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commit e643aaa940725d05c9e2c5827d9b05f7bd0cdb6b Merge: ef4e6f6 7eb4c6f Author: Ximin Luo <[email protected]> Date: Sat Dec 10 16:11:32 2016 +0100 Merge tag 'upstream/2.10.1.dfsg' Upstream version 2.10.1.dfsg # gpg: Signature made Sat 10 Dec 2016 16:11:29 CET # gpg: using RSA key 3667486A326DB2766D255546860DEF3B8F650B79 # gpg: Good signature from "Ximin Luo <[email protected]>" [ultimate] # gpg: aka "Ximin Luo <[email protected]>" [ultimate] # gpg: aka "Ximin Luo <[email protected]>" [ultimate] # gpg: aka "Ximin Luo <[email protected]>" [ultimate] # gpg: aka "Satoshi Nakamoto (www.bitcoin.org) <[email protected]>" [ultimate] JalviewApplet.jpx | 150 +- JalviewX.jpx | 94 +- README | 2 +- build.xml | 1439 ++-- doc/AddingGroovySupport.html | 27 +- doc/AnnotationPostAnalysis.txt | 59 + doc/JalviewRNASupport.html | 84 + doc/UnitTesting.html | 110 + doc/biojsmsa-templates.html | 101 + doc/building.html | 50 +- doc/developing.html | 103 +- doc/i18n.html | 96 + doc/index.html | 327 +- 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src/jalview/commands/ChangeCaseCommand.java | 30 +- src/jalview/commands/CommandI.java | 13 +- src/jalview/commands/EditCommand.java | 703 +- src/jalview/commands/OrderCommand.java | 55 +- src/jalview/commands/RemoveGapColCommand.java | 26 +- src/jalview/commands/RemoveGapsCommand.java | 28 +- src/jalview/commands/SlideSequencesCommand.java | 44 +- src/jalview/commands/TrimRegionCommand.java | 155 +- src/jalview/controller/AlignViewController.java | 467 ++ .../controller/FeatureSettingsController.java | 35 + .../controller/FeatureSettingsControllerGuiI.java | 26 + src/jalview/datamodel/ASequence.java | 33 + src/jalview/datamodel/ASequenceI.java | 32 + src/jalview/datamodel/AlignedCodon.java | 114 + src/jalview/datamodel/AlignedCodonFrame.java | 1101 ++- src/jalview/datamodel/Alignment.java | 1118 ++- src/jalview/datamodel/AlignmentAnnotation.java | 785 +- src/jalview/datamodel/AlignmentExportData.java | 83 + src/jalview/datamodel/AlignmentI.java | 282 +- src/jalview/datamodel/AlignmentOrder.java | 56 +- src/jalview/datamodel/AlignmentView.java | 2423 +++--- src/jalview/datamodel/AnnotatedCollectionI.java | 46 + src/jalview/datamodel/Annotation.java | 109 +- src/jalview/datamodel/BinaryNode.java | 13 +- src/jalview/datamodel/BinarySequence.java | 109 +- src/jalview/datamodel/CigarArray.java | 780 +- src/jalview/datamodel/CigarBase.java | 1307 ++-- src/jalview/datamodel/CigarCigar.java | 125 +- src/jalview/datamodel/CigarSimple.java | 67 +- src/jalview/datamodel/ColumnSelection.java | 3061 ++++---- src/jalview/datamodel/DBRefEntry.java | 226 +- src/jalview/datamodel/DBRefSource.java | 257 +- src/jalview/datamodel/FeatureProperties.java | 120 +- src/jalview/datamodel/GraphLine.java | 29 +- src/jalview/datamodel/HiddenSequences.java | 193 +- .../datamodel/IncompleteCodonException.java | 33 + src/jalview/datamodel/Mapping.java | 406 +- src/jalview/datamodel/MappingType.java | 83 + src/jalview/datamodel/NodeTransformI.java | 13 +- src/jalview/datamodel/PDBEntry.java | 382 +- src/jalview/datamodel/Profile.java | 163 + src/jalview/datamodel/ProfileI.java | 87 + src/jalview/datamodel/Profiles.java | 63 + src/jalview/datamodel/ProfilesI.java | 32 + src/jalview/datamodel/Provenance.java | 15 +- src/jalview/datamodel/ProvenanceEntry.java | 13 +- src/jalview/datamodel/ResidueCount.java | 641 ++ src/jalview/datamodel/RnaViewerModel.java | 64 + src/jalview/datamodel/SearchResultMatchI.java | 50 + src/jalview/datamodel/SearchResults.java | 328 +- src/jalview/datamodel/SearchResultsI.java | 104 + .../datamodel/SecondaryStructureAnnotation.java | 52 + src/jalview/datamodel/SeqCigar.java | 261 +- src/jalview/datamodel/Sequence.java | 781 +- src/jalview/datamodel/SequenceCollectionI.java | 67 + src/jalview/datamodel/SequenceDummy.java | 63 + src/jalview/datamodel/SequenceFeature.java | 322 +- src/jalview/datamodel/SequenceGroup.java | 518 +- src/jalview/datamodel/SequenceI.java | 217 +- src/jalview/datamodel/SequenceNode.java | 15 +- src/jalview/datamodel/SequencePoint.java | 13 +- src/jalview/datamodel/StructureViewerModel.java | 225 + src/jalview/datamodel/UniprotEntry.java | 44 +- src/jalview/datamodel/UniprotFile.java | 25 +- src/jalview/datamodel/UniprotProteinName.java | 84 +- src/jalview/datamodel/UniprotSequence.java | 39 +- src/jalview/datamodel/xdb/embl/BasePosition.java | 59 - src/jalview/datamodel/xdb/embl/EmblEntry.java | 1137 +-- src/jalview/datamodel/xdb/embl/EmblError.java | 18 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 48 +- .../datamodel/xdb/embl/EmblFeatureLocElement.java | 116 - .../datamodel/xdb/embl/EmblFeatureLocations.java | 168 - src/jalview/datamodel/xdb/embl/EmblFile.java | 115 +- src/jalview/datamodel/xdb/embl/EmblSequence.java | 59 +- src/jalview/datamodel/xdb/embl/Qualifier.java | 21 +- src/jalview/exceptions/JalviewException.java | 45 + .../exceptions/NoFileSelectedException.java | 30 + src/jalview/ext/android/ContainerHelpers.java | 108 + src/jalview/ext/android/SparseIntArray.java | 432 ++ src/jalview/ext/android/SparseShortArray.java | 442 ++ src/jalview/ext/ensembl/EnsemblCdna.java | 131 + src/jalview/ext/ensembl/EnsemblCds.java | 138 + src/jalview/ext/ensembl/EnsemblFeatures.java | 160 + src/jalview/ext/ensembl/EnsemblGene.java | 615 ++ src/jalview/ext/ensembl/EnsemblGenome.java | 115 + src/jalview/ext/ensembl/EnsemblGenomes.java | 65 + src/jalview/ext/ensembl/EnsemblInfo.java | 91 + src/jalview/ext/ensembl/EnsemblLookup.java | 180 + src/jalview/ext/ensembl/EnsemblProtein.java | 147 + src/jalview/ext/ensembl/EnsemblRestClient.java | 567 ++ src/jalview/ext/ensembl/EnsemblSeqProxy.java | 955 +++ .../ext/ensembl/EnsemblSequenceFetcher.java | 133 + src/jalview/ext/ensembl/EnsemblSymbol.java | 159 + src/jalview/ext/ensembl/EnsemblXref.java | 224 + src/jalview/ext/ensembl/Species.java | 52 + src/jalview/ext/htsjdk/HtsContigDb.java | 232 + src/jalview/ext/jmol/JalviewJmolBinding.java | 3015 ++++---- src/jalview/ext/jmol/JmolCommands.java | 338 +- src/jalview/ext/jmol/JmolParser.java | 658 ++ src/jalview/ext/paradise/Annotate3D.java | 255 + src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 293 + src/jalview/ext/rbvi/chimera/ChimeraListener.java | 149 + .../ext/rbvi/chimera/JalviewChimeraBinding.java | 1127 +++ src/jalview/ext/so/SequenceOntology.java | 474 ++ src/jalview/ext/varna/JalviewVarnaBinding.java | 35 + src/jalview/ext/varna/RnaModel.java | 52 + src/jalview/ext/varna/VarnaCommands.java | 170 + src/jalview/fts/api/FTSData.java | 46 + src/jalview/fts/api/FTSDataColumnI.java | 161 + src/jalview/fts/api/FTSRestClientI.java | 139 + src/jalview/fts/api/GFTSPanelI.java | 140 + .../fts/core/DecimalFormatTableCellRenderer.java | 80 + src/jalview/fts/core/FTSDataColumnPreferences.java | 338 + src/jalview/fts/core/FTSRestClient.java | 506 ++ src/jalview/fts/core/FTSRestRequest.java | 190 + src/jalview/fts/core/FTSRestResponse.java | 174 + src/jalview/fts/core/GFTSPanel.java | 992 +++ src/jalview/fts/service/pdb/PDBFTSPanel.java | 279 + src/jalview/fts/service/pdb/PDBFTSRestClient.java | 426 ++ .../fts/service/uniprot/UniProtFTSRestClient.java | 323 + .../fts/service/uniprot/UniprotFTSPanel.java | 238 + src/jalview/gui/AlignExportSettings.java | 118 + src/jalview/gui/AlignFrame.java | 3384 +++++---- src/jalview/gui/AlignViewport.java | 2425 ++---- src/jalview/gui/AlignmentPanel.java | 1255 ++-- src/jalview/gui/AnnotationChooser.java | 657 ++ src/jalview/gui/AnnotationColourChooser.java | 531 +- src/jalview/gui/AnnotationColumnChooser.java | 922 +++ src/jalview/gui/AnnotationExporter.java | 628 +- src/jalview/gui/AnnotationLabels.java | 990 ++- src/jalview/gui/AnnotationPanel.java | 1518 ++-- src/jalview/gui/AnnotationRowFilter.java | 407 + src/jalview/gui/AppJmol.java | 1123 ++- src/jalview/gui/AppJmolBinding.java | 146 +- src/jalview/gui/AppVarna.java | 752 ++ src/jalview/gui/AppVarnaBinding.java | 577 ++ src/jalview/gui/AssociatePdbFileWithSeq.java | 107 +- src/jalview/gui/BlogReader.java | 121 +- src/jalview/gui/ChimeraViewFrame.java | 1147 +++ src/jalview/gui/ConservationThread.java | 103 - src/jalview/gui/Console.java | 42 +- src/jalview/gui/CrossRefAction.java | 312 + src/jalview/gui/CutAndPasteHtmlTransfer.java | 252 + src/jalview/gui/CutAndPasteTransfer.java | 215 +- src/jalview/gui/DasSourceBrowser.java | 1826 +++-- src/jalview/gui/Desktop.java | 1861 +++-- src/jalview/gui/EPSOptions.java | 47 +- src/jalview/gui/EditNameDialog.java | 30 +- src/jalview/gui/FeatureColourChooser.java | 233 +- src/jalview/gui/FeatureRenderer.java | 1209 +-- src/jalview/gui/FeatureSettings.java | 884 ++- src/jalview/gui/Finder.java | 220 +- src/jalview/gui/FontChooser.java | 173 +- src/jalview/gui/HTMLOptions.java | 162 + src/jalview/gui/Help.java | 110 + src/jalview/gui/IProgressIndicator.java | 107 +- src/jalview/gui/IProgressIndicatorHandler.java | 73 +- src/jalview/gui/IdCanvas.java | 164 +- src/jalview/gui/IdPanel.java | 338 +- src/jalview/gui/IdwidthAdjuster.java | 50 +- src/jalview/gui/JDatabaseTree.java | 596 ++ src/jalview/gui/Jalview2XML.java | 4913 ++++++++---- src/jalview/gui/Jalview2XML_V1.java | 976 +-- src/jalview/gui/JalviewAppender.java | 13 +- src/jalview/gui/JalviewChangeSupport.java | 32 +- src/jalview/gui/JalviewChimeraBindingModel.java | 144 + src/jalview/gui/JalviewDialog.java | 102 +- src/jalview/gui/JvSwingUtils.java | 184 +- src/jalview/gui/MenuChooser.java | 99 + src/jalview/gui/OOMWarning.java | 177 +- src/jalview/gui/OptsAndParamsPage.java | 224 +- src/jalview/gui/OptsParametersContainerI.java | 26 +- src/jalview/gui/OverviewPanel.java | 169 +- src/jalview/gui/PCAPanel.java | 476 +- src/jalview/gui/PaintRefresher.java | 134 +- src/jalview/gui/PairwiseAlignPanel.java | 50 +- src/jalview/gui/PopupMenu.java | 1420 ++-- src/jalview/gui/Preferences.java | 715 +- src/jalview/gui/ProgressBar.java | 255 + src/jalview/gui/PromptUserConfig.java | 24 +- src/jalview/gui/RedundancyPanel.java | 157 +- src/jalview/gui/RestInputParamEditDialog.java | 155 +- src/jalview/gui/RestServiceEditorPane.java | 318 +- src/jalview/gui/RotatableCanvas.java | 81 +- src/jalview/gui/SVGOptions.java | 162 + src/jalview/gui/ScalePanel.java | 443 +- src/jalview/gui/ScriptWindow.java | 732 -- src/jalview/gui/SeqCanvas.java | 312 +- src/jalview/gui/SeqPanel.java | 1090 +-- src/jalview/gui/SequenceFetcher.java | 1090 +-- src/jalview/gui/SequenceRenderer.java | 196 +- src/jalview/gui/SliderPanel.java | 96 +- src/jalview/gui/SplashScreen.java | 304 +- src/jalview/gui/SplitFrame.java | 756 ++ src/jalview/gui/StructureChooser.java | 1178 +++ src/jalview/gui/StructureViewer.java | 248 + src/jalview/gui/StructureViewerBase.java | 555 ++ src/jalview/gui/TextColourChooser.java | 103 +- src/jalview/gui/TreeCanvas.java | 311 +- src/jalview/gui/TreePanel.java | 211 +- src/jalview/gui/UserDefinedColours.java | 322 +- src/jalview/gui/UserQuestionnaireCheck.java | 34 +- src/jalview/gui/VamsasApplication.java | 69 +- src/jalview/gui/ViewSelectionMenu.java | 165 +- src/jalview/gui/WebserviceInfo.java | 170 +- src/jalview/gui/WsJobParameters.java | 379 +- src/jalview/gui/WsParamSetManager.java | 43 +- src/jalview/gui/WsPreferences.java | 303 +- src/jalview/httpserver/AbstractRequestHandler.java | 205 + src/jalview/httpserver/HttpServer.java | 300 + src/jalview/io/AMSAFile.java | 16 +- src/jalview/io/AlignFile.java | 192 +- src/jalview/io/AlignmentProperties.java | 35 +- src/jalview/io/AnnotationFile.java | 3291 ++++---- src/jalview/io/AppletFormatAdapter.java | 472 +- src/jalview/io/BLCFile.java | 28 +- src/jalview/io/BioJsHTMLOutput.java | 315 + src/jalview/io/ClansFile.java | 57 +- src/jalview/io/ClustalFile.java | 79 +- src/jalview/io/DBRefFile.java | 91 +- src/jalview/io/FastaFile.java | 78 +- src/jalview/io/FeaturesFile.java | 2181 +++--- src/jalview/io/FileLoader.java | 206 +- src/jalview/io/FileParse.java | 272 +- src/jalview/io/FormatAdapter.java | 141 +- src/jalview/io/HTMLOutput.java | 456 +- src/jalview/io/HtmlFile.java | 193 + src/jalview/io/HtmlSvgOutput.java | 307 + src/jalview/io/IdentifyFile.java | 268 +- src/jalview/io/InputStreamParser.java | 57 + src/jalview/io/JPredFile.java | 39 +- src/jalview/io/JSONFile.java | 895 +++ src/jalview/io/JalviewFileChooser.java | 119 +- src/jalview/io/JalviewFileFilter.java | 19 +- src/jalview/io/JalviewFileView.java | 33 +- src/jalview/io/JnetAnnotationMaker.java | 210 +- src/jalview/io/MSFfile.java | 121 +- src/jalview/io/MatrixFile.java | 69 +- src/jalview/io/ModellerDescription.java | 98 +- src/jalview/io/NewickFile.java | 48 +- src/jalview/io/PDBFeatureSettings.java | 85 + src/jalview/io/PIRFile.java | 25 +- src/jalview/io/PfamFile.java | 124 +- src/jalview/io/PhylipFile.java | 329 + src/jalview/io/PileUpfile.java | 40 +- src/jalview/io/RnamlFile.java | 244 + src/jalview/io/SequenceAnnotationReport.java | 469 ++ src/jalview/io/SimpleBlastFile.java | 28 +- src/jalview/io/StockholmFile.java | 1781 +++-- src/jalview/io/StructureFile.java | 508 ++ src/jalview/io/TCoffeeScoreFile.java | 651 ++ src/jalview/io/VamsasAppDatastore.java | 191 +- src/jalview/io/WSWUBlastClient.java | 67 +- src/jalview/io/gff/ExonerateHelper.java | 365 + src/jalview/io/gff/Gff2Helper.java | 71 + src/jalview/io/gff/Gff3Helper.java | 425 ++ src/jalview/io/gff/GffConstants.java | 43 + src/jalview/io/gff/GffHelperBase.java | 426 ++ src/jalview/io/gff/GffHelperFactory.java | 89 + src/jalview/io/gff/GffHelperI.java | 63 + src/jalview/io/gff/InterProScanHelper.java | 138 + src/jalview/io/gff/SequenceOntologyFactory.java | 48 + src/jalview/io/gff/SequenceOntologyI.java | 80 + src/jalview/io/gff/SequenceOntologyLite.java | 240 + src/jalview/io/packed/DataProvider.java | 47 +- src/jalview/io/packed/JalviewDataset.java | 290 +- src/jalview/io/packed/ParsePackedSet.java | 70 +- src/jalview/io/packed/SimpleDataProvider.java | 41 +- src/jalview/io/vamsas/Datasetsequence.java | 553 +- src/jalview/io/vamsas/DatastoreItem.java | 68 +- src/jalview/io/vamsas/DatastoreRegistry.java | 23 +- src/jalview/io/vamsas/Dbref.java | 17 +- src/jalview/io/vamsas/LocalDocSyncObject.java | 13 +- src/jalview/io/vamsas/Rangetype.java | 46 +- src/jalview/io/vamsas/Sequencefeature.java | 724 +- src/jalview/io/vamsas/Sequencemapping.java | 60 +- src/jalview/io/vamsas/Tree.java | 82 +- src/jalview/javascript/JSFunctionExec.java | 544 +- src/jalview/javascript/JalviewLiteJsApi.java | 166 +- src/jalview/javascript/JsCallBack.java | 26 +- src/jalview/javascript/JsSelectionSender.java | 50 +- src/jalview/javascript/MouseOverListener.java | 39 +- .../javascript/MouseOverStructureListener.java | 629 +- src/jalview/jbgui/GAlignExportSettings.java | 192 + src/jalview/jbgui/GAlignFrame.java | 2273 ++++-- src/jalview/jbgui/GAlignmentPanel.java | 26 +- src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 275 + src/jalview/jbgui/GCutAndPasteTransfer.java | 63 +- src/jalview/jbgui/GDasSourceBrowser.java | 472 +- src/jalview/jbgui/GDesktop.java | 125 +- src/jalview/jbgui/GFinder.java | 103 +- src/jalview/jbgui/GFontChooser.java | 202 +- src/jalview/jbgui/GPCAPanel.java | 185 +- src/jalview/jbgui/GPairwiseAlignPanel.java | 28 +- src/jalview/jbgui/GPreferences.java | 1606 ++-- src/jalview/jbgui/GRestInputParamEditDialog.java | 118 +- src/jalview/jbgui/GRestServiceEditorPane.java | 273 +- src/jalview/jbgui/GRnaStructureViewer.java | 43 + src/jalview/jbgui/GSequenceLink.java | 85 +- src/jalview/jbgui/GSliderPanel.java | 43 +- src/jalview/jbgui/GSplitFrame.java | 224 + src/jalview/jbgui/GStructureChooser.java | 819 ++ src/jalview/jbgui/GStructureViewer.java | 313 +- src/jalview/jbgui/GTreePanel.java | 72 +- src/jalview/jbgui/GUserDefinedColours.java | 72 +- src/jalview/jbgui/GWebserviceInfo.java | 45 +- src/jalview/jbgui/GWsPreferences.java | 121 +- .../json/binding/biojs/BioJSReleasePojo.java | 66 + .../json/binding/biojs/BioJSRepositoryPojo.java | 111 + .../biojson/v1/AlignmentAnnotationPojo.java | 149 + .../json/binding/biojson/v1/AlignmentPojo.java | 158 + .../biojson/v1/AnnotationDisplaySettingPojo.java | 118 + .../json/binding/biojson/v1/AnnotationPojo.java | 101 + .../binding/biojson/v1/ColourSchemeMapper.java | 111 + .../binding/biojson/v1/SequenceFeaturesPojo.java | 183 + .../json/binding/biojson/v1/SequenceGrpPojo.java | 181 + .../json/binding/biojson/v1/SequencePojo.java | 143 + src/jalview/math/AlignmentDimension.java | 55 + src/jalview/math/Matrix.java | 44 +- src/jalview/math/RotatableMatrix.java | 13 +- src/jalview/renderer/AnnotationRenderer.java | 1622 ++++ src/jalview/renderer/AwtRenderPanelI.java | 62 + src/jalview/renderer/ScaleRenderer.java | 132 + .../renderer/seqfeatures/FeatureRenderer.java | 465 ++ src/jalview/rest/RestHandler.java | 115 + src/jalview/schemabinding/version2/.castor.cdr | 45 - src/jalview/schemabinding/version2/AlcodMap.java | 349 +- src/jalview/schemabinding/version2/Alcodon.java | 501 +- .../schemabinding/version2/AlcodonFrame.java | 845 +-- src/jalview/schemabinding/version2/Annotation.java | 2456 +++--- .../version2/AnnotationColourScheme.java | 497 ++ .../schemabinding/version2/AnnotationColours.java | 465 +- .../schemabinding/version2/AnnotationElement.java | 669 +- .../schemabinding/version2/CalcIdParam.java | 300 + src/jalview/schemabinding/version2/Colour.java | 957 ++- src/jalview/schemabinding/version2/DBRef.java | 425 +- src/jalview/schemabinding/version2/Feature.java | 1042 +-- .../schemabinding/version2/FeatureSettings.java | 841 +-- src/jalview/schemabinding/version2/Features.java | 195 +- src/jalview/schemabinding/version2/Group.java | 386 +- .../schemabinding/version2/HiddenColumns.java | 416 +- src/jalview/schemabinding/version2/JGroup.java | 2385 +++--- src/jalview/schemabinding/version2/JSeq.java | 1842 +++-- .../schemabinding/version2/JalviewModel.java | 429 +- .../version2/JalviewModelSequence.java | 1886 ++--- .../schemabinding/version2/JalviewUserColours.java | 638 +- .../schemabinding/version2/MapListFrom.java | 416 +- src/jalview/schemabinding/version2/MapListTo.java | 416 +- .../schemabinding/version2/MapListType.java | 1152 ++- src/jalview/schemabinding/version2/Mapping.java | 307 +- .../schemabinding/version2/MappingChoice.java | 325 +- src/jalview/schemabinding/version2/OtherData.java | 324 +- src/jalview/schemabinding/version2/Pdbentry.java | 688 +- .../schemabinding/version2/PdbentryItem.java | 369 +- src/jalview/schemabinding/version2/Pdbids.java | 498 +- src/jalview/schemabinding/version2/Property.java | 324 +- src/jalview/schemabinding/version2/RnaViewer.java | 668 ++ .../schemabinding/version2/SecondaryStructure.java | 290 + src/jalview/schemabinding/version2/Sequence.java | 596 +- .../schemabinding/version2/SequenceSet.java | 1654 ++-- .../version2/SequenceSetProperties.java | 326 +- .../schemabinding/version2/SequenceType.java | 426 +- src/jalview/schemabinding/version2/Setting.java | 1330 ++-- .../schemabinding/version2/StructureState.java | 1357 ++-- .../schemabinding/version2/ThresholdLine.java | 469 +- src/jalview/schemabinding/version2/Tree.java | 1705 ++--- .../schemabinding/version2/UserColourScheme.java | 199 +- .../schemabinding/version2/UserColours.java | 325 +- src/jalview/schemabinding/version2/VAMSAS.java | 830 ++- .../schemabinding/version2/VamsasModel.java | 195 +- src/jalview/schemabinding/version2/Viewport.java | 5128 +++++++------ .../version2/WebServiceParameterSet.java | 836 +-- .../version2/descriptors/AlcodMapDescriptor.java | 448 +- .../version2/descriptors/AlcodonDescriptor.java | 540 +- .../descriptors/AlcodonFrameDescriptor.java | 460 +- .../AnnotationColourSchemeDescriptor.java | 573 ++ .../descriptors/AnnotationColoursDescriptor.java | 529 +- .../version2/descriptors/AnnotationDescriptor.java | 2161 +++--- .../descriptors/AnnotationElementDescriptor.java | 806 +- .../descriptors/CalcIdParamDescriptor.java | 313 + .../version2/descriptors/ColourDescriptor.java | 1059 +-- .../version2/descriptors/DBRefDescriptor.java | 584 +- .../version2/descriptors/FeatureDescriptor.java | 980 +-- .../descriptors/FeatureSettingsDescriptor.java | 460 +- .../version2/descriptors/FeaturesDescriptor.java | 276 +- .../version2/descriptors/GroupDescriptor.java | 443 +- .../descriptors/HiddenColumnsDescriptor.java | 440 +- .../version2/descriptors/JGroupDescriptor.java | 2162 +++--- .../version2/descriptors/JSeqDescriptor.java | 1146 +-- .../descriptors/JalviewModelDescriptor.java | 600 +- .../JalviewModelSequenceDescriptor.java | 815 +- .../descriptors/JalviewUserColoursDescriptor.java | 541 +- .../descriptors/MapListFromDescriptor.java | 442 +- .../version2/descriptors/MapListToDescriptor.java | 442 +- .../descriptors/MapListTypeDescriptor.java | 652 +- .../descriptors/MappingChoiceDescriptor.java | 440 +- .../version2/descriptors/MappingDescriptor.java | 371 +- .../version2/descriptors/OtherDataDescriptor.java | 448 +- .../version2/descriptors/PdbentryDescriptor.java | 605 +- .../descriptors/PdbentryItemDescriptor.java | 387 +- .../version2/descriptors/PdbidsDescriptor.java | 390 +- .../version2/descriptors/PropertyDescriptor.java | 448 +- .../version2/descriptors/RnaViewerDescriptor.java | 634 ++ .../descriptors/SecondaryStructureDescriptor.java | 345 + .../version2/descriptors/SequenceDescriptor.java | 431 +- .../descriptors/SequenceSetDescriptor.java | 815 +- .../SequenceSetPropertiesDescriptor.java | 440 +- .../descriptors/SequenceTypeDescriptor.java | 594 +- .../version2/descriptors/SettingDescriptor.java | 1296 ++-- .../descriptors/StructureStateDescriptor.java | 1218 +-- .../descriptors/ThresholdLineDescriptor.java | 536 +- .../version2/descriptors/TreeDescriptor.java | 1719 +++-- .../descriptors/UserColourSchemeDescriptor.java | 277 +- .../descriptors/UserColoursDescriptor.java | 445 +- .../version2/descriptors/VAMSASDescriptor.java | 471 +- .../descriptors/VamsasModelDescriptor.java | 276 +- .../version2/descriptors/ViewportDescriptor.java | 4612 +++++++----- .../WebServiceParameterSetDescriptor.java | 693 +- src/jalview/schemes/AnnotationColourGradient.java | 318 +- src/jalview/schemes/Blosum62ColourScheme.java | 48 +- src/jalview/schemes/BuriedColourScheme.java | 19 +- src/jalview/schemes/ClustalxColourScheme.java | 227 +- src/jalview/schemes/ColourSchemeI.java | 103 +- src/jalview/schemes/ColourSchemeProperty.java | 180 +- src/jalview/schemes/Consensus.java | 13 +- src/jalview/schemes/CovariationColourScheme.java | 124 + src/jalview/schemes/FeatureColour.java | 696 ++ src/jalview/schemes/FeatureSettingsAdapter.java | 68 + src/jalview/schemes/FollowerColourScheme.java | 69 + src/jalview/schemes/GraduatedColor.java | 295 - src/jalview/schemes/HelixColourScheme.java | 19 +- src/jalview/schemes/HydrophobicColourScheme.java | 19 +- src/jalview/schemes/NucleotideColourScheme.java | 24 +- src/jalview/schemes/PIDColourScheme.java | 45 +- .../schemes/PurinePyrimidineColourScheme.java | 90 + src/jalview/schemes/RNAHelicesColour.java | 205 + src/jalview/schemes/RNAHelicesColourChooser.java | 137 + .../schemes/RNAInteractionColourScheme.java | 85 + src/jalview/schemes/ResidueColourScheme.java | 271 +- src/jalview/schemes/ResidueProperties.java | 2662 +++++-- src/jalview/schemes/ScoreColourScheme.java | 25 +- src/jalview/schemes/ScoreMatrix.java | 259 +- src/jalview/schemes/StrandColourScheme.java | 19 +- src/jalview/schemes/TCoffeeColourScheme.java | 144 + src/jalview/schemes/TaylorColourScheme.java | 15 +- src/jalview/schemes/TurnColourScheme.java | 19 +- src/jalview/schemes/UserColourScheme.java | 54 +- src/jalview/schemes/ZappoColourScheme.java | 15 +- .../structure/AlignmentViewPanelListener.java | 26 +- src/jalview/structure/AtomSpec.java | 85 + src/jalview/structure/CommandListener.java | 55 + .../structure/SecondaryStructureListener.java | 39 + src/jalview/structure/SelectionListener.java | 13 +- src/jalview/structure/SelectionSource.java | 13 +- src/jalview/structure/SequenceListener.java | 23 +- src/jalview/structure/StructureImportSettings.java | 153 + src/jalview/structure/StructureListener.java | 71 +- src/jalview/structure/StructureMapping.java | 112 +- .../structure/StructureMappingcommandSet.java | 49 +- .../structure/StructureSelectionManager.java | 1284 +++- src/jalview/structure/VamsasListener.java | 75 +- src/jalview/structure/VamsasSource.java | 30 +- .../structures/models/AAStructureBindingModel.java | 680 ++ .../models/SequenceStructureBindingModel.java | 72 + src/jalview/util/AWTConsole.java | 35 +- src/jalview/util/ArrayUtils.java | 47 + src/jalview/util/BrowserLauncher.java | 194 +- src/jalview/util/CaseInsensitiveString.java | 77 + src/jalview/util/ColorUtils.java | 194 + src/jalview/util/Comparison.java | 294 +- src/jalview/util/DBRefUtils.java | 575 +- src/jalview/util/DnaUtils.java | 153 + src/jalview/util/Format.java | 93 +- src/jalview/util/GroupUrlLink.java | 59 +- src/jalview/util/HttpUtils.java | 67 + src/jalview/util/ImageMaker.java | 251 +- src/jalview/util/LinkedIdentityHashSet.java | 143 + src/jalview/util/MapList.java | 942 ++- src/jalview/util/MappingUtils.java | 937 +++ src/jalview/util/MessageManager.java | 127 + src/jalview/util/ParseHtmlBodyAndLinks.java | 185 +- src/jalview/util/Platform.java | 184 +- src/jalview/util/QuickSort.java | 561 +- src/jalview/util/ReverseListIterator.java | 63 + src/jalview/util/ShiftList.java | 297 +- src/jalview/util/SparseCount.java | 174 + src/jalview/util/StringUtils.java | 406 + src/jalview/util/TableSorter.java | 1213 +-- src/jalview/util/UrlConstants.java | 55 + src/jalview/util/UrlLink.java | 1018 ++- src/jalview/util/jarInputStreamProvider.java | 93 +- src/jalview/viewmodel/AlignmentViewport.java | 2875 +++++++ src/jalview/viewmodel/PCAModel.java | 246 + .../AnnotationFilterParameter.java | 122 + .../seqfeatures/FeatureRendererModel.java | 947 +++ .../seqfeatures/FeatureRendererSettings.java | 110 + .../seqfeatures/FeatureSettingsModel.java | 28 + .../viewmodel/seqfeatures/FeaturesDisplayed.java | 114 + src/jalview/viewmodel/styles/ViewStyle.java | 1097 +++ src/jalview/workers/AlignCalcManager.java | 399 + src/jalview/workers/AlignCalcWorker.java | 139 + .../workers/AlignmentAnnotationFactory.java | 148 + src/jalview/workers/AnnotationProviderI.java | 37 + src/jalview/workers/AnnotationWorker.java | 144 + src/jalview/workers/ColumnCounterWorker.java | 244 + src/jalview/workers/ComplementConsensusThread.java | 118 + src/jalview/workers/ConsensusThread.java | 220 + src/jalview/workers/ConservationThread.java | 140 + src/jalview/workers/FeatureCounterI.java | 83 + src/jalview/workers/StrucConsensusThread.java | 170 + src/jalview/ws/AWSThread.java | 111 +- src/jalview/ws/AWsJob.java | 13 +- src/jalview/ws/DBRefFetcher.java | 1578 ++-- src/jalview/ws/DasSequenceFeatureFetcher.java | 1829 ++--- src/jalview/ws/EnfinEnvision2OneWay.java | 709 -- src/jalview/ws/HttpClientUtils.java | 169 + src/jalview/ws/JobStateSummary.java | 36 +- src/jalview/ws/SequenceFetcher.java | 582 +- src/jalview/ws/SequenceFetcherFactory.java | 52 + src/jalview/ws/WSClient.java | 15 +- src/jalview/ws/WSClientI.java | 13 +- src/jalview/ws/WSMenuEntryProviderI.java | 17 +- src/jalview/ws/dbsources/DasSequenceSource.java | 176 - .../ws/dbsources/EbiFileRetrievedProxy.java | 130 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 88 - src/jalview/ws/dbsources/EmblCdsSource.java | 101 + src/jalview/ws/dbsources/EmblSource.java | 259 +- src/jalview/ws/dbsources/EmblXmlSource.java | 301 +- src/jalview/ws/dbsources/GeneDbSource.java | 265 +- src/jalview/ws/dbsources/Pdb.java | 504 +- src/jalview/ws/dbsources/Pfam.java | 315 +- src/jalview/ws/dbsources/PfamFull.java | 142 +- src/jalview/ws/dbsources/PfamSeed.java | 140 +- src/jalview/ws/dbsources/Rfam.java | 119 + src/jalview/ws/dbsources/RfamFull.java | 85 + src/jalview/ws/dbsources/RfamSeed.java | 89 + src/jalview/ws/dbsources/Uniprot.java | 312 +- src/jalview/ws/dbsources/UniprotName.java | 46 + src/jalview/ws/dbsources/UnprotName.java | 41 - src/jalview/ws/dbsources/Xfam.java | 95 + .../dbsources/das/DasSequenceSourceListener.java | 165 - .../ws/dbsources/das/api/DasSourceRegistryI.java | 57 + .../ws/dbsources/das/api/jalviewSourceI.java | 87 + .../dbsources/das/datamodel/DasSequenceSource.java | 355 + .../dbsources/das/datamodel/DasSourceRegistry.java | 486 ++ .../ws/dbsources/das/datamodel/JalviewSource.java | 383 + src/jalview/ws/ebi/EBIFetchClient.java | 523 +- src/jalview/ws/io/mime/HttpContentHandler.java | 25 +- .../ws/io/mime/JalviewMimeContentHandler.java | 77 +- src/jalview/ws/io/mime/MimeTypes.java | 67 +- src/jalview/ws/jws1/Annotate3D.java | 282 + src/jalview/ws/jws1/Discoverer.java | 58 +- src/jalview/ws/jws1/JPredClient.java | 69 +- src/jalview/ws/jws1/JPredThread.java | 205 +- src/jalview/ws/jws1/JWS1Thread.java | 21 +- src/jalview/ws/jws1/MsaWSClient.java | 61 +- src/jalview/ws/jws1/MsaWSThread.java | 90 +- src/jalview/ws/jws1/SeqSearchWSClient.java | 64 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 95 +- src/jalview/ws/jws1/WS1Client.java | 20 +- src/jalview/ws/jws1/WSJob.java | 13 +- src/jalview/ws/jws2/AAConClient.java | 128 + src/jalview/ws/jws2/AADisorderClient.java | 379 + src/jalview/ws/jws2/AWS2Thread.java | 13 +- src/jalview/ws/jws2/AbstractJabaCalcWorker.java | 621 ++ src/jalview/ws/jws2/JPred301Client.java | 299 + src/jalview/ws/jws2/JWs2Job.java | 17 +- src/jalview/ws/jws2/JabaParamStore.java | 121 +- src/jalview/ws/jws2/JabaPreset.java | 30 +- src/jalview/ws/jws2/JabaWsServerQuery.java | 236 +- src/jalview/ws/jws2/JabawsCalcWorker.java | 237 + .../ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java | 226 + src/jalview/ws/jws2/Jws2Client.java | 377 +- src/jalview/ws/jws2/Jws2Discoverer.java | 758 +- src/jalview/ws/jws2/MsaWSClient.java | 278 +- src/jalview/ws/jws2/MsaWSThread.java | 401 +- src/jalview/ws/jws2/ParameterUtils.java | 34 +- src/jalview/ws/jws2/RNAalifoldClient.java | 404 + .../ws/jws2/SequenceAnnotationWSClient.java | 258 + src/jalview/ws/jws2/dm/AAConSettings.java | 153 + src/jalview/ws/jws2/dm/JabaOption.java | 30 +- src/jalview/ws/jws2/dm/JabaParameter.java | 15 +- src/jalview/ws/jws2/dm/JabaValueConstrain.java | 31 +- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 35 +- src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 252 + .../ws/jws2/jabaws2/Jws2InstanceFactory.java | 97 + src/jalview/ws/params/ArgumentI.java | 14 +- src/jalview/ws/params/AutoCalcSetting.java | 90 + .../ws/params/InvalidArgumentException.java | 22 +- src/jalview/ws/params/OptionI.java | 13 +- src/jalview/ws/params/ParamDatastoreI.java | 13 +- src/jalview/ws/params/ParamManager.java | 15 +- src/jalview/ws/params/ParameterI.java | 17 +- src/jalview/ws/params/ValueConstrainI.java | 23 +- src/jalview/ws/params/WsParamSetI.java | 13 +- src/jalview/ws/params/simple/BooleanOption.java | 38 +- src/jalview/ws/params/simple/IntegerParameter.java | 75 +- src/jalview/ws/params/simple/Option.java | 62 +- src/jalview/ws/params/simple/Parameter.java | 33 +- .../ws/params/simple/StringChoiceParameter.java | 23 +- src/jalview/ws/rest/AlignmentProcessor.java | 32 +- src/jalview/ws/rest/HttpResultSet.java | 36 +- src/jalview/ws/rest/InputType.java | 312 +- src/jalview/ws/rest/NoValidInputDataException.java | 31 +- src/jalview/ws/rest/RestClient.java | 279 +- src/jalview/ws/rest/RestJob.java | 129 +- src/jalview/ws/rest/RestJobThread.java | 45 +- src/jalview/ws/rest/RestServiceDescription.java | 375 +- src/jalview/ws/rest/params/Alignment.java | 57 +- src/jalview/ws/rest/params/AnnotationFile.java | 91 +- src/jalview/ws/rest/params/JobConstant.java | 56 +- .../ws/rest/params/SeqGroupIndexVector.java | 142 +- src/jalview/ws/rest/params/SeqIdVector.java | 39 +- src/jalview/ws/rest/params/SeqVector.java | 74 +- src/jalview/ws/rest/params/Tree.java | 57 +- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 793 +- src/jalview/ws/seqfetcher/DbSourceProxy.java | 312 +- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 297 +- src/jalview/ws/sifts/MappingOutputPojo.java | 137 + src/jalview/ws/sifts/SiftsClient.java | 1094 +++ src/jalview/ws/sifts/SiftsException.java | 32 + src/jalview/ws/sifts/SiftsSettings.java | 78 + src/jalview/ws/uimodel/AlignAnalysisUIText.java | 133 + src/jalview/xml/binding/sifts/Alignment.java | 2310 ++++++ src/jalview/xml/binding/sifts/EntityType.java | 62 + src/jalview/xml/binding/sifts/Entry.java | 2818 +++++++ src/jalview/xml/binding/sifts/ObjectFactory.java | 319 + src/jalview/xml/binding/sifts/package-info.java | 9 + .../biojava/dasobert/das/DAS_FeatureRetrieve.java | 287 - .../biojava/dasobert/das/DAS_Feature_Handler.java | 314 - .../biojava/dasobert/das/DAS_Sequence_Handler.java | 161 - src/org/biojava/dasobert/das/FeatureThread.java | 198 - src/org/biojava/dasobert/das/SequenceThread.java | 299 - src/org/biojava/dasobert/das2/Das2Capability.java | 51 - .../biojava/dasobert/das2/Das2CapabilityImpl.java | 131 - src/org/biojava/dasobert/das2/Das2Source.java | 42 - src/org/biojava/dasobert/das2/Das2SourceImpl.java | 157 - .../biojava/dasobert/das2/DasSourceConverter.java | 92 - .../dasobert/das2/io/DAS2SourceHandler.java | 216 - .../biojava/dasobert/das2/io/DasSourceReader.java | 33 - .../dasobert/das2/io/DasSourceReaderImpl.java | 183 - .../biojava/dasobert/dasregistry/Das1Source.java | 305 - .../dasobert/dasregistry/Das2Validator.java | 44 - .../dasregistry/DasCoordSysComparator.java | 128 - .../dasobert/dasregistry/DasCoordinateSystem.java | 233 - .../biojava/dasobert/dasregistry/DasSource.java | 130 - .../dasobert/dasregistry/DasSourceComparator.java | 190 - .../dasobert/eventmodel/AbstractDasEvent.java | 43 - .../biojava/dasobert/eventmodel/FeatureEvent.java | 96 - .../dasobert/eventmodel/FeatureListener.java | 48 - .../dasobert/eventmodel/ObjectListener.java | 51 - .../biojava/dasobert/eventmodel/SequenceEvent.java | 62 - .../dasobert/eventmodel/SequenceListener.java | 64 - .../dasobert/feature/AbstractFeatureTrack.java | 278 - .../biojava/dasobert/feature/AbstractSegment.java | 256 - .../dasobert/feature/FeatureComparator.java | 87 - .../dasobert/feature/FeatureMapComparator.java | 68 - src/org/biojava/dasobert/feature/FeatureTrack.java | 127 - .../dasobert/feature/FeatureTrackConverter.java | 526 -- .../biojava/dasobert/feature/FeatureTrackImpl.java | 68 - .../biojava/dasobert/feature/HistogramFeature.java | 95 - .../biojava/dasobert/feature/HistogramSegment.java | 67 - src/org/biojava/dasobert/feature/Segment.java | 84 - .../dasobert/feature/SegmentComparator.java | 45 - src/org/biojava/dasobert/feature/SegmentImpl.java | 83 - src/org/jibble/epsgraphics/EpsDocument.java | 47 +- src/org/jibble/epsgraphics/EpsException.java | 34 +- src/org/jibble/epsgraphics/EpsGraphics2D.java | 112 +- src/uk/ac/ebi/picr/model/CrossReference.java | 675 +- .../ac/ebi/picr/model/CrossReference_Helper.java | 253 +- src/uk/ac/ebi/picr/model/UPEntry.java | 591 +- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 215 +- src/uk/ac/ebi/www/Data.java | 21 +- src/uk/ac/ebi/www/InputParams.java | 21 +- src/uk/ac/ebi/www/WSFile.java | 21 +- src/uk/ac/ebi/www/WSWUBlast.java | 13 +- src/uk/ac/ebi/www/WSWUBlastService.java | 13 +- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 23 +- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 39 +- .../AccessionMapperBindingStub.java | 795 +- .../AccessionMapperInterface.java | 71 +- .../AccessionMapperService.java | 61 +- .../AccessionMapperServiceLocator.java | 385 +- src/vamsas/IMsaWS.java | 18 +- src/vamsas/objects/simple/Alignment.java | 25 +- src/vamsas/objects/simple/Alignment_Helper.java | 13 +- src/vamsas/objects/simple/JpredResult.java | 21 +- src/vamsas/objects/simple/JpredResult_Helper.java | 13 +- src/vamsas/objects/simple/MsaResult.java | 40 +- src/vamsas/objects/simple/MsaResult_Helper.java | 30 +- src/vamsas/objects/simple/Msfalignment.java | 21 +- src/vamsas/objects/simple/Msfalignment_Helper.java | 13 +- src/vamsas/objects/simple/Object.java | 26 +- src/vamsas/objects/simple/Object_Helper.java | 13 +- src/vamsas/objects/simple/Result.java | 25 +- src/vamsas/objects/simple/Result_Helper.java | 13 +- src/vamsas/objects/simple/Secstructpred.java | 19 +- .../objects/simple/Secstructpred_Helper.java | 13 +- src/vamsas/objects/simple/SeqSearchResult.java | 381 +- .../objects/simple/SeqSearchResult_Helper.java | 175 +- src/vamsas/objects/simple/Sequence.java | 25 +- src/vamsas/objects/simple/SequenceSet.java | 25 +- src/vamsas/objects/simple/SequenceSet_Helper.java | 13 +- src/vamsas/objects/simple/Sequence_Helper.java | 13 +- src/vamsas/objects/simple/WsJobId.java | 25 +- src/vamsas/objects/simple/WsJobId_Helper.java | 13 +- 1123 files changed, 234438 insertions(+), 122373 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/jalview.git 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