JAL-1807 includes ?j2sdebug flag and DebugJS._(msg)
authorhansonr <hansonr@stolaf.edu>
Fri, 24 Jul 2015 09:27:35 +0000 (10:27 +0100)
committerhansonr <hansonr@stolaf.edu>
Fri, 24 Jul 2015 09:27:35 +0000 (10:27 +0100)
712 files changed:
.j2s
bin/.gitignore [new file with mode: 0644]
bin/MCview/Atom.js
bin/MCview/Bond.js
bin/MCview/PDBChain.class
bin/MCview/PDBChain.js
bin/MCview/PDBfile.class
bin/MCview/PDBfile.js
bin/MCview/Residue.js
bin/awt2swing/Button.js
bin/awt2swing/Canvas.js
bin/awt2swing/Checkbox.js
bin/awt2swing/CheckboxMenuItem.js
bin/awt2swing/Choice.js
bin/awt2swing/Frame.js
bin/awt2swing/Label.js
bin/awt2swing/Menu.js
bin/awt2swing/MenuBar.js
bin/awt2swing/MenuItem.js
bin/awt2swing/Panel.js
bin/awt2swing/PopupMenu.js
bin/awt2swing/ScrollPane.js
bin/awt2swing/Scrollbar.js
bin/awt2swing/TextArea.js
bin/awt2swing/TextField.js
bin/com/stevesoft/pat/AmpersandRule.js
bin/com/stevesoft/pat/Any.js
bin/com/stevesoft/pat/BackG.js
bin/com/stevesoft/pat/BackMatch.js
bin/com/stevesoft/pat/BackRefRule.js
bin/com/stevesoft/pat/Backup.js
bin/com/stevesoft/pat/BasicStringBufferLike.js
bin/com/stevesoft/pat/Bits.js
bin/com/stevesoft/pat/Boundary.js
bin/com/stevesoft/pat/Bracket.js
bin/com/stevesoft/pat/CaseMgr.js
bin/com/stevesoft/pat/ChangeRule.js
bin/com/stevesoft/pat/CodeRule.js
bin/com/stevesoft/pat/Ctrl.js
bin/com/stevesoft/pat/Custom.js
bin/com/stevesoft/pat/CustomEndpoint.js
bin/com/stevesoft/pat/DirFileRegex.js
bin/com/stevesoft/pat/DotMulti.class
bin/com/stevesoft/pat/DotMulti.js
bin/com/stevesoft/pat/End.js
bin/com/stevesoft/pat/FastBracket.js
bin/com/stevesoft/pat/FastMulti.class
bin/com/stevesoft/pat/FastMulti.js
bin/com/stevesoft/pat/FileRegex.js
bin/com/stevesoft/pat/Group.js
bin/com/stevesoft/pat/LeftRule.js
bin/com/stevesoft/pat/MessageManager.js
bin/com/stevesoft/pat/Multi.js
bin/com/stevesoft/pat/MultiMin.js
bin/com/stevesoft/pat/Multi_stage2.js
bin/com/stevesoft/pat/NoPattern.js
bin/com/stevesoft/pat/NonDirFileRegex.js
bin/com/stevesoft/pat/NotImplementedError.js
bin/com/stevesoft/pat/NullPattern.js
bin/com/stevesoft/pat/NullRule.js
bin/com/stevesoft/pat/Or.js
bin/com/stevesoft/pat/OrMark.js
bin/com/stevesoft/pat/PartialBuffer.js
bin/com/stevesoft/pat/Pattern.js
bin/com/stevesoft/pat/PatternSub.js
bin/com/stevesoft/pat/PopRule.js
bin/com/stevesoft/pat/Prop.js
bin/com/stevesoft/pat/Pthings.js
bin/com/stevesoft/pat/PushRule.js
bin/com/stevesoft/pat/RBuffer.js
bin/com/stevesoft/pat/Range.js
bin/com/stevesoft/pat/RegOpt.class
bin/com/stevesoft/pat/RegOpt.js
bin/com/stevesoft/pat/RegRes.js
bin/com/stevesoft/pat/RegSyntax.js
bin/com/stevesoft/pat/RegSyntaxError.js
bin/com/stevesoft/pat/Regex.class
bin/com/stevesoft/pat/Regex.js
bin/com/stevesoft/pat/RegexReader.class
bin/com/stevesoft/pat/RegexReader.js
bin/com/stevesoft/pat/RegexTokenizer.js
bin/com/stevesoft/pat/RegexWriter.class
bin/com/stevesoft/pat/RegexWriter.js
bin/com/stevesoft/pat/ReplaceRule.class
bin/com/stevesoft/pat/ReplaceRule.js
bin/com/stevesoft/pat/Replacer.class
bin/com/stevesoft/pat/Replacer.js
bin/com/stevesoft/pat/RightRule.js
bin/com/stevesoft/pat/Rthings.js
bin/com/stevesoft/pat/RuleHolder.js
bin/com/stevesoft/pat/Skip.js
bin/com/stevesoft/pat/Skip2.js
bin/com/stevesoft/pat/SkipBMH.js
bin/com/stevesoft/pat/Skipped.js
bin/com/stevesoft/pat/SpecialRule.js
bin/com/stevesoft/pat/Start.js
bin/com/stevesoft/pat/StrPos.class
bin/com/stevesoft/pat/StrPos.js
bin/com/stevesoft/pat/StringBufferLike.class
bin/com/stevesoft/pat/StringBufferLike.js
bin/com/stevesoft/pat/StringLike.js
bin/com/stevesoft/pat/StringRule.js
bin/com/stevesoft/pat/SubMark.js
bin/com/stevesoft/pat/TransPat.js
bin/com/stevesoft/pat/Transformer.js
bin/com/stevesoft/pat/UniValidator.js
bin/com/stevesoft/pat/Util.js
bin/com/stevesoft/pat/Validator.js
bin/com/stevesoft/pat/WantMoreTextReplaceRule.js
bin/com/stevesoft/pat/lookAhead.js
bin/com/stevesoft/pat/oneChar.js
bin/com/stevesoft/pat/package.js
bin/com/stevesoft/pat/parsePerl.class
bin/com/stevesoft/pat/parsePerl.js
bin/com/stevesoft/pat/patInf.js
bin/com/stevesoft/pat/patInt.js
bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js
bin/com/stevesoft/pat/wrap/CharArrayWrap.js
bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js
bin/com/stevesoft/pat/wrap/StringBufferWrap.js
bin/com/stevesoft/pat/wrap/StringWrap.js
bin/com/stevesoft/pat/wrap/WriterWrap.js
bin/fr/orsay/lri/varna/models/rna/RNA.js
bin/jalview/analysis/AAFrequency.class
bin/jalview/analysis/AAFrequency.js
bin/jalview/analysis/AlignSeq.class
bin/jalview/analysis/AlignSeq.js
bin/jalview/analysis/AlignmentAnnotationUtils.class
bin/jalview/analysis/AlignmentAnnotationUtils.js
bin/jalview/analysis/AlignmentSorter.class
bin/jalview/analysis/AlignmentSorter.js
bin/jalview/analysis/AlignmentUtils.class
bin/jalview/analysis/AlignmentUtils.js
bin/jalview/analysis/AnnotationSorter.js
bin/jalview/analysis/CodingUtils.js
bin/jalview/analysis/CodonComparator.js
bin/jalview/analysis/Conservation.class
bin/jalview/analysis/Conservation.js
bin/jalview/analysis/Dna.class
bin/jalview/analysis/Dna.js
bin/jalview/analysis/Finder.class
bin/jalview/analysis/Finder.js
bin/jalview/analysis/Grouping.js
bin/jalview/analysis/NJTree.class
bin/jalview/analysis/NJTree.js
bin/jalview/analysis/PCA.js
bin/jalview/analysis/ParseProperties.js
bin/jalview/analysis/Rna.js
bin/jalview/analysis/SecStrConsensus.class
bin/jalview/analysis/SecStrConsensus.js
bin/jalview/analysis/SeqsetUtils.js
bin/jalview/analysis/SequenceIdMatcher$SeqIdName.class
bin/jalview/analysis/SequenceIdMatcher.js
bin/jalview/analysis/StructureFrequency.class
bin/jalview/analysis/StructureFrequency.js
bin/jalview/analysis/WUSSParseException.js
bin/jalview/analysis/package.js
bin/jalview/analysis/scoremodels/FeatureScoreModel.js
bin/jalview/analysis/scoremodels/PIDScoreModel.js
bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
bin/jalview/analysis/scoremodels/SWScoreModel.js
bin/jalview/api/AlignCalcManagerI.js
bin/jalview/api/AlignCalcWorkerI.js
bin/jalview/api/AlignExportSettingI.js
bin/jalview/api/AlignViewControllerGuiI.js
bin/jalview/api/AlignViewControllerI.js
bin/jalview/api/AlignViewportI.js
bin/jalview/api/AlignmentViewPanel.js
bin/jalview/api/ComplexAlignFile.js
bin/jalview/api/FeatureRenderer.js
bin/jalview/api/FeatureSettingsControllerI.js
bin/jalview/api/FeatureSettingsModelI.js
bin/jalview/api/FeaturesDisplayedI.js
bin/jalview/api/OOMHandlerI.js
bin/jalview/api/RotatableCanvasI.js
bin/jalview/api/SequenceRenderer.js
bin/jalview/api/SequenceStructureBinding.js
bin/jalview/api/SplitContainerI.js
bin/jalview/api/StructureSelectionManagerProvider.js
bin/jalview/api/ViewStyleI.js
bin/jalview/api/analysis/ScoreModelI.js
bin/jalview/api/analysis/ViewBasedAnalysisI.js
bin/jalview/api/structures/JalviewStructureDisplayI.js
bin/jalview/appletgui/APopupMenu.class
bin/jalview/appletgui/APopupMenu.js
bin/jalview/appletgui/AlignFrame.class
bin/jalview/appletgui/AlignFrame.js
bin/jalview/appletgui/AlignViewport.js
bin/jalview/appletgui/AlignmentPanel.class
bin/jalview/appletgui/AlignmentPanel.js
bin/jalview/appletgui/AnnotationColourChooser.class
bin/jalview/appletgui/AnnotationColourChooser.js
bin/jalview/appletgui/AnnotationColumnChooser.class
bin/jalview/appletgui/AnnotationColumnChooser.js
bin/jalview/appletgui/AnnotationLabels.class
bin/jalview/appletgui/AnnotationLabels.js
bin/jalview/appletgui/AnnotationPanel.class
bin/jalview/appletgui/AnnotationPanel.js
bin/jalview/appletgui/AnnotationRowFilter.js
bin/jalview/appletgui/AppletJmol.js
bin/jalview/appletgui/AppletJmolBinding.js
bin/jalview/appletgui/CutAndPasteTransfer.class
bin/jalview/appletgui/CutAndPasteTransfer.js
bin/jalview/appletgui/EditNameDialog.js
bin/jalview/appletgui/EmbmenuFrame.js
bin/jalview/appletgui/ExtJmol.js
bin/jalview/appletgui/FeatureColourChooser.class
bin/jalview/appletgui/FeatureColourChooser.js
bin/jalview/appletgui/FeatureRenderer.class
bin/jalview/appletgui/FeatureRenderer.js
bin/jalview/appletgui/FeatureSettings.js
bin/jalview/appletgui/Finder.js
bin/jalview/appletgui/FontChooser.js
bin/jalview/appletgui/IdCanvas.class
bin/jalview/appletgui/IdCanvas.js
bin/jalview/appletgui/IdPanel.js
bin/jalview/appletgui/IdwidthAdjuster.js
bin/jalview/appletgui/JVDialog.js
bin/jalview/appletgui/OverviewPanel.class
bin/jalview/appletgui/OverviewPanel.js
bin/jalview/appletgui/PCAPanel.class
bin/jalview/appletgui/PCAPanel.js
bin/jalview/appletgui/PaintRefresher.class
bin/jalview/appletgui/PaintRefresher.js
bin/jalview/appletgui/PairwiseAlignPanel.class
bin/jalview/appletgui/PairwiseAlignPanel.js
bin/jalview/appletgui/RedundancyPanel.js
bin/jalview/appletgui/RotatableCanvas.js
bin/jalview/appletgui/ScalePanel.class
bin/jalview/appletgui/ScalePanel.js
bin/jalview/appletgui/SeqCanvas.class
bin/jalview/appletgui/SeqCanvas.js
bin/jalview/appletgui/SeqPanel.class
bin/jalview/appletgui/SeqPanel.js
bin/jalview/appletgui/SequenceRenderer.class
bin/jalview/appletgui/SequenceRenderer.js
bin/jalview/appletgui/SliderPanel.class
bin/jalview/appletgui/SliderPanel.js
bin/jalview/appletgui/SplitFrame.js
bin/jalview/appletgui/TitledPanel.js
bin/jalview/appletgui/Tooltip.js
bin/jalview/appletgui/TreeCanvas.class
bin/jalview/appletgui/TreeCanvas.js
bin/jalview/appletgui/TreePanel$TreeLoader.class
bin/jalview/appletgui/TreePanel.class
bin/jalview/appletgui/TreePanel.js
bin/jalview/appletgui/UserDefinedColours.class
bin/jalview/appletgui/UserDefinedColours.js
bin/jalview/bin/Cache.js
bin/jalview/bin/JalviewLite$4.class
bin/jalview/bin/JalviewLite$LoadJmolThread.class
bin/jalview/bin/JalviewLite$LoadingThread.class
bin/jalview/bin/JalviewLite.class
bin/jalview/bin/JalviewLite.js
bin/jalview/commands/ChangeCaseCommand.js
bin/jalview/commands/CommandI.js
bin/jalview/commands/EditCommand.class
bin/jalview/commands/EditCommand.js
bin/jalview/commands/OrderCommand.js
bin/jalview/commands/RemoveGapColCommand.js
bin/jalview/commands/RemoveGapsCommand.js
bin/jalview/commands/SlideSequencesCommand.js
bin/jalview/commands/TrimRegionCommand.class
bin/jalview/commands/TrimRegionCommand.js
bin/jalview/controller/AlignViewController.class
bin/jalview/controller/AlignViewController.js
bin/jalview/controller/FeatureSettingsController.js
bin/jalview/controller/FeatureSettingsControllerGuiI.js
bin/jalview/datamodel/ASequence.js
bin/jalview/datamodel/ASequenceI.js
bin/jalview/datamodel/AlignedCodon.js
bin/jalview/datamodel/AlignedCodonFrame.class
bin/jalview/datamodel/AlignedCodonFrame.js
bin/jalview/datamodel/Alignment.class
bin/jalview/datamodel/Alignment.js
bin/jalview/datamodel/AlignmentAnnotation.class
bin/jalview/datamodel/AlignmentAnnotation.js
bin/jalview/datamodel/AlignmentI.js
bin/jalview/datamodel/AlignmentOrder.js
bin/jalview/datamodel/AlignmentView.class
bin/jalview/datamodel/AlignmentView.js
bin/jalview/datamodel/AnnotatedCollectionI.js
bin/jalview/datamodel/Annotation.class
bin/jalview/datamodel/Annotation.js
bin/jalview/datamodel/BinaryNode.js
bin/jalview/datamodel/BinarySequence.js
bin/jalview/datamodel/CigarArray.class
bin/jalview/datamodel/CigarArray.js
bin/jalview/datamodel/CigarBase.class
bin/jalview/datamodel/CigarBase.js
bin/jalview/datamodel/CigarCigar.js
bin/jalview/datamodel/CigarSimple.js
bin/jalview/datamodel/ColumnSelection.class
bin/jalview/datamodel/ColumnSelection.js
bin/jalview/datamodel/DBRefEntry.js
bin/jalview/datamodel/DBRefSource.js
bin/jalview/datamodel/FeatureProperties.js
bin/jalview/datamodel/GraphLine.js
bin/jalview/datamodel/HiddenSequences.class
bin/jalview/datamodel/HiddenSequences.js
bin/jalview/datamodel/IncompleteCodonException.js
bin/jalview/datamodel/Mapping.js
bin/jalview/datamodel/NodeTransformI.js
bin/jalview/datamodel/PDBEntry.js
bin/jalview/datamodel/Provenance.js
bin/jalview/datamodel/ProvenanceEntry.js
bin/jalview/datamodel/RnaViewerModel.js
bin/jalview/datamodel/SearchResults.js
bin/jalview/datamodel/SecondaryStructureAnnotation.js
bin/jalview/datamodel/SeqCigar.class
bin/jalview/datamodel/SeqCigar.js
bin/jalview/datamodel/Sequence.class
bin/jalview/datamodel/Sequence.js
bin/jalview/datamodel/SequenceCollectionI.js
bin/jalview/datamodel/SequenceDummy.js
bin/jalview/datamodel/SequenceFeature.js
bin/jalview/datamodel/SequenceGroup.class
bin/jalview/datamodel/SequenceGroup.js
bin/jalview/datamodel/SequenceI.js
bin/jalview/datamodel/SequenceNode.js
bin/jalview/datamodel/SequencePoint.js
bin/jalview/datamodel/StructureViewerModel.js
bin/jalview/datamodel/UniprotEntry.js
bin/jalview/datamodel/UniprotFile.js
bin/jalview/datamodel/UniprotProteinName.js
bin/jalview/datamodel/UniprotSequence.js
bin/jalview/ext/jmol/JmolCommands.class
bin/jalview/ext/jmol/JmolCommands.js
bin/jalview/ext/varna/JalviewVarnaBinding.js
bin/jalview/ext/varna/RnaModel.js
bin/jalview/ext/varna/VarnaCommands.class
bin/jalview/ext/varna/VarnaCommands.js
bin/jalview/io/AlignFile.js
bin/jalview/io/AlignmentProperties.js
bin/jalview/io/AnnotationFile.class
bin/jalview/io/AnnotationFile.js
bin/jalview/io/AppletFormatAdapter.class
bin/jalview/io/AppletFormatAdapter.js
bin/jalview/io/FastaFile.class
bin/jalview/io/FastaFile.js
bin/jalview/io/FeaturesFile.class
bin/jalview/io/FeaturesFile.js
bin/jalview/io/FileParse.class
bin/jalview/io/FileParse.js
bin/jalview/io/IdentifyFile.class
bin/jalview/io/IdentifyFile.js
bin/jalview/io/JPredFile.class
bin/jalview/io/JPredFile.js
bin/jalview/io/JnetAnnotationMaker.class
bin/jalview/io/JnetAnnotationMaker.js
bin/jalview/io/MSFfile.class
bin/jalview/io/MSFfile.js
bin/jalview/io/ModellerDescription.class
bin/jalview/io/ModellerDescription.js
bin/jalview/io/NewickFile.class
bin/jalview/io/NewickFile.js
bin/jalview/io/PIRFile.class
bin/jalview/io/PIRFile.js
bin/jalview/io/PfamFile.js
bin/jalview/io/PhylipFile.js
bin/jalview/io/PileUpfile.class
bin/jalview/io/PileUpfile.js
bin/jalview/io/SequenceAnnotationReport.class
bin/jalview/io/SequenceAnnotationReport.js
bin/jalview/io/TCoffeeScoreFile.class
bin/jalview/io/TCoffeeScoreFile.js
bin/jalview/javascript/JSFunctionExec$1.class
bin/jalview/javascript/JSFunctionExec.class
bin/jalview/javascript/JSFunctionExec.js
bin/jalview/javascript/JalviewLiteJsApi.js
bin/jalview/javascript/JsCallBack.js
bin/jalview/javascript/JsSelectionSender.js
bin/jalview/javascript/MouseOverListener.js
bin/jalview/javascript/MouseOverStructureListener.js
bin/jalview/jsdev/Constants.js
bin/jalview/jsdev/GenericFileAdapter.js
bin/jalview/jsdev/JSRegex.js
bin/jalview/jsdev/JavaScriptRegExp.js
bin/jalview/jsdev/RegExp.js
bin/jalview/jsdev/api/RegExpInterface.js
bin/jalview/jsdev/api/VarnaRNA.js
bin/jalview/math/AlignmentDimension.js
bin/jalview/math/Matrix.class
bin/jalview/math/Matrix.js
bin/jalview/math/RotatableMatrix.js
bin/jalview/renderer/AnnotationRenderer.class
bin/jalview/renderer/AnnotationRenderer.js
bin/jalview/renderer/AwtRenderPanelI.js
bin/jalview/renderer/seqfeatures/FeatureRenderer.class
bin/jalview/renderer/seqfeatures/FeatureRenderer.js
bin/jalview/schemes/AnnotationColourGradient.class
bin/jalview/schemes/AnnotationColourGradient.js
bin/jalview/schemes/Blosum62ColourScheme.class
bin/jalview/schemes/Blosum62ColourScheme.js
bin/jalview/schemes/BuriedColourScheme.js
bin/jalview/schemes/ClustalxColourScheme.js
bin/jalview/schemes/ColourSchemeI.js
bin/jalview/schemes/ColourSchemeProperty.js
bin/jalview/schemes/Consensus.js
bin/jalview/schemes/CovariationColourScheme.js
bin/jalview/schemes/FollowerColourScheme.js
bin/jalview/schemes/GraduatedColor.js
bin/jalview/schemes/HelixColourScheme.js
bin/jalview/schemes/HydrophobicColourScheme.js
bin/jalview/schemes/NucleotideColourScheme.js
bin/jalview/schemes/PIDColourScheme.js
bin/jalview/schemes/PurinePyrimidineColourScheme.js
bin/jalview/schemes/RNAHelicesColour.js
bin/jalview/schemes/RNAHelicesColourChooser.js
bin/jalview/schemes/RNAInteractionColourScheme.js
bin/jalview/schemes/ResidueColourScheme.js
bin/jalview/schemes/ResidueProperties.class
bin/jalview/schemes/ResidueProperties.js
bin/jalview/schemes/ScoreColourScheme.js
bin/jalview/schemes/ScoreMatrix.js
bin/jalview/schemes/StrandColourScheme.js
bin/jalview/schemes/TCoffeeColourScheme.js
bin/jalview/schemes/TaylorColourScheme.js
bin/jalview/schemes/TurnColourScheme.js
bin/jalview/schemes/UserColourScheme.class
bin/jalview/schemes/UserColourScheme.js
bin/jalview/schemes/ZappoColourScheme.js
bin/jalview/schemes/package.js
bin/jalview/structure/AlignmentViewPanelListener.js
bin/jalview/structure/AtomSpec.js
bin/jalview/structure/CommandListener.js
bin/jalview/structure/SecondaryStructureListener.js
bin/jalview/structure/SelectionListener.js
bin/jalview/structure/SelectionSource.js
bin/jalview/structure/SequenceListener.js
bin/jalview/structure/StructureListener.js
bin/jalview/structure/StructureMapping.js
bin/jalview/structure/StructureMappingcommandSet.js
bin/jalview/structure/StructureSelectionManager.class
bin/jalview/structure/StructureSelectionManager.js
bin/jalview/structure/VamsasListener.js
bin/jalview/structure/VamsasSource.js
bin/jalview/structures/models/AAStructureBindingModel.class
bin/jalview/structures/models/AAStructureBindingModel.js
bin/jalview/structures/models/SequenceStructureBindingModel.js
bin/jalview/util/AWTConsole.js [deleted file]
bin/jalview/util/BrowserLauncher.js [deleted file]
bin/jalview/util/ColorUtils.js
bin/jalview/util/Comparison.class
bin/jalview/util/Comparison.js
bin/jalview/util/DBRefUtils.class
bin/jalview/util/DBRefUtils.js
bin/jalview/util/Format.class
bin/jalview/util/Format.js
bin/jalview/util/GroupUrlLink.class
bin/jalview/util/GroupUrlLink.js
bin/jalview/util/MapList.class
bin/jalview/util/MapList.js
bin/jalview/util/MappingUtils.js
bin/jalview/util/MessageManager.class
bin/jalview/util/MessageManager.js
bin/jalview/util/ParseHtmlBodyAndLinks.class
bin/jalview/util/ParseHtmlBodyAndLinks.js
bin/jalview/util/Platform.js
bin/jalview/util/QuickSort.js
bin/jalview/util/ReverseListIterator.js
bin/jalview/util/ShiftList.js
bin/jalview/util/StringUtils.js
bin/jalview/util/TableSorter.js
bin/jalview/util/UrlLink.class
bin/jalview/util/UrlLink.js
bin/jalview/util/jarInputStreamProvider.js [deleted file]
bin/jalview/viewmodel/AlignmentViewport.js
bin/jalview/viewmodel/PCAModel.class
bin/jalview/viewmodel/PCAModel.js
bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js
bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.class
bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js
bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js
bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
bin/jalview/viewmodel/styles/ViewStyle.js
bin/jalview/workers/AlignCalcManager.js
bin/jalview/workers/AlignCalcWorker.js
bin/jalview/workers/ComplementConsensusThread.js
bin/jalview/workers/ConsensusThread.js
bin/jalview/workers/ConservationThread.js
bin/jalview/workers/StrucConsensusThread.class
bin/jalview/workers/StrucConsensusThread.js
bin/java.policy.applet [deleted file]
bin/javajs/J2SIgnoreImport.js
bin/javajs/J2SRequireImport.js
bin/javajs/api/BytePoster.js
bin/javajs/api/EigenInterface.js
bin/javajs/api/EventManager.js
bin/javajs/api/FontManager.js
bin/javajs/api/GenericBinaryDocument.js
bin/javajs/api/GenericCifDataParser.js
bin/javajs/api/GenericColor.js
bin/javajs/api/GenericFileInterface.js
bin/javajs/api/GenericImageDialog.js
bin/javajs/api/GenericImageEncoder.js
bin/javajs/api/GenericLineReader.js
bin/javajs/api/GenericMenuInterface.js
bin/javajs/api/GenericMouseInterface.js
bin/javajs/api/GenericPlatform.js
bin/javajs/api/GenericZipInputStream.js
bin/javajs/api/GenericZipTools.js
bin/javajs/api/HTMLElement.js
bin/javajs/api/HTMLWindowEvent.js
bin/javajs/api/Interface.js
bin/javajs/api/JSInterface.js
bin/javajs/api/JSONEncodable.js
bin/javajs/api/JmolObjectInterface.js
bin/javajs/api/PlatformViewer.js
bin/javajs/api/SC.js
bin/javajs/api/SwingController.js
bin/javajs/api/ZInputStream.js
bin/javajs/awt/BorderLayout.js
bin/javajs/awt/Color.js
bin/javajs/awt/Component.js
bin/javajs/awt/Container.js
bin/javajs/awt/Dimension.js
bin/javajs/awt/Font.js
bin/javajs/awt/LayoutManager.js
bin/javajs/awt/event/ActionEvent.js
bin/javajs/awt/event/ActionListener.js
bin/javajs/awt/event/Event.js
bin/javajs/awt/event/ItemEvent.js
bin/javajs/awt/event/WindowEvent.js
bin/javajs/awt/event/WindowListener.js
bin/javajs/export/PDFCreator.js
bin/javajs/export/PDFObject.class
bin/javajs/export/PDFObject.js
bin/javajs/img/BMPDecoder.js
bin/javajs/img/CRCEncoder.js
bin/javajs/img/GifEncoder$ColorCell.class
bin/javajs/img/GifEncoder.class
bin/javajs/img/GifEncoder.js
bin/javajs/img/ImageEncoder.js
bin/javajs/img/Jpg64Encoder.js
bin/javajs/img/JpgEncoder.js
bin/javajs/img/PdfEncoder.js
bin/javajs/img/PngEncoder.js
bin/javajs/img/PpmEncoder.js
bin/javajs/img/package.js
bin/javajs/swing/AbstractButton.js
bin/javajs/swing/AbstractTableModel.js
bin/javajs/swing/ButtonGroup.js
bin/javajs/swing/Cell.js
bin/javajs/swing/ColumnSelectionModel.js
bin/javajs/swing/Document.js
bin/javajs/swing/FlowLayout.js
bin/javajs/swing/Grid.js
bin/javajs/swing/GridBagConstraints.js
bin/javajs/swing/GridBagLayout.js
bin/javajs/swing/Insets.js
bin/javajs/swing/JButton.js
bin/javajs/swing/JCheckBox.js
bin/javajs/swing/JCheckBoxMenuItem.js
bin/javajs/swing/JComboBox.js
bin/javajs/swing/JComponent.js
bin/javajs/swing/JComponentImp.js
bin/javajs/swing/JContentPane.js
bin/javajs/swing/JDialog.js
bin/javajs/swing/JEditorPane.js
bin/javajs/swing/JLabel.js
bin/javajs/swing/JMenu.js
bin/javajs/swing/JMenuItem.js
bin/javajs/swing/JPanel.js
bin/javajs/swing/JPopupMenu.js
bin/javajs/swing/JRadioButtonMenuItem.js
bin/javajs/swing/JScrollPane.js
bin/javajs/swing/JSplitPane.js
bin/javajs/swing/JTable.js
bin/javajs/swing/JTextField.js
bin/javajs/swing/JTextPane.js
bin/javajs/swing/ListSelectionModel.js
bin/javajs/swing/SwingConstants.js
bin/javajs/swing/TableCellRenderer.js
bin/javajs/swing/TableColumn.js
bin/javajs/util/A4.js
bin/javajs/util/AU.js
bin/javajs/util/AjaxURLConnection.js
bin/javajs/util/AjaxURLStreamHandler.js
bin/javajs/util/AjaxURLStreamHandlerFactory.js
bin/javajs/util/ArrayDataReader.js
bin/javajs/util/BArray.js
bin/javajs/util/BC.js
bin/javajs/util/BS.js
bin/javajs/util/Base64.js
bin/javajs/util/BinaryDocument.js
bin/javajs/util/CU.js
bin/javajs/util/CifDataParser.class
bin/javajs/util/CifDataParser.js
bin/javajs/util/CompoundDocDirEntry.js
bin/javajs/util/CompoundDocHeader.js
bin/javajs/util/CompoundDocument.class
bin/javajs/util/CompoundDocument.js
bin/javajs/util/DF.js
bin/javajs/util/DataReader.js
bin/javajs/util/Eigen.js
bin/javajs/util/Encoding.js
bin/javajs/util/LimitedLineReader.js
bin/javajs/util/ListDataReader.js
bin/javajs/util/Lst.js
bin/javajs/util/M3.js
bin/javajs/util/M34.js
bin/javajs/util/M4.js
bin/javajs/util/Matrix.js
bin/javajs/util/Measure.class
bin/javajs/util/Measure.js
bin/javajs/util/OC.class
bin/javajs/util/OC.js
bin/javajs/util/P3.js
bin/javajs/util/P3i.js
bin/javajs/util/P4.js
bin/javajs/util/PT.class
bin/javajs/util/PT.js
bin/javajs/util/Quat.js
bin/javajs/util/Rdr.class
bin/javajs/util/Rdr.js
bin/javajs/util/SB.js
bin/javajs/util/StringDataReader.js
bin/javajs/util/T3.js
bin/javajs/util/T3d.js
bin/javajs/util/T3i.js
bin/javajs/util/T4.js
bin/javajs/util/V3.js
bin/javajs/util/V3d.js
bin/javajs/util/XmlUtil.js
bin/javajs/util/ZipData.js
bin/javajs/util/ZipTools.class
bin/javajs/util/ZipTools.js
bin/lang/Messages.properties [deleted file]
bin/lang/Messages_es.properties [deleted file]
bin/netscape/javascript/JSException.js
bin/netscape/javascript/JSObject.js
bin/org/exolab/castor/mapping/Mapping.js
bin/org/exolab/castor/xml/Unmarshaller.js
bin/org/jmol/viewer/Viewer.js
bin/swingjs/JSEvent.js [deleted file]
bin/swingjs/JSThread.js
bin/swingjs/api/DOMNode.js
bin/swingjs/api/JSFunction.js
bin/uniref50.fa [deleted file]
resources/.cvsignore
resources/authors.props
resources/biojs_templates/BioJsMSA_1.0.txt
resources/biojs_templates/BioJsMSA_1.1.txt
resources/biojs_templates/Latest_BioJsMSA_1.2.txt
resources/embl_mapping.xml
resources/images/.cvsignore
resources/lang/Messages.properties
resources/lang/Messages_es.properties
resources/uniprot_mapping.xml
site/j2s/JU/DebugJS.js [new file with mode: 0644]
site/j2s/awt2swing/Scrollbar.js
site/j2s/core/core.js [new file with mode: 0644]
site/j2s/core/core.z.js
site/j2s/core/coreswingjs.js [new file with mode: 0644]
site/j2s/core/coreswingjs.z.js
site/j2s/jalview/analysis/AlignSeq.js
site/j2s/jalview/analysis/Conservation.js
site/j2s/jalview/datamodel/Annotation.js
site/j2s/jalview/io/AnnotationFile.js
site/j2s/jalview/io/FeaturesFile.js
site/j2s/jalview/io/SequenceAnnotationReport.js
site/j2s/jalview/viewmodel/PCAModel.js
site/j2s/jalview/workers/StrucConsensusThread.js
site/j2s/swingjs/JSImage.js
site/j2s/swingjs/JSToolkit.js
site/j2s/swingjs/plaf/HTML5LookAndFeel.java
site/j2s/swingjs/plaf/JSButtonListener.java
site/j2s/swingjs/plaf/JSButtonUI.java
site/j2s/swingjs/plaf/JSCheckBoxMenuItemUI.java
site/j2s/swingjs/plaf/JSCheckBoxUI.java
site/j2s/swingjs/plaf/JSComboBoxUI.java
site/j2s/swingjs/plaf/JSFormattedTextFieldUI.java
site/j2s/swingjs/plaf/JSLabelUI.java
site/j2s/swingjs/plaf/JSMenuBarUI.java
site/j2s/swingjs/plaf/JSMenuItemUI.java
site/j2s/swingjs/plaf/JSMenuUI.java
site/j2s/swingjs/plaf/JSPanelUI.java
site/j2s/swingjs/plaf/JSPasswordFieldUI.java
site/j2s/swingjs/plaf/JSPopupMenuUI.java
site/j2s/swingjs/plaf/JSRadioButtonMenuItemUI.java
site/j2s/swingjs/plaf/JSRadioButtonUI.java
site/j2s/swingjs/plaf/JSRootPaneUI.java
site/j2s/swingjs/plaf/JSScrollBarUI.java
site/j2s/swingjs/plaf/JSScrollBarUI.js
site/j2s/swingjs/plaf/JSScrollPaneUI.java
site/j2s/swingjs/plaf/JSSeparatorUI.java
site/j2s/swingjs/plaf/JSSliderUI.java
site/j2s/swingjs/plaf/JSSliderUI.js
site/j2s/swingjs/plaf/JSTextAreaUI.java
site/j2s/swingjs/plaf/JSTextFieldUI.java
site/j2s/swingjs/plaf/JSTextUI.java
site/j2s/swingjs/plaf/JSToolBarSeparatorUI.java
site/j2s/swingjs/plaf/JSViewportUI.java
site/j2s/swingjs/plaf/LazyActionMap.java
site/j2s/swingjs/plaf/TextListener.java
site/js/JSmol.js
site/js/SwingJS.js
site/js/SwingJSJavaExt.js [new file with mode: 0644]
site/js/SwingJSjQueryExt.js [new file with mode: 0644]
site/js/j2sSwingJS.js [new file with mode: 0644]
site/test.htm
site/test_2.htm
src/awt2swing/Scrollbar.java
src/fr/orsay/lri/varna/models/rna/RNA.java
src/jalview/analysis/Conservation.java
src/jalview/datamodel/SecondaryStructureAnnotation.java
src/jalview/ext/varna/RnaModel.java
src/jalview/workers/StrucConsensusThread.java
src/javajs/api/Interface.java
src/javajs/util/DebugJS.java [new file with mode: 0644]

diff --git a/.j2s b/.j2s
index c403133..e061f63 100644 (file)
--- a/.j2s
+++ b/.j2s
@@ -1,8 +1,8 @@
-#Java2Script Configuration\r
-#Thu Jul 23 11:58:58 BST 2015\r
-j2s.compiler.abbreviation=false\r
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efFetcher.js,bin/jalview/ws/AWsJob.js,bin/jalview/ws/AWSThread.js,bin/jalview/workers/StrucConsensusThread.js,bin/jalview/workers/ConservationThread.js,bin/jalview/workers/ConsensusThread.js,bin/jalview/workers/ComplementConsensusThread.js,bin/jalview/workers/AlignCalcWorker.js,bin/jalview/workers/AlignCalcManager.js,bin/jalview/viewmodel/styles/ViewStyle.js,bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js,bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js,bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js,bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js,bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js,bin/jalview/viewmodel/PCAModel.js,bin/jalview/viewmodel/AlignmentViewport.js,bin/jalview/util/jarInputStreamProvider.js,bin/jalview/util/UrlLink.js,bin/jalview/util/TableSorter.js,bin/jalview/util/StringUtils.js,bin/jalview/util/ShiftList.js,bin/jalview/util/ReverseListIterator.js,bin/jalview/util/QuickSort.js,bin/jalview/util/Platform.js,bin/jalview/util/ParseHtmlBodyAndLinks.js,bin/jalview/util/MessageManager.js,bin/jalview/util/MappingUtils.js,bin/jalview/util/MapList.js,bin/jalview/util/ImageMaker.js,bin/jalview/util/GroupUrlLink.js,bin/jalview/util/Format.js,bin/jalview/util/DBRefUtils.js,bin/jalview/util/Comparison.js,bin/jalview/util/ColorUtils.js,bin/jalview/util/BrowserLauncher.js,bin/jalview/util/AWTConsole.js,bin/jalview/structures/models/SequenceStructureBindingModel.js,bin/jalview/structures/models/AAStructureBindingModel.js,bin/jalview/structure/VamsasSource.js,bin/jalview/structure/VamsasListener.js,bin/jalview/structure/StructureSelectionManager.js,bin/jalview/structure/StructureMappingcommandSet.js,bin/jalview/structure/StructureMapping.js,bin/jalview/structure/StructureListener.js,bin/jalview/structure/SequenceListener.js,bin/jalview/structure/SelectionSource.js,bin/jalview/structure/SelectionListener.js,bin/jalview/structure/SecondaryStructureListener.js,bin/jalview/structure/CommandListener.js,bin/jalview/structure/AtomSpec.js,bin/jalview/structure/AlignmentViewPanelListener.js,bin/jalview/schemes/ZappoColourScheme.js,bin/jalview/schemes/UserColourScheme.js,bin/jalview/schemes/TurnColourScheme.js,bin/jalview/schemes/TaylorColourScheme.js,bin/jalview/schemes/TCoffeeColourScheme.js,bin/jalview/schemes/StrandColourScheme.js,bin/jalview/schemes/ScoreMatrix.js,bin/jalview/schemes/ScoreColourScheme.js,bin/jalview/schemes/ResidueProperties.js,bin/jalview/schemes/ResidueColourScheme.js,bin/jalview/schemes/RNAInteractionColourScheme.js,bin/jalview/schemes/RNAHelicesColourChooser.js,bin/jalview/schemes/RNAHelicesColour.js,bin/jalview/schemes/PurinePyrimidineColourScheme.js,bin/jalview/schemes/PIDColourScheme.js,bin/jalview/schemes/NucleotideColourScheme.js,bin/jalview/schemes/HydrophobicColourScheme.js,bin/jalview/schemes/HelixColourScheme.js,bin/jalview/schemes/GraduatedColor.js,bin/jalview/schemes/FollowerColourScheme.js,bin/jalview/schemes/CovariationColourScheme.js,bin/jalview/schemes/Consensus.js,bin/jalview/schemes/ColourSchemeProperty.js,bin/jalview/schemes/ColourSchemeI.js,bin/jalview/schemes/ClustalxColourScheme.js,bin/jalview/schemes/BuriedColourScheme.js,bin/jalview/schemes/Blosum62ColourScheme.js,bin/jalview/schemes/AnnotationColourGradient.js,bin/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.js,bin/jalview/schemabinding/version2/descriptors/ViewportDescriptor.js,bin/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.js,bin/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.js,bin/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.js,bin/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/TreeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.js,bin/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SettingDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.js,bin/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PropertyDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.js,bin/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MappingDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.j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efFetcher.js,bin/jalview/ws/AWsJob.js,bin/jalview/ws/AWSThread.js,bin/jalview/workers/StrucConsensusThread.js,bin/jalview/workers/ConservationThread.js,bin/jalview/workers/ConsensusThread.js,bin/jalview/workers/ComplementConsensusThread.js,bin/jalview/workers/AlignCalcWorker.js,bin/jalview/workers/AlignCalcManager.js,bin/jalview/viewmodel/styles/ViewStyle.js,bin/jalview/viewmodel/seqfeatures/FeaturesDisplayed.js,bin/jalview/viewmodel/seqfeatures/FeatureSettingsModel.js,bin/jalview/viewmodel/seqfeatures/FeatureRendererSettings.js,bin/jalview/viewmodel/seqfeatures/FeatureRendererModel.js,bin/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js,bin/jalview/viewmodel/PCAModel.js,bin/jalview/viewmodel/AlignmentViewport.js,bin/jalview/util/jarInputStreamProvider.js,bin/jalview/util/UrlLink.js,bin/jalview/util/TableSorter.js,bin/jalview/util/StringUtils.js,bin/jalview/util/ShiftList.js,bin/jalview/util/ReverseListIterator.js,bin/jalview/util/QuickSort.js,bin/jalview/util/Platform.js,bin/jalview/util/ParseHtmlBodyAndLinks.js,bin/jalview/util/MessageManager.js,bin/jalview/util/MappingUtils.js,bin/jalview/util/MapList.js,bin/jalview/util/ImageMaker.js,bin/jalview/util/GroupUrlLink.js,bin/jalview/util/Format.js,bin/jalview/util/DBRefUtils.js,bin/jalview/util/Comparison.js,bin/jalview/util/ColorUtils.js,bin/jalview/util/BrowserLauncher.js,bin/jalview/util/AWTConsole.js,bin/jalview/structures/models/SequenceStructureBindingModel.js,bin/jalview/structures/models/AAStructureBindingModel.js,bin/jalview/structure/VamsasSource.js,bin/jalview/structure/VamsasListener.js,bin/jalview/structure/StructureSelectionManager.js,bin/jalview/structure/StructureMappingcommandSet.js,bin/jalview/structure/StructureMapping.js,bin/jalview/structure/StructureListener.js,bin/jalview/structure/SequenceListener.js,bin/jalview/structure/SelectionSource.js,bin/jalview/structure/SelectionListener.js,bin/jalview/structure/SecondaryStructureListener.js,bin/jalview/structure/CommandListener.js,bin/jalview/structure/AtomSpec.js,bin/jalview/structure/AlignmentViewPanelListener.js,bin/jalview/schemes/ZappoColourScheme.js,bin/jalview/schemes/UserColourScheme.js,bin/jalview/schemes/TurnColourScheme.js,bin/jalview/schemes/TaylorColourScheme.js,bin/jalview/schemes/TCoffeeColourScheme.js,bin/jalview/schemes/StrandColourScheme.js,bin/jalview/schemes/ScoreMatrix.js,bin/jalview/schemes/ScoreColourScheme.js,bin/jalview/schemes/ResidueProperties.js,bin/jalview/schemes/ResidueColourScheme.js,bin/jalview/schemes/RNAInteractionColourScheme.js,bin/jalview/schemes/RNAHelicesColourChooser.js,bin/jalview/schemes/RNAHelicesColour.js,bin/jalview/schemes/PurinePyrimidineColourScheme.js,bin/jalview/schemes/PIDColourScheme.js,bin/jalview/schemes/NucleotideColourScheme.js,bin/jalview/schemes/HydrophobicColourScheme.js,bin/jalview/schemes/HelixColourScheme.js,bin/jalview/schemes/GraduatedColor.js,bin/jalview/schemes/FollowerColourScheme.js,bin/jalview/schemes/CovariationColourScheme.js,bin/jalview/schemes/Consensus.js,bin/jalview/schemes/ColourSchemeProperty.js,bin/jalview/schemes/ColourSchemeI.js,bin/jalview/schemes/ClustalxColourScheme.js,bin/jalview/schemes/BuriedColourScheme.js,bin/jalview/schemes/Blosum62ColourScheme.js,bin/jalview/schemes/AnnotationColourGradient.js,bin/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.js,bin/jalview/schemabinding/version2/descriptors/ViewportDescriptor.js,bin/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.js,bin/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.js,bin/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.js,bin/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/TreeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.js,bin/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SettingDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SequenceDescriptor.js,bin/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.js,bin/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PropertyDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.js,bin/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.js,bin/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MappingDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.js,bin/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.j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odel.js,bin/javajs/swing/JTextPane.js,bin/javajs/swing/JTextField.js,bin/javajs/swing/JTable.js,bin/javajs/swing/JSplitPane.js,bin/javajs/swing/JScrollPane.js,bin/javajs/swing/JRadioButtonMenuItem.js,bin/javajs/swing/JPopupMenu.js,bin/javajs/swing/JPanel.js,bin/javajs/swing/JMenuItem.js,bin/javajs/swing/JMenu.js,bin/javajs/swing/JLabel.js,bin/javajs/swing/JEditorPane.js,bin/javajs/swing/JDialog.js,bin/javajs/swing/JContentPane.js,bin/javajs/swing/JComponentImp.js,bin/javajs/swing/JComponent.js,bin/javajs/swing/JComboBox.js,bin/javajs/swing/JCheckBoxMenuItem.js,bin/javajs/swing/JCheckBox.js,bin/javajs/swing/JButton.js,bin/javajs/swing/Insets.js,bin/javajs/swing/GridBagLayout.js,bin/javajs/swing/GridBagConstraints.js,bin/javajs/swing/Grid.js,bin/javajs/swing/FlowLayout.js,bin/javajs/swing/Document.js,bin/javajs/swing/ColumnSelectionModel.js,bin/javajs/swing/Cell.js,bin/javajs/swing/ButtonGroup.js,bin/javajs/swing/AbstractTableModel.js,bin/javajs/swing/AbstractButton.js,bin/javajs/img/PpmEncoder.js,bin/javajs/img/PngEncoder.js,bin/javajs/img/PdfEncoder.js,bin/javajs/img/JpgEncoder.js,bin/javajs/img/Jpg64Encoder.js,bin/javajs/img/ImageEncoder.js,bin/javajs/img/GifEncoder.js,bin/javajs/img/CRCEncoder.js,bin/javajs/img/BMPDecoder.js,bin/javajs/export/PDFObject.js,bin/javajs/export/PDFCreator.js,bin/javajs/awt/event/WindowListener.js,bin/javajs/awt/event/WindowEvent.js,bin/javajs/awt/event/ItemEvent.js,bin/javajs/awt/event/Event.js,bin/javajs/awt/event/ActionListener.js,bin/javajs/awt/event/ActionEvent.js,bin/javajs/awt/LayoutManager.js,bin/javajs/awt/Font.js,bin/javajs/awt/Dimension.js,bin/javajs/awt/Container.js,bin/javajs/awt/Component.js,bin/javajs/awt/Color.js,bin/javajs/awt/BorderLayout.js,bin/javajs/api/ZInputStream.js,bin/javajs/api/SwingController.js,bin/javajs/api/SC.js,bin/javajs/api/PlatformViewer.js,bin/javajs/api/JmolObjectInterface.js,bin/javajs/api/JSONEncodable.js,bin/javajs/api/JSInterface.js,bin/javajs/api/Interface.js,bin/javajs/api/HTMLWindowEvent.js,bin/javajs/api/HTMLElement.js,bin/javajs/api/GenericZipTools.js,bin/javajs/api/GenericZipInputStream.js,bin/javajs/api/GenericPlatform.js,bin/javajs/api/GenericMouseInterface.js,bin/javajs/api/GenericMenuInterface.js,bin/javajs/api/GenericLineReader.js,bin/javajs/api/GenericImageEncoder.js,bin/javajs/api/GenericImageDialog.js,bin/javajs/api/GenericFileInterface.js,bin/javajs/api/GenericColor.js,bin/javajs/api/GenericCifDataParser.js,bin/javajs/api/GenericBinaryDocument.js,bin/javajs/api/FontManager.js,bin/javajs/api/EventManager.js,bin/javajs/api/EigenInterface.js,bin/javajs/api/BytePoster.js,bin/javajs/J2SRequireImport.js,bin/javajs/J2SIgnoreImport.js,bin/jalview/jsdev/api/VarnaRNA.js,bin/jalview/jsdev/GenericFileAdapter.js,bin/jalview/jsdev/Constants.js,bin/fr/orsay/lri/varna/models/rna/RNA.js,bin/com/stevesoft/pat/wrap/WriterWrap.js,bin/com/stevesoft/pat/wrap/StringWrap.js,bin/com/stevesoft/pat/wrap/StringBufferWrap.js,bin/com/stevesoft/pat/wrap/RandomAccessFileWrap.js,bin/com/stevesoft/pat/wrap/CharArrayWrap.js,bin/com/stevesoft/pat/wrap/CharArrayBufferWrap.js,bin/com/stevesoft/pat/patInt.js,bin/com/stevesoft/pat/patInf.js,bin/com/stevesoft/pat/parsePerl.js,bin/com/stevesoft/pat/oneChar.js,bin/com/stevesoft/pat/lookAhead.js,bin/com/stevesoft/pat/WantMoreTextReplaceRule.js,bin/com/stevesoft/pat/Validator.js,bin/com/stevesoft/pat/UniValidator.js,bin/com/stevesoft/pat/Transformer.js,bin/com/stevesoft/pat/TransPat.js,bin/com/stevesoft/pat/SubMark.js,bin/com/stevesoft/pat/StringRule.js,bin/com/stevesoft/pat/StringLike.js,bin/com/stevesoft/pat/StringBufferLike.js,bin/com/stevesoft/pat/StrPos.js,bin/com/stevesoft/pat/Start.js,bin/com/stevesoft/pat/SpecialRule.js,bin/com/stevesoft/pat/Skipped.js,bin/com/stevesoft/pat/SkipBMH.js,bin/com/stevesoft/pat/Skip2.js,bin/com/stevesoft/pat/Skip.js,bin/com/stevesoft/pat/RuleHolder.js,bin/com/stevesoft/pat/Rthings.js,bin/com/stevesoft/pat/RightRule.js,bin/com/stevesoft/pat/Replacer.js,bin/com/stevesoft/pat/ReplaceRule.js,bin/com/stevesoft/pat/RegexWriter.js,bin/com/stevesoft/pat/RegexTokenizer.js,bin/com/stevesoft/pat/RegexReader.js,bin/com/stevesoft/pat/Regex.js,bin/com/stevesoft/pat/RegSyntaxError.js,bin/com/stevesoft/pat/RegSyntax.js,bin/com/stevesoft/pat/RegRes.js,bin/com/stevesoft/pat/RegOpt.js,bin/com/stevesoft/pat/Range.js,bin/com/stevesoft/pat/RBuffer.js,bin/com/stevesoft/pat/PushRule.js,bin/com/stevesoft/pat/Pthings.js,bin/com/stevesoft/pat/Prop.js,bin/com/stevesoft/pat/PopRule.js,bin/com/stevesoft/pat/PatternSub.js,bin/com/stevesoft/pat/Pattern.js,bin/com/stevesoft/pat/PartialBuffer.js,bin/com/stevesoft/pat/OrMark.js,bin/com/stevesoft/pat/Or.js,bin/com/stevesoft/pat/NullRule.js,bin/com/stevesoft/pat/NullPattern.js,bin/com/stevesoft/pat/NotImplementedError.js,bin/com/stevesoft/pat/NonDirFileRegex.js,bin/com/stevesoft/pat/NoPattern.js,bin/com/stevesoft/pat/Multi_stage2.js,bin/com/stevesoft/pat/MultiMin.js,bin/com/stevesoft/pat/Multi.js,bin/com/stevesoft/pat/LeftRule.js,bin/com/stevesoft/pat/Group.js,bin/com/stevesoft/pat/FileRegex.js,bin/com/stevesoft/pat/FastMulti.js,bin/com/stevesoft/pat/FastBracket.js,bin/com/stevesoft/pat/End.js,bin/com/stevesoft/pat/DotMulti.js,bin/com/stevesoft/pat/DirFileRegex.js,bin/com/stevesoft/pat/CustomEndpoint.js,bin/com/stevesoft/pat/Custom.js,bin/com/stevesoft/pat/Ctrl.js,bin/com/stevesoft/pat/CodeRule.js,bin/com/stevesoft/pat/ChangeRule.js,bin/com/stevesoft/pat/CaseMgr.js,bin/com/stevesoft/pat/Bracket.js,bin/com/stevesoft/pat/Boundary.js,bin/com/stevesoft/pat/Bits.js,bin/com/stevesoft/pat/BasicStringBufferLike.js,bin/com/stevesoft/pat/Backup.js,bin/com/stevesoft/pat/BackRefRule.js,bin/com/stevesoft/pat/BackMatch.js,bin/com/stevesoft/pat/BackG.js,bin/com/stevesoft/pat/Any.js,bin/com/stevesoft/pat/AmpersandRule.js,bin/awt2swing/TextField.js,bin/awt2swing/TextArea.js,bin/awt2swing/Scrollbar.js,bin/awt2swing/ScrollPane.js,bin/awt2swing/PopupMenu.js,bin/awt2swing/Panel.js,bin/awt2swing/MenuItem.js,bin/awt2swing/MenuBar.js,bin/awt2swing/Menu.js,bin/awt2swing/Label.js,bin/awt2swing/Frame.js,bin/awt2swing/CheckboxMenuItem.js,bin/awt2swing/Checkbox.js,bin/MCview/Residue.js,bin/MCview/PDBfile.js,bin/MCview/PDBChain.js,bin/MCview/Bond.js,bin/MCview/Atom.js,bin/awt2swing/Button.js,bin/awt2swing/Canvas.js,bin/awt2swing/Choice.js,bin/jalview/appletgui/Cache.js,bin/com/stevesoft/pat/Util.js,bin/jalview/jsdev/Regex.js,bin/jalview/jsdev/RegexJS.js,bin/com/stevesoft/pat/MessageManager.js,bin/jalview/jsdev/api/RegexInterface.js,bin/jalview/jsdev/api/RegExpInterface.js,bin/jalview/jsdev/RegExp.js,bin/jalview/jsdev/JavaScriptRegExp.js,bin/jalview/jsdev/JSRegex.js,bin/swingjs/JSEvent.js,bin/swingjs/JSThread.js,bin/swingjs/api/JSFunction.js,bin/swingjs/JSImage.js,bin/swingjs/api/DOMNode.js
+j2s.compiler.abbreviation.prefix=$_
+j2s.abandoned.resources.list=
+j2s.output.path=bin
+j2s.compiler.status=enable
diff --git a/bin/.gitignore b/bin/.gitignore
new file mode 100644 (file)
index 0000000..77d60bf
--- /dev/null
@@ -0,0 +1,9 @@
+/MCview/
+/awt2swing/
+/com/
+/fr/
+/jalview/
+/javajs/
+/netscape/
+/org/
+/swingjs/
index 1f4c66f..ff57b47 100644 (file)
@@ -1,55 +1,55 @@
-Clazz.declarePackage ("MCview");\r
-Clazz.load (["java.awt.Color"], "MCview.Atom", ["java.lang.Float"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.x = 0;\r
-this.y = 0;\r
-this.z = 0;\r
-this.number = 0;\r
-this.name = null;\r
-this.resName = null;\r
-this.resNumber = 0;\r
-this.insCode = ' ';\r
-this.resNumIns = null;\r
-this.type = 0;\r
-this.color = null;\r
-this.chain = null;\r
-this.alignmentMapping = -1;\r
-this.atomIndex = 0;\r
-this.occupancy = 0;\r
-this.tfactor = 0;\r
-this.isSelected = false;\r
-Clazz.instantialize (this, arguments);\r
-}, MCview, "Atom");\r
-Clazz.prepareFields (c$, function () {\r
-this.color = java.awt.Color.lightGray;\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (str) {\r
-this.atomIndex = Integer.parseInt (str.substring (6, 11).trim ());\r
-this.name = str.substring (12, 15).trim ();\r
-this.resName = str.substring (17, 20);\r
-this.chain = str.substring (21, 22);\r
-this.resNumber = Integer.parseInt (str.substring (22, 26).trim ());\r
-this.resNumIns = str.substring (22, 27).trim ();\r
-this.insCode = str.substring (26, 27).charAt (0);\r
-this.x = ( new Float (str.substring (30, 38).trim ()).floatValue ());\r
-this.y = ( new Float (str.substring (38, 46).trim ()).floatValue ());\r
-this.z = ( new Float (str.substring (47, 55).trim ()).floatValue ());\r
-var tm = str.substring (54, 60).trim ();\r
-if (tm.length > 0) {\r
-this.occupancy = ( new Float (tm)).floatValue ();\r
-} else {\r
-this.occupancy = 1;\r
-}tm = str.substring (60, 66).trim ();\r
-if (tm.length > 0) {\r
-this.tfactor = ( new Float (tm).floatValue ());\r
-} else {\r
-this.tfactor = 1;\r
-}}, "~S");\r
-Clazz.makeConstructor (c$, \r
-function (x, y, z) {\r
-this.x = x;\r
-this.y = y;\r
-this.z = z;\r
-}, "~N,~N,~N");\r
-});\r
+Clazz.declarePackage ("MCview");
+Clazz.load (["java.awt.Color"], "MCview.Atom", ["java.lang.Float"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.x = 0;
+this.y = 0;
+this.z = 0;
+this.number = 0;
+this.name = null;
+this.resName = null;
+this.resNumber = 0;
+this.insCode = ' ';
+this.resNumIns = null;
+this.type = 0;
+this.color = null;
+this.chain = null;
+this.alignmentMapping = -1;
+this.atomIndex = 0;
+this.occupancy = 0;
+this.tfactor = 0;
+this.isSelected = false;
+Clazz.instantialize (this, arguments);
+}, MCview, "Atom");
+Clazz.prepareFields (c$, function () {
+this.color = java.awt.Color.lightGray;
+});
+Clazz.makeConstructor (c$, 
+function (str) {
+this.atomIndex = Integer.parseInt (str.substring (6, 11).trim ());
+this.name = str.substring (12, 15).trim ();
+this.resName = str.substring (17, 20);
+this.chain = str.substring (21, 22);
+this.resNumber = Integer.parseInt (str.substring (22, 26).trim ());
+this.resNumIns = str.substring (22, 27).trim ();
+this.insCode = str.substring (26, 27).charAt (0);
+this.x = ( new Float (str.substring (30, 38).trim ()).floatValue ());
+this.y = ( new Float (str.substring (38, 46).trim ()).floatValue ());
+this.z = ( new Float (str.substring (47, 55).trim ()).floatValue ());
+var tm = str.substring (54, 60).trim ();
+if (tm.length > 0) {
+this.occupancy = ( new Float (tm)).floatValue ();
+} else {
+this.occupancy = 1;
+}tm = str.substring (60, 66).trim ();
+if (tm.length > 0) {
+this.tfactor = ( new Float (tm).floatValue ());
+} else {
+this.tfactor = 1;
+}}, "~S");
+Clazz.makeConstructor (c$, 
+function (x, y, z) {
+this.x = x;
+this.y = y;
+this.z = z;
+}, "~N,~N,~N");
+});
index 539e323..9aaba45 100644 (file)
@@ -1,34 +1,34 @@
-Clazz.declarePackage ("MCview");\r
-Clazz.load (["java.awt.Color"], "MCview.Bond", null, function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.start = null;\r
-this.end = null;\r
-this.startCol = null;\r
-this.endCol = null;\r
-this.at1 = null;\r
-this.at2 = null;\r
-Clazz.instantialize (this, arguments);\r
-}, MCview, "Bond");\r
-Clazz.prepareFields (c$, function () {\r
-this.startCol = java.awt.Color.lightGray;\r
-this.endCol = java.awt.Color.lightGray;\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (at1, at2) {\r
-this.start =  Clazz.newFloatArray (-1, [at1.x, at1.y, at1.z]);\r
-this.end =  Clazz.newFloatArray (-1, [at2.x, at2.y, at2.z]);\r
-this.startCol = at1.color;\r
-this.endCol = at2.color;\r
-this.at1 = at1;\r
-this.at2 = at2;\r
-}, "MCview.Atom,MCview.Atom");\r
-Clazz.defineMethod (c$, "translate", \r
-function (x, y, z) {\r
-this.start[0] = this.start[0] + x;\r
-this.end[0] = this.end[0] + x;\r
-this.start[1] = this.start[1] + y;\r
-this.end[1] = this.end[1] + y;\r
-this.start[2] = this.start[2] + z;\r
-this.end[2] = this.end[2] + z;\r
-}, "~N,~N,~N");\r