From 17e77c3f2949a0729322b4a8d907f3f34b6a9914 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 11:25:10 +0100 Subject: [PATCH] JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob --- build.xml | 4 ++-- doc/AddingGroovySupport.html | 4 ++-- doc/AnnotationPostAnalysis.txt | 4 ++-- doc/JalviewRNASupport.html | 4 ++-- doc/UnitTesting.html | 4 ++-- doc/biojsmsa-templates.html | 4 ++-- doc/building.html | 4 ++-- doc/developing.html | 24 ++------------------ doc/i18n.html | 4 ++-- doc/index.html | 24 ++------------------ doc/newdmobj.html | 4 ++-- examples/appletParameters.html | 4 ++-- examples/applets.html | 4 ++-- examples/css/ie6.css | 4 ++-- examples/css/ie7.css | 4 ++-- examples/css/reset.css | 4 ++-- examples/css/style.css | 4 ++-- examples/embedded.html | 4 ++-- examples/exampleFeatures.txt | 4 ++-- examples/formComplete.html | 4 ++-- examples/groovy/JvLoadTestHarness.groovy | 4 ++-- examples/groovy/JvLoadTester.groovy | 4 ++-- 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src/jalview/gui/PaintRefresher.java | 4 ++-- src/jalview/gui/PairwiseAlignPanel.java | 4 ++-- src/jalview/gui/PopupMenu.java | 4 ++-- src/jalview/gui/Preferences.java | 4 ++-- src/jalview/gui/ProgressBar.java | 4 ++-- src/jalview/gui/PromptUserConfig.java | 4 ++-- src/jalview/gui/RedundancyPanel.java | 4 ++-- src/jalview/gui/RestInputParamEditDialog.java | 4 ++-- src/jalview/gui/RestServiceEditorPane.java | 4 ++-- src/jalview/gui/RotatableCanvas.java | 4 ++-- src/jalview/gui/SVGOptions.java | 4 ++-- src/jalview/gui/ScalePanel.java | 4 ++-- src/jalview/gui/SeqCanvas.java | 4 ++-- src/jalview/gui/SeqPanel.java | 4 ++-- src/jalview/gui/SequenceFetcher.java | 4 ++-- src/jalview/gui/SequenceRenderer.java | 4 ++-- src/jalview/gui/SliderPanel.java | 4 ++-- src/jalview/gui/SplashScreen.java | 4 ++-- src/jalview/gui/SplitFrame.java | 4 ++-- src/jalview/gui/StructureViewer.java | 4 ++-- src/jalview/gui/StructureViewerBase.java | 4 ++-- src/jalview/gui/TextColourChooser.java | 4 ++-- src/jalview/gui/TreeCanvas.java | 4 ++-- src/jalview/gui/TreePanel.java | 4 ++-- src/jalview/gui/UserDefinedColours.java | 4 ++-- src/jalview/gui/UserQuestionnaireCheck.java | 4 ++-- src/jalview/gui/VamsasApplication.java | 4 ++-- src/jalview/gui/ViewSelectionMenu.java | 4 ++-- src/jalview/gui/WebserviceInfo.java | 4 ++-- src/jalview/gui/WsJobParameters.java | 4 ++-- src/jalview/gui/WsParamSetManager.java | 4 ++-- src/jalview/gui/WsPreferences.java | 4 ++-- src/jalview/httpserver/AbstractRequestHandler.java | 4 ++-- src/jalview/httpserver/HttpServer.java | 4 ++-- src/jalview/io/AMSAFile.java | 4 ++-- src/jalview/io/AlignFile.java | 4 ++-- src/jalview/io/AlignmentProperties.java | 4 ++-- src/jalview/io/AnnotationFile.java | 4 ++-- src/jalview/io/AppletFormatAdapter.java | 4 ++-- src/jalview/io/BLCFile.java | 4 ++-- src/jalview/io/BioJsHTMLOutput.java | 4 ++-- src/jalview/io/ClansFile.java | 4 ++-- src/jalview/io/ClustalFile.java | 4 ++-- src/jalview/io/DBRefFile.java | 4 ++-- src/jalview/io/FastaFile.java | 4 ++-- src/jalview/io/FeaturesFile.java | 4 ++-- src/jalview/io/FileLoader.java | 4 ++-- src/jalview/io/FileParse.java | 4 ++-- src/jalview/io/FormatAdapter.java | 4 ++-- src/jalview/io/Gff3File.java | 4 ++-- src/jalview/io/HTMLOutput.java | 4 ++-- src/jalview/io/HtmlFile.java | 4 ++-- src/jalview/io/HtmlSvgOutput.java | 4 ++-- src/jalview/io/IdentifyFile.java | 4 ++-- src/jalview/io/InputStreamParser.java | 4 ++-- src/jalview/io/JPredFile.java | 4 ++-- src/jalview/io/JSONFile.java | 4 ++-- src/jalview/io/JalviewFileChooser.java | 4 ++-- src/jalview/io/JalviewFileFilter.java | 4 ++-- src/jalview/io/JalviewFileView.java | 4 ++-- src/jalview/io/JnetAnnotationMaker.java | 4 ++-- src/jalview/io/MSFfile.java | 4 ++-- src/jalview/io/MatrixFile.java | 4 ++-- src/jalview/io/ModellerDescription.java | 4 ++-- src/jalview/io/NewickFile.java | 4 ++-- src/jalview/io/PIRFile.java | 4 ++-- src/jalview/io/PfamFile.java | 4 ++-- src/jalview/io/PhylipFile.java | 4 ++-- src/jalview/io/PileUpfile.java | 4 ++-- src/jalview/io/RnamlFile.java | 4 ++-- src/jalview/io/SequenceAnnotationReport.java | 4 ++-- src/jalview/io/SimpleBlastFile.java | 4 ++-- src/jalview/io/StockholmFile.java | 4 ++-- src/jalview/io/TCoffeeScoreFile.java | 4 ++-- src/jalview/io/VamsasAppDatastore.java | 4 ++-- src/jalview/io/WSWUBlastClient.java | 4 ++-- src/jalview/io/packed/DataProvider.java | 4 ++-- src/jalview/io/packed/JalviewDataset.java | 4 ++-- src/jalview/io/packed/ParsePackedSet.java | 4 ++-- src/jalview/io/packed/SimpleDataProvider.java | 4 ++-- src/jalview/io/vamsas/Datasetsequence.java | 4 ++-- src/jalview/io/vamsas/DatastoreItem.java | 4 ++-- src/jalview/io/vamsas/DatastoreRegistry.java | 4 ++-- src/jalview/io/vamsas/Dbref.java | 4 ++-- src/jalview/io/vamsas/LocalDocSyncObject.java | 4 ++-- src/jalview/io/vamsas/Rangetype.java | 4 ++-- src/jalview/io/vamsas/Sequencefeature.java | 4 ++-- src/jalview/io/vamsas/Sequencemapping.java | 4 ++-- src/jalview/io/vamsas/Tree.java | 4 ++-- src/jalview/javascript/JSFunctionExec.java | 4 ++-- src/jalview/javascript/JalviewLiteJsApi.java | 4 ++-- src/jalview/javascript/JsCallBack.java | 4 ++-- src/jalview/javascript/JsSelectionSender.java | 4 ++-- src/jalview/javascript/MouseOverListener.java | 4 ++-- .../javascript/MouseOverStructureListener.java | 4 ++-- src/jalview/jbgui/GAlignExportSettings.java | 4 ++-- src/jalview/jbgui/GAlignFrame.java | 4 ++-- src/jalview/jbgui/GAlignmentPanel.java | 4 ++-- src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 4 ++-- src/jalview/jbgui/GCutAndPasteTransfer.java | 4 ++-- src/jalview/jbgui/GDasSourceBrowser.java | 4 ++-- src/jalview/jbgui/GDesktop.java | 4 ++-- src/jalview/jbgui/GFinder.java | 4 ++-- src/jalview/jbgui/GFontChooser.java | 4 ++-- src/jalview/jbgui/GPCAPanel.java | 4 ++-- src/jalview/jbgui/GPairwiseAlignPanel.java | 4 ++-- src/jalview/jbgui/GPreferences.java | 4 ++-- src/jalview/jbgui/GRestInputParamEditDialog.java | 4 ++-- src/jalview/jbgui/GRestServiceEditorPane.java | 4 ++-- src/jalview/jbgui/GRnaStructureViewer.java | 4 ++-- src/jalview/jbgui/GSequenceLink.java | 4 ++-- src/jalview/jbgui/GSliderPanel.java | 4 ++-- src/jalview/jbgui/GSplitFrame.java | 4 ++-- src/jalview/jbgui/GStructureViewer.java | 4 ++-- src/jalview/jbgui/GTreePanel.java | 4 ++-- src/jalview/jbgui/GUserDefinedColours.java | 4 ++-- src/jalview/jbgui/GWebserviceInfo.java | 4 ++-- src/jalview/jbgui/GWsPreferences.java | 4 ++-- src/jalview/jbgui/PDBDocFieldPreferences.java | 4 ++-- .../json/binding/biojs/BioJSReleasePojo.java | 4 ++-- .../json/binding/biojs/BioJSRepositoryPojo.java | 4 ++-- .../biojson/v1/AlignmentAnnotationPojo.java | 4 ++-- .../json/binding/biojson/v1/AlignmentPojo.java | 4 ++-- .../json/binding/biojson/v1/AnnotationPojo.java | 4 ++-- .../biojson/v1/JalviewBioJsColorSchemeMapper.java | 4 ++-- .../binding/biojson/v1/SequenceFeaturesPojo.java | 4 ++-- .../json/binding/biojson/v1/SequenceGrpPojo.java | 4 ++-- .../json/binding/biojson/v1/SequencePojo.java | 4 ++-- src/jalview/math/AlignmentDimension.java | 4 ++-- src/jalview/math/Matrix.java | 4 ++-- src/jalview/math/RotatableMatrix.java | 4 ++-- src/jalview/renderer/AnnotationRenderer.java | 4 ++-- src/jalview/renderer/AwtRenderPanelI.java | 4 ++-- .../renderer/seqfeatures/FeatureRenderer.java | 4 ++-- src/jalview/rest/RestHandler.java | 4 ++-- src/jalview/schemes/AnnotationColourGradient.java | 4 ++-- src/jalview/schemes/Blosum62ColourScheme.java | 4 ++-- src/jalview/schemes/BuriedColourScheme.java | 4 ++-- src/jalview/schemes/ClustalxColourScheme.java | 4 ++-- src/jalview/schemes/ColourSchemeI.java | 4 ++-- src/jalview/schemes/ColourSchemeProperty.java | 4 ++-- src/jalview/schemes/Consensus.java | 4 ++-- src/jalview/schemes/CovariationColourScheme.java | 4 ++-- src/jalview/schemes/FollowerColourScheme.java | 4 ++-- src/jalview/schemes/GraduatedColor.java | 4 ++-- src/jalview/schemes/HelixColourScheme.java | 4 ++-- src/jalview/schemes/HydrophobicColourScheme.java | 4 ++-- src/jalview/schemes/NucleotideColourScheme.java | 4 ++-- src/jalview/schemes/PIDColourScheme.java | 4 ++-- .../schemes/PurinePyrimidineColourScheme.java | 4 ++-- src/jalview/schemes/RNAHelicesColour.java | 4 ++-- src/jalview/schemes/RNAHelicesColourChooser.java | 4 ++-- .../schemes/RNAInteractionColourScheme.java | 4 ++-- src/jalview/schemes/ResidueColourScheme.java | 4 ++-- src/jalview/schemes/ResidueProperties.java | 4 ++-- src/jalview/schemes/ScoreColourScheme.java | 4 ++-- src/jalview/schemes/ScoreMatrix.java | 4 ++-- src/jalview/schemes/StrandColourScheme.java | 4 ++-- src/jalview/schemes/TCoffeeColourScheme.java | 4 ++-- src/jalview/schemes/TaylorColourScheme.java | 4 ++-- src/jalview/schemes/TurnColourScheme.java | 4 ++-- src/jalview/schemes/UserColourScheme.java | 4 ++-- src/jalview/schemes/ZappoColourScheme.java | 4 ++-- .../structure/AlignmentViewPanelListener.java | 4 ++-- src/jalview/structure/AtomSpec.java | 4 ++-- src/jalview/structure/CommandListener.java | 4 ++-- .../structure/SecondaryStructureListener.java | 4 ++-- src/jalview/structure/SelectionListener.java | 4 ++-- src/jalview/structure/SelectionSource.java | 4 ++-- src/jalview/structure/SequenceListener.java | 4 ++-- src/jalview/structure/StructureListener.java | 4 ++-- src/jalview/structure/StructureMapping.java | 4 ++-- .../structure/StructureMappingcommandSet.java | 4 ++-- .../structure/StructureSelectionManager.java | 4 ++-- src/jalview/structure/VamsasListener.java | 4 ++-- src/jalview/structure/VamsasSource.java | 4 ++-- .../structures/models/AAStructureBindingModel.java | 4 ++-- .../models/SequenceStructureBindingModel.java | 4 ++-- src/jalview/util/AWTConsole.java | 4 ++-- src/jalview/util/BrowserLauncher.java | 4 ++-- src/jalview/util/ColorUtils.java | 4 ++-- src/jalview/util/Comparison.java | 4 ++-- src/jalview/util/DBRefUtils.java | 4 ++-- src/jalview/util/Format.java | 4 ++-- src/jalview/util/GroupUrlLink.java | 4 ++-- src/jalview/util/ImageMaker.java | 4 ++-- src/jalview/util/MapList.java | 4 ++-- src/jalview/util/MappingUtils.java | 4 ++-- src/jalview/util/MessageManager.java | 4 ++-- src/jalview/util/ParseHtmlBodyAndLinks.java | 4 ++-- src/jalview/util/Platform.java | 4 ++-- src/jalview/util/QuickSort.java | 4 ++-- src/jalview/util/ReverseListIterator.java | 4 ++-- src/jalview/util/ShiftList.java | 4 ++-- src/jalview/util/StringUtils.java | 4 ++-- src/jalview/util/TableSorter.java | 4 ++-- src/jalview/util/UrlLink.java | 4 ++-- src/jalview/util/jarInputStreamProvider.java | 4 ++-- src/jalview/viewmodel/AlignmentViewport.java | 4 ++-- src/jalview/viewmodel/PCAModel.java | 4 ++-- .../AnnotationFilterParameter.java | 4 ++-- .../seqfeatures/FeatureRendererModel.java | 4 ++-- .../seqfeatures/FeatureRendererSettings.java | 4 ++-- .../seqfeatures/FeatureSettingsModel.java | 4 ++-- .../viewmodel/seqfeatures/FeaturesDisplayed.java | 4 ++-- src/jalview/viewmodel/styles/ViewStyle.java | 4 ++-- src/jalview/workers/AlignCalcManager.java | 4 ++-- src/jalview/workers/AlignCalcWorker.java | 4 ++-- src/jalview/workers/ComplementConsensusThread.java | 4 ++-- src/jalview/workers/ConsensusThread.java | 4 ++-- src/jalview/workers/ConservationThread.java | 4 ++-- src/jalview/workers/StrucConsensusThread.java | 4 ++-- src/jalview/ws/AWSThread.java | 4 ++-- src/jalview/ws/AWsJob.java | 4 ++-- src/jalview/ws/DBRefFetcher.java | 4 ++-- src/jalview/ws/DasSequenceFeatureFetcher.java | 4 ++-- src/jalview/ws/HttpClientUtils.java | 4 ++-- src/jalview/ws/JobStateSummary.java | 4 ++-- src/jalview/ws/SequenceFetcher.java | 4 ++-- src/jalview/ws/WSClient.java | 4 ++-- src/jalview/ws/WSClientI.java | 4 ++-- src/jalview/ws/WSMenuEntryProviderI.java | 4 ++-- .../ws/dbsources/EbiFileRetrievedProxy.java | 4 ++-- src/jalview/ws/dbsources/EmblCdsSouce.java | 4 ++-- src/jalview/ws/dbsources/EmblSource.java | 4 ++-- src/jalview/ws/dbsources/EmblXmlSource.java | 4 ++-- src/jalview/ws/dbsources/GeneDbSource.java | 4 ++-- src/jalview/ws/dbsources/PDBRestClient.java | 4 ++-- src/jalview/ws/dbsources/Pdb.java | 4 ++-- src/jalview/ws/dbsources/Pfam.java | 4 ++-- src/jalview/ws/dbsources/PfamFull.java | 4 ++-- src/jalview/ws/dbsources/PfamSeed.java | 4 ++-- src/jalview/ws/dbsources/Rfam.java | 4 ++-- src/jalview/ws/dbsources/RfamFull.java | 4 ++-- src/jalview/ws/dbsources/RfamSeed.java | 4 ++-- src/jalview/ws/dbsources/Uniprot.java | 4 ++-- src/jalview/ws/dbsources/UnprotName.java | 4 ++-- src/jalview/ws/dbsources/Xfam.java | 4 ++-- .../ws/dbsources/das/api/DasSourceRegistryI.java | 4 ++-- .../ws/dbsources/das/api/jalviewSourceI.java | 4 ++-- .../dbsources/das/datamodel/DasSequenceSource.java | 4 ++-- .../dbsources/das/datamodel/DasSourceRegistry.java | 4 ++-- .../ws/dbsources/das/datamodel/JalviewSource.java | 4 ++-- src/jalview/ws/ebi/EBIFetchClient.java | 4 ++-- src/jalview/ws/io/mime/HttpContentHandler.java | 4 ++-- .../ws/io/mime/JalviewMimeContentHandler.java | 4 ++-- src/jalview/ws/io/mime/MimeTypes.java | 4 ++-- src/jalview/ws/jws1/Annotate3D.java | 4 ++-- src/jalview/ws/jws1/Discoverer.java | 4 ++-- src/jalview/ws/jws1/JPredClient.java | 4 ++-- src/jalview/ws/jws1/JPredThread.java | 4 ++-- src/jalview/ws/jws1/JWS1Thread.java | 4 ++-- src/jalview/ws/jws1/MsaWSClient.java | 4 ++-- src/jalview/ws/jws1/MsaWSThread.java | 4 ++-- src/jalview/ws/jws1/SeqSearchWSClient.java | 4 ++-- src/jalview/ws/jws1/SeqSearchWSThread.java | 4 ++-- src/jalview/ws/jws1/WS1Client.java | 4 ++-- src/jalview/ws/jws1/WSJob.java | 4 ++-- src/jalview/ws/jws2/AAConClient.java | 4 ++-- src/jalview/ws/jws2/AADisorderClient.java | 4 ++-- src/jalview/ws/jws2/AWS2Thread.java | 4 ++-- src/jalview/ws/jws2/AbstractJabaCalcWorker.java | 4 ++-- src/jalview/ws/jws2/JPred301Client.java | 4 ++-- src/jalview/ws/jws2/JWs2Job.java | 4 ++-- src/jalview/ws/jws2/JabaParamStore.java | 4 ++-- src/jalview/ws/jws2/JabaPreset.java | 4 ++-- src/jalview/ws/jws2/JabaWsServerQuery.java | 4 ++-- src/jalview/ws/jws2/JabawsCalcWorker.java | 4 ++-- .../ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java | 4 ++-- src/jalview/ws/jws2/Jws2Client.java | 4 ++-- src/jalview/ws/jws2/Jws2Discoverer.java | 4 ++-- src/jalview/ws/jws2/MsaWSClient.java | 4 ++-- src/jalview/ws/jws2/MsaWSThread.java | 4 ++-- src/jalview/ws/jws2/ParameterUtils.java | 4 ++-- src/jalview/ws/jws2/RNAalifoldClient.java | 4 ++-- .../ws/jws2/SequenceAnnotationWSClient.java | 4 ++-- src/jalview/ws/jws2/dm/AAConSettings.java | 4 ++-- src/jalview/ws/jws2/dm/JabaOption.java | 4 ++-- src/jalview/ws/jws2/dm/JabaParameter.java | 4 ++-- src/jalview/ws/jws2/dm/JabaValueConstrain.java | 4 ++-- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 4 ++-- src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 4 ++-- .../ws/jws2/jabaws2/Jws2InstanceFactory.java | 4 ++-- src/jalview/ws/params/ArgumentI.java | 4 ++-- src/jalview/ws/params/AutoCalcSetting.java | 4 ++-- .../ws/params/InvalidArgumentException.java | 4 ++-- src/jalview/ws/params/OptionI.java | 4 ++-- src/jalview/ws/params/ParamDatastoreI.java | 4 ++-- src/jalview/ws/params/ParamManager.java | 4 ++-- src/jalview/ws/params/ParameterI.java | 4 ++-- src/jalview/ws/params/ValueConstrainI.java | 4 ++-- src/jalview/ws/params/WsParamSetI.java | 4 ++-- src/jalview/ws/params/simple/BooleanOption.java | 4 ++-- src/jalview/ws/params/simple/IntegerParameter.java | 4 ++-- src/jalview/ws/params/simple/Option.java | 4 ++-- src/jalview/ws/params/simple/Parameter.java | 4 ++-- .../ws/params/simple/StringChoiceParameter.java | 4 ++-- src/jalview/ws/rest/AlignmentProcessor.java | 4 ++-- src/jalview/ws/rest/HttpResultSet.java | 4 ++-- src/jalview/ws/rest/InputType.java | 4 ++-- src/jalview/ws/rest/NoValidInputDataException.java | 4 ++-- src/jalview/ws/rest/RestClient.java | 4 ++-- src/jalview/ws/rest/RestJob.java | 4 ++-- src/jalview/ws/rest/RestJobThread.java | 4 ++-- src/jalview/ws/rest/RestServiceDescription.java | 4 ++-- src/jalview/ws/rest/params/Alignment.java | 4 ++-- src/jalview/ws/rest/params/AnnotationFile.java | 4 ++-- src/jalview/ws/rest/params/JobConstant.java | 4 ++-- .../ws/rest/params/SeqGroupIndexVector.java | 4 ++-- src/jalview/ws/rest/params/SeqIdVector.java | 4 ++-- src/jalview/ws/rest/params/SeqVector.java | 4 ++-- src/jalview/ws/rest/params/Tree.java | 4 ++-- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 4 ++-- src/jalview/ws/seqfetcher/DbSourceProxy.java | 4 ++-- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 4 ++-- src/jalview/ws/uimodel/AlignAnalysisUIText.java | 4 ++-- src/org/jibble/epsgraphics/EpsDocument.java | 4 ++-- src/org/jibble/epsgraphics/EpsException.java | 4 ++-- src/org/jibble/epsgraphics/EpsGraphics2D.java | 4 ++-- src/uk/ac/ebi/picr/model/CrossReference.java | 4 ++-- .../ac/ebi/picr/model/CrossReference_Helper.java | 4 ++-- src/uk/ac/ebi/picr/model/UPEntry.java | 4 ++-- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 4 ++-- src/uk/ac/ebi/www/Data.java | 4 ++-- src/uk/ac/ebi/www/InputParams.java | 4 ++-- src/uk/ac/ebi/www/WSFile.java | 4 ++-- src/uk/ac/ebi/www/WSWUBlast.java | 4 ++-- src/uk/ac/ebi/www/WSWUBlastService.java | 4 ++-- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 4 ++-- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 4 ++-- .../AccessionMapperBindingStub.java | 4 ++-- .../AccessionMapperInterface.java | 4 ++-- .../AccessionMapperService.java | 4 ++-- .../AccessionMapperServiceLocator.java | 4 ++-- src/vamsas/IMsaWS.java | 4 ++-- src/vamsas/objects/simple/Alignment.java | 4 ++-- src/vamsas/objects/simple/Alignment_Helper.java | 4 ++-- src/vamsas/objects/simple/JpredResult.java | 4 ++-- src/vamsas/objects/simple/JpredResult_Helper.java | 4 ++-- src/vamsas/objects/simple/MsaResult.java | 4 ++-- src/vamsas/objects/simple/MsaResult_Helper.java | 4 ++-- src/vamsas/objects/simple/Msfalignment.java | 4 ++-- src/vamsas/objects/simple/Msfalignment_Helper.java | 4 ++-- src/vamsas/objects/simple/Object.java | 4 ++-- src/vamsas/objects/simple/Object_Helper.java | 4 ++-- src/vamsas/objects/simple/Result.java | 4 ++-- src/vamsas/objects/simple/Result_Helper.java | 4 ++-- src/vamsas/objects/simple/Secstructpred.java | 4 ++-- .../objects/simple/Secstructpred_Helper.java | 4 ++-- src/vamsas/objects/simple/SeqSearchResult.java | 4 ++-- .../objects/simple/SeqSearchResult_Helper.java | 4 ++-- src/vamsas/objects/simple/Sequence.java | 4 ++-- src/vamsas/objects/simple/SequenceSet.java | 4 ++-- src/vamsas/objects/simple/SequenceSet_Helper.java | 4 ++-- src/vamsas/objects/simple/Sequence_Helper.java | 4 ++-- src/vamsas/objects/simple/WsJobId.java | 4 ++-- src/vamsas/objects/simple/WsJobId_Helper.java | 4 ++-- test/MCview/AtomTest.java | 4 ++-- test/MCview/BondTest.java | 4 ++-- test/MCview/PDBChainTest.java | 4 ++-- test/MCview/PDBfileTest.java | 4 ++-- test/MCview/ResidueTest.java | 4 ++-- test/com/stevesoft/pat/RegexWriterTest.java | 4 ++-- test/jalview/analysis/AAFrequencyTest.java | 4 ++-- test/jalview/analysis/AlignSeqTest.java | 4 ++-- .../analysis/AlignmentAnnotationUtilsTest.java | 4 ++-- test/jalview/analysis/AlignmentUtilsTests.java | 4 ++-- test/jalview/analysis/AnnotationSorterTest.java | 4 ++-- test/jalview/analysis/CodingUtilsTest.java | 4 ++-- test/jalview/analysis/CrossRefTest.java | 4 ++-- test/jalview/analysis/DnaAlignmentGenerator.java | 4 ++-- test/jalview/analysis/DnaTest.java | 4 ++-- test/jalview/analysis/GroupingTest.java | 4 ++-- test/jalview/analysis/ParsePropertiesTest.java | 4 ++-- test/jalview/analysis/RnaTest.java | 4 ++-- test/jalview/analysis/TestAlignSeq.java | 4 ++-- .../scoremodels/FeatureScoreModelTest.java | 4 ++-- test/jalview/bin/CommandLineOperations.java | 4 ++-- test/jalview/commands/EditCommandTest.java | 4 ++-- test/jalview/datamodel/AlignedCodonFrameTest.java | 4 ++-- .../datamodel/AlignedCodonIteratorTest.java | 4 ++-- test/jalview/datamodel/AlignedCodonTest.java | 4 ++-- .../datamodel/AlignmentAnnotationTests.java | 4 ++-- test/jalview/datamodel/AlignmentTest.java | 4 ++-- test/jalview/datamodel/AlignmentViewTest.java | 4 ++-- test/jalview/datamodel/ColumnSelectionTest.java | 4 ++-- test/jalview/datamodel/DBRefEntryTest.java | 4 ++-- test/jalview/datamodel/MappingTest.java | 4 ++-- test/jalview/datamodel/MatchTest.java | 4 ++-- test/jalview/datamodel/PDBEntryTest.java | 4 ++-- test/jalview/datamodel/SearchResultsTest.java | 4 ++-- test/jalview/datamodel/SeqCigarTest.java | 4 ++-- test/jalview/datamodel/SequenceDummyTest.java | 4 ++-- test/jalview/datamodel/SequenceTest.java | 4 ++-- test/jalview/datamodel/xdb/embl/EmblFileTest.java | 4 ++-- test/jalview/ext/jmol/JmolViewerTest.java | 4 ++-- test/jalview/ext/jmol/PDBFileWithJmolTest.java | 4 ++-- test/jalview/ext/paradise/TestAnnotate3D.java | 4 ++-- test/jalview/ext/rbvi/chimera/AllTests.java | 4 ++-- .../ext/rbvi/chimera/ChimeraCommandsTest.java | 4 ++-- test/jalview/ext/rbvi/chimera/ChimeraConnect.java | 4 ++-- .../ext/rbvi/chimera/JalviewChimeraView.java | 4 ++-- test/jalview/gui/AlignViewportTest.java | 4 ++-- test/jalview/gui/AnnotationChooserTest.java | 4 ++-- test/jalview/gui/AppVarnaTest.java | 4 ++-- test/jalview/gui/FontChooserTest.java | 4 ++-- test/jalview/gui/HelpTest.java | 4 ++-- test/jalview/gui/JAL1353bugdemo.java | 4 ++-- test/jalview/gui/JvSwingUtilsTest.java | 4 ++-- test/jalview/gui/PDBSearchPanelTest.java | 4 ++-- test/jalview/gui/PaintRefresherTest.java | 4 ++-- test/jalview/gui/PopupMenuTest.java | 4 ++-- test/jalview/gui/ProgressBarTest.java | 4 ++-- test/jalview/gui/SequenceRendererTest.java | 4 ++-- test/jalview/gui/StructureChooserTest.java | 4 ++-- test/jalview/io/AnnotatedPDBFileInputTest.java | 4 ++-- test/jalview/io/AnnotationFileIOTest.java | 4 ++-- test/jalview/io/BioJsHTMLOutputTest.java | 4 ++-- test/jalview/io/FileIOTester.java | 4 ++-- test/jalview/io/Gff3tests.java | 4 ++-- test/jalview/io/HtmlFileTest.java | 4 ++-- test/jalview/io/IdentifyFileTest.java | 4 ++-- test/jalview/io/JSONFileTest.java | 4 ++-- test/jalview/io/Jalview2xmlTests.java | 4 ++-- test/jalview/io/JalviewExportPropertiesTests.java | 4 ++-- test/jalview/io/NewickFileTests.java | 4 ++-- test/jalview/io/PhylipFileTests.java | 4 ++-- test/jalview/io/RNAMLfileTest.java | 4 ++-- test/jalview/io/StockholmFileTest.java | 4 ++-- test/jalview/io/TCoffeeScoreFileTest.java | 4 ++-- test/jalview/schemes/DnaCodonTests.java | 4 ++-- test/jalview/schemes/ResiduePropertiesTest.java | 4 ++-- test/jalview/schemes/ScoreMatrixPrinter.java | 4 ++-- test/jalview/structure/Mapping.java | 4 ++-- .../structure/StructureSelectionManagerTest.java | 4 ++-- .../models/AAStructureBindingModelTest.java | 4 ++-- test/jalview/util/ColorUtilsTest.java | 4 ++-- test/jalview/util/ComparisonTest.java | 4 ++-- test/jalview/util/DBRefUtilsTest.java | 4 ++-- test/jalview/util/MapListTest.java | 4 ++-- test/jalview/util/MappingUtilsTest.java | 4 ++-- test/jalview/util/QuickSortTest.java | 4 ++-- test/jalview/util/ShiftListTest.java | 4 ++-- test/jalview/util/StringUtilsTest.java | 4 ++-- test/jalview/viewmodel/styles/ViewStyleTest.java | 4 ++-- test/jalview/ws/PDBSequenceFetcherTest.java | 4 ++-- test/jalview/ws/dbsources/PDBRestClientTest.java | 4 ++-- test/jalview/ws/dbsources/UniprotTest.java | 4 ++-- test/jalview/ws/gui/Jws2ParamView.java | 4 ++-- .../ws/jabaws/DisorderAnnotExportImport.java | 4 ++-- test/jalview/ws/jabaws/JalviewJabawsTestUtils.java | 4 ++-- .../ws/jabaws/JpredJabaStructExportImport.java | 4 ++-- test/jalview/ws/jabaws/MinJabawsClientTests.java | 4 ++-- test/jalview/ws/jabaws/RNAStructExportImport.java | 4 ++-- test/jalview/ws/jws2/ParameterUtilsTest.java | 4 ++-- test/jalview/ws/rest/RestClientTest.java | 4 ++-- test/jalview/ws/rest/ShmmrRSBSService.java | 4 ++-- test/jalview/ws/seqfetcher/DasSequenceFetcher.java | 4 ++-- test/jalview/ws/seqfetcher/DbRefFetcherTest.java | 4 ++-- utils/InstallAnywhere/Jalview.iap_xml | 4 ++-- utils/InstallAnywhere/jalview_buildinstaller.xml | 4 ++-- utils/eclipse/JalviewCodeStyle.xml | 4 ++-- utils/getJavaVersion.java | 4 ++-- utils/gff2annot.pl | 4 ++-- utils/help2Website.java | 4 ++-- utils/jalview_testng.xml | 4 ++-- utils/jarunsigner.pl | 4 ++-- utils/patchGt.pl | 4 ++-- utils/splitstockholm.pl | 4 ++-- 895 files changed, 1790 insertions(+), 1830 deletions(-) diff --git a/build.xml b/build.xml index e9006ca..de0d7a8 100755 --- a/build.xml +++ b/build.xml @@ -1,7 +1,7 @@