src/jalview/gui/ViewSelectionMenu.java | 2 +- src/jalview/gui/WebserviceInfo.java | 2 +- src/jalview/gui/WsJobParameters.java | 2 +- src/jalview/gui/WsParamSetManager.java | 2 +- src/jalview/gui/WsPreferences.java | 2 +- src/jalview/io/AMSAFile.java | 2 +- src/jalview/io/AlignFile.java | 2 +- src/jalview/io/AlignmentProperties.java | 2 +- src/jalview/io/AnnotationFile.java | 2 +- src/jalview/io/AppletFormatAdapter.java | 2 +- src/jalview/io/BLCFile.java | 2 +- src/jalview/io/ClansFile.java | 2 +- src/jalview/io/ClustalFile.java | 2 +- src/jalview/io/DBRefFile.java | 2 +- src/jalview/io/FastaFile.java | 2 +- src/jalview/io/FeaturesFile.java | 2 +- src/jalview/io/FileLoader.java | 2 +- src/jalview/io/FileParse.java | 2 +- src/jalview/io/FormatAdapter.java | 2 +- src/jalview/io/HTMLOutput.java | 2 +- src/jalview/io/IdentifyFile.java | 2 +- src/jalview/io/InputStreamParser.java | 2 +- src/jalview/io/JPredFile.java | 2 +- src/jalview/io/JalviewFileChooser.java | 2 +- src/jalview/io/JalviewFileFilter.java | 2 +- src/jalview/io/JalviewFileView.java | 2 +- src/jalview/io/JnetAnnotationMaker.java | 2 +- src/jalview/io/MSFfile.java | 2 +- src/jalview/io/MatrixFile.java | 2 +- src/jalview/io/ModellerDescription.java | 2 +- src/jalview/io/NewickFile.java | 2 +- src/jalview/io/PIRFile.java | 2 +- src/jalview/io/PfamFile.java | 2 +- src/jalview/io/PileUpfile.java | 2 +- src/jalview/io/RnamlFile.java | 2 +- src/jalview/io/SequenceAnnotationReport.java | 2 +- src/jalview/io/SimpleBlastFile.java | 2 +- src/jalview/io/StockholmFile.java | 2 +- src/jalview/io/TCoffeeScoreFile.java | 2 +- src/jalview/io/VamsasAppDatastore.java | 2 +- src/jalview/io/WSWUBlastClient.java | 2 +- src/jalview/io/packed/DataProvider.java | 2 +- src/jalview/io/packed/JalviewDataset.java | 2 +- src/jalview/io/packed/ParsePackedSet.java | 2 +- src/jalview/io/packed/SimpleDataProvider.java | 2 +- src/jalview/io/vamsas/Datasetsequence.java | 2 +- src/jalview/io/vamsas/DatastoreItem.java | 2 +- src/jalview/io/vamsas/DatastoreRegistry.java | 2 +- src/jalview/io/vamsas/Dbref.java | 2 +- src/jalview/io/vamsas/LocalDocSyncObject.java | 2 +- src/jalview/io/vamsas/Rangetype.java | 2 +- src/jalview/io/vamsas/Sequencefeature.java | 2 +- src/jalview/io/vamsas/Sequencemapping.java | 2 +- src/jalview/io/vamsas/Tree.java | 2 +- src/jalview/javascript/JSFunctionExec.java | 2 +- src/jalview/javascript/JalviewLiteJsApi.java | 2 +- src/jalview/javascript/JsCallBack.java | 2 +- src/jalview/javascript/JsSelectionSender.java | 2 +- src/jalview/javascript/MouseOverListener.java | 2 +- .../javascript/MouseOverStructureListener.java | 2 +- src/jalview/jbgui/GAlignFrame.java | 2 +- src/jalview/jbgui/GAlignmentPanel.java | 2 +- src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 2 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 2 +- src/jalview/jbgui/GDasSourceBrowser.java | 2 +- src/jalview/jbgui/GDesktop.java | 2 +- src/jalview/jbgui/GFinder.java | 2 +- src/jalview/jbgui/GFontChooser.java | 2 +- src/jalview/jbgui/GPCAPanel.java | 2 +- src/jalview/jbgui/GPairwiseAlignPanel.java | 2 +- src/jalview/jbgui/GPreferences.java | 2 +- src/jalview/jbgui/GRestInputParamEditDialog.java | 2 +- src/jalview/jbgui/GRestServiceEditorPane.java | 2 +- src/jalview/jbgui/GRnaStructureViewer.java | 2 +- src/jalview/jbgui/GSequenceLink.java | 2 +- src/jalview/jbgui/GSliderPanel.java | 2 +- src/jalview/jbgui/GStructureViewer.java | 2 +- src/jalview/jbgui/GTreePanel.java | 2 +- src/jalview/jbgui/GUserDefinedColours.java | 2 +- src/jalview/jbgui/GWebserviceInfo.java | 2 +- src/jalview/jbgui/GWsPreferences.java | 2 +- src/jalview/math/Matrix.java | 2 +- src/jalview/math/RotatableMatrix.java | 2 +- src/jalview/renderer/AnnotationRenderer.java | 2 +- src/jalview/renderer/AwtRenderPanelI.java | 2 +- src/jalview/schemabinding/version2/AlcodMap.java | 2 +- src/jalview/schemabinding/version2/Alcodon.java | 2 +- .../schemabinding/version2/AlcodonFrame.java | 2 +- .../version2/AnnotationColourScheme.java | 2 +- .../schemabinding/version2/AnnotationColours.java | 2 +- .../schemabinding/version2/AnnotationElement.java | 2 +- .../schemabinding/version2/CalcIdParam.java | 2 +- src/jalview/schemabinding/version2/Colour.java | 2 +- src/jalview/schemabinding/version2/DBRef.java | 2 +- src/jalview/schemabinding/version2/Feature.java | 2 +- .../schemabinding/version2/FeatureSettings.java | 2 +- src/jalview/schemabinding/version2/Features.java | 2 +- src/jalview/schemabinding/version2/Group.java | 2 +- .../schemabinding/version2/HiddenColumns.java | 2 +- src/jalview/schemabinding/version2/JGroup.java | 2 +- src/jalview/schemabinding/version2/JSeq.java | 2 +- .../schemabinding/version2/JalviewModel.java | 2 +- .../version2/JalviewModelSequence.java | 2 +- .../schemabinding/version2/JalviewUserColours.java | 2 +- .../schemabinding/version2/MapListFrom.java | 2 +- src/jalview/schemabinding/version2/MapListTo.java | 2 +- .../schemabinding/version2/MapListType.java | 2 +- src/jalview/schemabinding/version2/Mapping.java | 2 +- .../schemabinding/version2/MappingChoice.java | 2 +- src/jalview/schemabinding/version2/OtherData.java | 2 +- src/jalview/schemabinding/version2/Pdbentry.java | 2 +- .../schemabinding/version2/PdbentryItem.java | 2 +- src/jalview/schemabinding/version2/Pdbids.java | 2 +- src/jalview/schemabinding/version2/Sequence.java | 2 +- .../schemabinding/version2/SequenceSet.java | 2 +- .../version2/SequenceSetProperties.java | 2 +- .../schemabinding/version2/SequenceType.java | 2 +- src/jalview/schemabinding/version2/Setting.java | 2 +- .../schemabinding/version2/StructureState.java | 2 +- .../schemabinding/version2/ThresholdLine.java | 2 +- src/jalview/schemabinding/version2/Tree.java | 2 +- .../schemabinding/version2/UserColourScheme.java | 2 +- .../schemabinding/version2/UserColours.java | 2 +- src/jalview/schemabinding/version2/VAMSAS.java | 2 +- .../schemabinding/version2/VamsasModel.java | 2 +- src/jalview/schemabinding/version2/Viewport.java | 2 +- .../version2/WebServiceParameterSet.java | 2 +- .../version2/descriptors/AlcodMapDescriptor.java | 2 +- .../version2/descriptors/AlcodonDescriptor.java | 2 +- .../descriptors/AlcodonFrameDescriptor.java | 2 +- .../AnnotationColourSchemeDescriptor.java | 2 +- .../descriptors/AnnotationColoursDescriptor.java | 2 +- .../version2/descriptors/AnnotationDescriptor.java | 2 +- .../descriptors/AnnotationElementDescriptor.java | 2 +- .../descriptors/CalcIdParamDescriptor.java | 2 +- .../version2/descriptors/ColourDescriptor.java | 2 +- .../version2/descriptors/DBRefDescriptor.java | 2 +- .../version2/descriptors/FeatureDescriptor.java | 2 +- .../descriptors/FeatureSettingsDescriptor.java | 2 +- .../version2/descriptors/FeaturesDescriptor.java | 2 +- .../version2/descriptors/GroupDescriptor.java | 2 +- .../descriptors/HiddenColumnsDescriptor.java | 2 +- .../version2/descriptors/JGroupDescriptor.java | 2 +- .../version2/descriptors/JSeqDescriptor.java | 2 +- .../descriptors/JalviewModelDescriptor.java | 2 +- .../JalviewModelSequenceDescriptor.java | 2 +- .../descriptors/JalviewUserColoursDescriptor.java | 2 +- .../descriptors/MapListFromDescriptor.java | 2 +- .../version2/descriptors/MapListToDescriptor.java | 2 +- .../descriptors/MapListTypeDescriptor.java | 2 +- .../descriptors/MappingChoiceDescriptor.java | 2 +- .../version2/descriptors/MappingDescriptor.java | 2 +- .../version2/descriptors/OtherDataDescriptor.java | 2 +- .../version2/descriptors/PdbentryDescriptor.java | 2 +- .../descriptors/PdbentryItemDescriptor.java | 2 +- .../version2/descriptors/PdbidsDescriptor.java | 2 +- .../version2/descriptors/PropertyDescriptor.java | 2 +- .../version2/descriptors/SequenceDescriptor.java | 2 +- .../descriptors/SequenceSetDescriptor.java | 2 +- .../SequenceSetPropertiesDescriptor.java | 2 +- .../descriptors/SequenceTypeDescriptor.java | 2 +- .../version2/descriptors/SettingDescriptor.java | 2 +- .../descriptors/StructureStateDescriptor.java | 2 +- .../descriptors/ThresholdLineDescriptor.java | 2 +- .../version2/descriptors/TreeDescriptor.java | 2 +- .../descriptors/UserColourSchemeDescriptor.java | 2 +- .../descriptors/UserColoursDescriptor.java | 2 +- .../version2/descriptors/VAMSASDescriptor.java | 2 +- .../descriptors/VamsasModelDescriptor.java | 2 +- .../version2/descriptors/ViewportDescriptor.java | 2 +- .../WebServiceParameterSetDescriptor.java | 2 +- src/jalview/schemes/AnnotationColourGradient.java | 2 +- src/jalview/schemes/Blosum62ColourScheme.java | 2 +- src/jalview/schemes/BuriedColourScheme.java | 2 +- src/jalview/schemes/ClustalxColourScheme.java | 2 +- src/jalview/schemes/ColourSchemeI.java | 2 +- src/jalview/schemes/ColourSchemeProperty.java | 2 +- src/jalview/schemes/Consensus.java | 2 +- src/jalview/schemes/CovariationColourScheme.java | 2 +- src/jalview/schemes/FollowerColourScheme.java | 2 +- src/jalview/schemes/GraduatedColor.java | 2 +- src/jalview/schemes/HelixColourScheme.java | 2 +- src/jalview/schemes/HydrophobicColourScheme.java | 2 +- src/jalview/schemes/NucleotideColourScheme.java | 2 +- src/jalview/schemes/PIDColourScheme.java | 2 +- .../schemes/PurinePyrimidineColourScheme.java | 2 +- src/jalview/schemes/RNAHelicesColour.java | 2 +- src/jalview/schemes/RNAHelicesColourChooser.java | 2 +- .../schemes/RNAInteractionColourScheme.java | 2 +- src/jalview/schemes/ResidueColourScheme.java | 2 +- src/jalview/schemes/ResidueProperties.java | 2 +- src/jalview/schemes/ScoreColourScheme.java | 2 +- src/jalview/schemes/ScoreMatrix.java | 2 +- src/jalview/schemes/StrandColourScheme.java | 2 +- src/jalview/schemes/TCoffeeColourScheme.java | 2 +- src/jalview/schemes/TaylorColourScheme.java | 2 +- src/jalview/schemes/TurnColourScheme.java | 2 +- src/jalview/schemes/UserColourScheme.java | 2 +- src/jalview/schemes/ZappoColourScheme.java | 2 +- .../structure/AlignmentViewPanelListener.java | 2 +- .../structure/SecondaryStructureListener.java | 2 +- src/jalview/structure/SelectionListener.java | 2 +- src/jalview/structure/SelectionSource.java | 2 +- src/jalview/structure/SequenceListener.java | 2 +- src/jalview/structure/StructureListener.java | 2 +- src/jalview/structure/StructureMapping.java | 2 +- .../structure/StructureMappingcommandSet.java | 2 +- .../structure/StructureSelectionManager.java | 2 +- src/jalview/structure/VamsasListener.java | 2 +- src/jalview/structure/VamsasSource.java | 2 +- .../models/SequenceStructureBindingModel.java | 2 +- src/jalview/util/AWTConsole.java | 2 +- src/jalview/util/BrowserLauncher.java | 2 +- src/jalview/util/ColorUtils.java | 2 +- src/jalview/util/Comparison.java | 2 +- src/jalview/util/DBRefUtils.java | 2 +- src/jalview/util/Format.java | 2 +- src/jalview/util/GroupUrlLink.java | 2 +- src/jalview/util/ImageMaker.java | 2 +- src/jalview/util/MapList.java | 2 +- src/jalview/util/MessageManager.java | 2 +- src/jalview/util/ParseHtmlBodyAndLinks.java | 2 +- src/jalview/util/Platform.java | 2 +- src/jalview/util/QuickSort.java | 2 +- src/jalview/util/ShiftList.java | 2 +- src/jalview/util/TableSorter.java | 2 +- src/jalview/util/UrlLink.java | 2 +- src/jalview/util/jarInputStreamProvider.java | 2 +- src/jalview/viewmodel/AlignmentViewport.java | 2 +- src/jalview/viewmodel/PCAModel.java | 2 +- src/jalview/workers/AlignCalcManager.java | 2 +- src/jalview/workers/AlignCalcWorker.java | 2 +- src/jalview/workers/ConsensusThread.java | 2 +- src/jalview/workers/ConservationThread.java | 2 +- src/jalview/workers/StrucConsensusThread.java | 2 +- src/jalview/ws/AWSThread.java | 2 +- src/jalview/ws/AWsJob.java | 2 +- src/jalview/ws/DBRefFetcher.java | 2 +- src/jalview/ws/DasSequenceFeatureFetcher.java | 2 +- src/jalview/ws/EnfinEnvision2OneWay.java | 2 +- src/jalview/ws/HttpClientUtils.java | 2 +- src/jalview/ws/JobStateSummary.java | 2 +- src/jalview/ws/SequenceFetcher.java | 2 +- src/jalview/ws/WSClient.java | 2 +- src/jalview/ws/WSClientI.java | 2 +- src/jalview/ws/WSMenuEntryProviderI.java | 2 +- .../ws/dbsources/EbiFileRetrievedProxy.java | 2 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 2 +- src/jalview/ws/dbsources/EmblSource.java | 2 +- src/jalview/ws/dbsources/EmblXmlSource.java | 2 +- src/jalview/ws/dbsources/GeneDbSource.java | 2 +- src/jalview/ws/dbsources/Pdb.java | 2 +- src/jalview/ws/dbsources/Pfam.java | 2 +- src/jalview/ws/dbsources/PfamFull.java | 2 +- src/jalview/ws/dbsources/PfamSeed.java | 2 +- src/jalview/ws/dbsources/Rfam.java | 2 +- src/jalview/ws/dbsources/RfamFull.java | 2 +- src/jalview/ws/dbsources/RfamSeed.java | 2 +- src/jalview/ws/dbsources/Uniprot.java | 2 +- src/jalview/ws/dbsources/UnprotName.java | 2 +- src/jalview/ws/dbsources/Xfam.java | 2 +- .../ws/dbsources/das/api/DasSourceRegistryI.java | 2 +- .../ws/dbsources/das/api/jalviewSourceI.java | 2 +- .../dbsources/das/datamodel/DasSequenceSource.java | 2 +- .../dbsources/das/datamodel/DasSourceRegistry.java | 2 +- .../ws/dbsources/das/datamodel/JalviewSource.java | 2 +- src/jalview/ws/ebi/EBIFetchClient.java | 2 +- src/jalview/ws/io/mime/HttpContentHandler.java | 2 +- .../ws/io/mime/JalviewMimeContentHandler.java | 2 +- src/jalview/ws/io/mime/MimeTypes.java | 2 +- src/jalview/ws/jws1/Annotate3D.java | 2 +- src/jalview/ws/jws1/Discoverer.java | 2 +- src/jalview/ws/jws1/JPredClient.java | 2 +- src/jalview/ws/jws1/JPredThread.java | 2 +- src/jalview/ws/jws1/JWS1Thread.java | 2 +- src/jalview/ws/jws1/MsaWSClient.java | 2 +- src/jalview/ws/jws1/MsaWSThread.java | 2 +- src/jalview/ws/jws1/SeqSearchWSClient.java | 2 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 2 +- src/jalview/ws/jws1/WS1Client.java | 2 +- src/jalview/ws/jws1/WSJob.java | 2 +- src/jalview/ws/jws2/AAConClient.java | 2 +- src/jalview/ws/jws2/AADisorderClient.java | 2 +- src/jalview/ws/jws2/AWS2Thread.java | 2 +- src/jalview/ws/jws2/JPred301Client.java | 2 +- src/jalview/ws/jws2/JWs2Job.java | 2 +- src/jalview/ws/jws2/JabaParamStore.java | 2 +- src/jalview/ws/jws2/JabaPreset.java | 2 +- src/jalview/ws/jws2/JabaWsServerQuery.java | 2 +- src/jalview/ws/jws2/JabawsCalcWorker.java | 2 +- .../ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java | 2 +- src/jalview/ws/jws2/Jws2Client.java | 2 +- src/jalview/ws/jws2/Jws2Discoverer.java | 2 +- src/jalview/ws/jws2/MsaWSClient.java | 2 +- src/jalview/ws/jws2/MsaWSThread.java | 2 +- src/jalview/ws/jws2/ParameterUtils.java | 2 +- src/jalview/ws/jws2/RNAalifoldClient.java | 2 +- .../ws/jws2/SequenceAnnotationWSClient.java | 2 +- src/jalview/ws/jws2/dm/AAConSettings.java | 2 +- src/jalview/ws/jws2/dm/JabaOption.java | 2 +- src/jalview/ws/jws2/dm/JabaParameter.java | 2 +- src/jalview/ws/jws2/dm/JabaValueConstrain.java | 2 +- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 2 +- src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 2 +- .../ws/jws2/jabaws2/Jws2InstanceFactory.java | 2 +- src/jalview/ws/params/ArgumentI.java | 2 +- src/jalview/ws/params/AutoCalcSetting.java | 2 +- .../ws/params/InvalidArgumentException.java | 2 +- src/jalview/ws/params/OptionI.java | 2 +- src/jalview/ws/params/ParamDatastoreI.java | 2 +- src/jalview/ws/params/ParamManager.java | 2 +- src/jalview/ws/params/ParameterI.java | 2 +- src/jalview/ws/params/ValueConstrainI.java | 2 +- src/jalview/ws/params/WsParamSetI.java | 2 +- src/jalview/ws/params/simple/BooleanOption.java | 2 +- src/jalview/ws/params/simple/IntegerParameter.java | 2 +- src/jalview/ws/params/simple/Option.java | 2 +- src/jalview/ws/params/simple/Parameter.java | 2 +- .../ws/params/simple/StringChoiceParameter.java | 2 +- src/jalview/ws/rest/AlignmentProcessor.java | 2 +- src/jalview/ws/rest/HttpResultSet.java | 2 +- src/jalview/ws/rest/InputType.java | 2 +- src/jalview/ws/rest/NoValidInputDataException.java | 2 +- src/jalview/ws/rest/RestClient.java | 2 +- src/jalview/ws/rest/RestJob.java | 2 +- src/jalview/ws/rest/RestJobThread.java | 2 +- src/jalview/ws/rest/RestServiceDescription.java | 2 +- src/jalview/ws/rest/params/Alignment.java | 2 +- src/jalview/ws/rest/params/AnnotationFile.java | 2 +- src/jalview/ws/rest/params/JobConstant.java | 2 +- .../ws/rest/params/SeqGroupIndexVector.java | 2 +- src/jalview/ws/rest/params/SeqIdVector.java | 2 +- src/jalview/ws/rest/params/SeqVector.java | 2 +- src/jalview/ws/rest/params/Tree.java | 2 +- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 2 +- src/jalview/ws/seqfetcher/DbSourceProxy.java | 2 +- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 2 +- src/jalview/ws/uimodel/AlignAnalysisUIText.java | 2 +- src/org/jibble/epsgraphics/EpsDocument.java | 2 +- src/org/jibble/epsgraphics/EpsException.java | 2 +- src/org/jibble/epsgraphics/EpsGraphics2D.java | 2 +- src/uk/ac/ebi/picr/model/CrossReference.java | 2 +- .../ac/ebi/picr/model/CrossReference_Helper.java | 2 +- src/uk/ac/ebi/picr/model/UPEntry.java | 2 +- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 2 +- src/uk/ac/ebi/www/Data.java | 2 +- src/uk/ac/ebi/www/InputParams.java | 2 +- src/uk/ac/ebi/www/WSFile.java | 2 +- src/uk/ac/ebi/www/WSWUBlast.java | 2 +- src/uk/ac/ebi/www/WSWUBlastService.java | 2 +- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 2 +- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 2 +- .../AccessionMapperBindingStub.java | 2 +- .../AccessionMapperInterface.java | 2 +- .../AccessionMapperService.java | 2 +- .../AccessionMapperServiceLocator.java | 2 +- src/vamsas/IMsaWS.java | 2 +- src/vamsas/objects/simple/Alignment.java | 2 +- src/vamsas/objects/simple/Alignment_Helper.java | 2 +- src/vamsas/objects/simple/JpredResult.java | 2 +- src/vamsas/objects/simple/JpredResult_Helper.java | 2 +- src/vamsas/objects/simple/MsaResult.java | 2 +- src/vamsas/objects/simple/MsaResult_Helper.java | 2 +- src/vamsas/objects/simple/Msfalignment.java | 2 +- src/vamsas/objects/simple/Msfalignment_Helper.java | 2 +- src/vamsas/objects/simple/Object.java | 2 +- src/vamsas/objects/simple/Object_Helper.java | 2 +- src/vamsas/objects/simple/Result.java | 2 +- src/vamsas/objects/simple/Result_Helper.java | 2 +- src/vamsas/objects/simple/Secstructpred.java | 2 +- .../objects/simple/Secstructpred_Helper.java | 2 +- src/vamsas/objects/simple/SeqSearchResult.java | 2 +- .../objects/simple/SeqSearchResult_Helper.java | 2 +- src/vamsas/objects/simple/Sequence.java | 2 +- src/vamsas/objects/simple/SequenceSet.java | 2 +- src/vamsas/objects/simple/SequenceSet_Helper.java | 2 +- src/vamsas/objects/simple/Sequence_Helper.java | 2 +- src/vamsas/objects/simple/WsJobId.java | 2 +- src/vamsas/objects/simple/WsJobId_Helper.java | 2 +- test/jalview/analysis/AlignmentUtilsTests.java | 2 +- test/jalview/analysis/DnaTranslation.java | 2 +- test/jalview/analysis/TestAlignSeq.java | 2 +- test/jalview/bin/CommandLineOperations.java | 2 +- test/jalview/ext/jmol/PDBFileWithJmolTest.java | 2 +- test/jalview/ext/paradise/TestAnnotate3D.java | 2 +- test/jalview/gui/JAL1353bugdemo.java | 2 +- test/jalview/io/AnnotationFileIOTest.java | 2 +- test/jalview/io/FileIOTester.java | 2 +- test/jalview/io/Jalview2xmlTests.java | 2 +- test/jalview/io/NewickFileTests.java | 2 +- test/jalview/io/RNAMLfileTest.java | 2 +- test/jalview/io/StockholmFileTest.java | 2 +- test/jalview/io/TCoffeeScoreFileTest.java | 2 +- test/jalview/schemes/DnaCodonTests.java | 2 +- test/jalview/schemes/ScoreMatrixPrinter.java | 2 +- test/jalview/ws/PDBSequenceFetcherTest.java | 2 +- test/jalview/ws/gui/Jws2ParamView.java | 2 +- .../ws/jabaws/DisorderAnnotExportImport.java | 2 +- test/jalview/ws/jabaws/JalviewJabawsTestUtils.java | 2 +- .../ws/jabaws/JpredJabaStructExportImport.java | 2 +- test/jalview/ws/jabaws/RNAStructExportImport.java | 2 +- test/jalview/ws/rest/ShmmrRSBSService.java | 2 +- test/jalview/ws/seqfetcher/DbRefFetcherTest.java | 2 +- utils/InstallAnywhere/jalview_buildinstaller.xml | 2 +- utils/eclipse/JalviewCodeStyle.xml | 2 +- utils/getJavaVersion.java | 2 +- utils/gff2annot.pl | 2 +- utils/help2Website.java | 2 +- utils/jarunsigner.pl | 2 +- utils/patchGt.pl | 2 +- utils/splitstockholm.pl | 2 +- 836 files changed, 855 insertions(+), 837 deletions(-) diff --git a/README b/README index 10f032b..cbc93b1 100755 --- a/README +++ b/README @@ -4,7 +4,7 @@ Jalview Readme The source is available as a tar file and comes complete with the GNU General Public License. -To build the application you will need a J2SDK 1.6+. +To build the application you will need a J2SDK 1.7+. An Ant build file (build.xml) is provided, you will need to install Apache Ant first. Run ant to view usage which will display a list of useful build targets. diff --git a/RELEASE b/RELEASE index 11598ab..72e42f6 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ -jalview.release=Release_2_8_2_Branch -jalview.version=2.8.2 +jalview.release=Release_2_8_2b1_Branch +jalview.version=2.8.2b1 diff --git a/build.xml b/build.xml index d8ebe1e..baadc25 100755 --- a/build.xml +++ b/build.xml @@ -1,6 +1,6 @@