JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory
authorhansonr <hansonr@STO24954W.ad.stolaf.edu>
Sun, 22 Jul 2018 22:58:16 +0000 (17:58 -0500)
committerhansonr <hansonr@STO24954W.ad.stolaf.edu>
Sun, 22 Jul 2018 22:58:16 +0000 (17:58 -0500)
commita1225b9392dc7657d5cef12907385b07527d6122
treec9e6ebd4777822a929bcc2eaeda5b68d04f0ee1a
parentb513684c725997c77341f30ce4e584cf9f7cdfed
JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

probably should put .gitignore on src2. Sorry about that.
344 files changed:
src2/fr/orsay/lri/varna/README_SWINGJS.txt [deleted file]
src2/fr/orsay/lri/varna/VARNA.java [deleted file]
src2/fr/orsay/lri/varna/VARNAPanel.java [deleted file]
src2/fr/orsay/lri/varna/applications/AlignmentDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/BasicINI.java [deleted file]
src2/fr/orsay/lri/varna/applications/FileNameExtensionFilter.java [deleted file]
src2/fr/orsay/lri/varna/applications/NussinovDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/NussinovDesignDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/SecStrConsensus.java [deleted file]
src2/fr/orsay/lri/varna/applications/SuperpositionDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAConsoleDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAEditor.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAGUI.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAOnlineDemo.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAPrinter.java [deleted file]
src2/fr/orsay/lri/varna/applications/VARNAcmd.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqCellEditor.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqCellRenderer.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqGUI.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqNode.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqRNASecStrModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqTree.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/fragseq/Watcher.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUI.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUICellEditor.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIRenderer.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITree.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITreeModel.java [deleted file]
src2/fr/orsay/lri/varna/applications/newGUI/Watcher.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/Connection.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/Couple.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/GraphicalTemplateElement.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/Helix.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/MouseControler.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEditor.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEditorPanelUI.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEdits.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java [deleted file]
src2/fr/orsay/lri/varna/applications/templateEditor/UnpairedRegion.java [deleted file]
src2/fr/orsay/lri/varna/components/ActionEditor.java [deleted file]
src2/fr/orsay/lri/varna/components/ActionRenderer.java [deleted file]
src2/fr/orsay/lri/varna/components/AnnotationTableModel.java [deleted file]
src2/fr/orsay/lri/varna/components/BaseSpecialColorEditor.java [deleted file]
src2/fr/orsay/lri/varna/components/BaseTableModel.java [deleted file]
src2/fr/orsay/lri/varna/components/ColorRenderer.java [deleted file]
src2/fr/orsay/lri/varna/components/GradientEditorPanel.java [deleted file]
src2/fr/orsay/lri/varna/components/ReorderableJList.java [deleted file]
src2/fr/orsay/lri/varna/components/VARNAConsole.java [deleted file]
src2/fr/orsay/lri/varna/components/ZoomWindow.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurBPHeightIncrement.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurBaseSpecialColorEditor.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurBlinkingThread.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurBorder.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurClicMovement.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurDemoTextField.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurDraggedMolette.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurGlobalRescale.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurGlobalRotation.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurInterpolator.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurJCheckBoxMenuItem.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurMenu.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurMolette.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurNumPeriod.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurScriptParser.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurSelectionHighlight.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurSliderLabel.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurSpaceBetweenBases.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurTableAnnotations.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurVARNAPanelKeys.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurVueAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/controlers/ControleurZoom.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionDrawingAlgorithm.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionEdgeEndpointAlreadyConnected.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionExportFailed.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionInvalidRNATemplate.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionJPEGEncoding.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionLoadingFailed.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionModeleStyleBaseSyntaxError.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionNAViewAlgorithm.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionNonEqualLength.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionParameterError.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionPermissionDenied.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionUnmatchedClosingParentheses.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionWritingForbidden.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionXMLGeneration.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/ExceptionXmlLoading.java [deleted file]
src2/fr/orsay/lri/varna/exceptions/MappingException.java [deleted file]
src2/fr/orsay/lri/varna/factories/RNAAlignment.java [deleted file]
src2/fr/orsay/lri/varna/factories/RNAFactory.java [deleted file]
src2/fr/orsay/lri/varna/factories/StockholmIO.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceParameterLoader.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceParseExport.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceVARNABasesListener.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceVARNAListener.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceVARNAObservable.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceVARNARNAListener.java [deleted file]
src2/fr/orsay/lri/varna/interfaces/InterfaceVARNASelectionListener.java [deleted file]
src2/fr/orsay/lri/varna/models/BaseList.java [deleted file]
src2/fr/orsay/lri/varna/models/FullBackup.java [deleted file]
src2/fr/orsay/lri/varna/models/VARNAConfig.java [deleted file]
src2/fr/orsay/lri/varna/models/VARNAConfigLoader.java [deleted file]
src2/fr/orsay/lri/varna/models/VARNAEdits.java [deleted file]
src2/fr/orsay/lri/varna/models/annotations/ChemProbAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/models/annotations/HighlightRegionAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/models/annotations/TextAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/models/export/ArcCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/CircleCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/ColorCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/FillCircleCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/FillPolygonCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/FontCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/GraphicElement.java [deleted file]
src2/fr/orsay/lri/varna/models/export/LineCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/PSExport.java [deleted file]
src2/fr/orsay/lri/varna/models/export/PolygonCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/RectangleCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/SVGExport.java [deleted file]
src2/fr/orsay/lri/varna/models/export/SecStrDrawingProducer.java [deleted file]
src2/fr/orsay/lri/varna/models/export/SecStrProducerGraphics.java [deleted file]
src2/fr/orsay/lri/varna/models/export/SwingGraphics.java [deleted file]
src2/fr/orsay/lri/varna/models/export/TextCommand.java [deleted file]
src2/fr/orsay/lri/varna/models/export/TikzExport.java [deleted file]
src2/fr/orsay/lri/varna/models/export/VueVARNAGraphics.java [deleted file]
src2/fr/orsay/lri/varna/models/export/XFIGExport.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/ComputeArcCenter.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/ComputeEllipseAxis.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/CubicBezierCurve.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/HalfEllipse.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/LinesIntersect.java [deleted file]
src2/fr/orsay/lri/varna/models/geom/MiscGeom.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/Base.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/Connection.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/Loop.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/NAView.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/Radloop.java [deleted file]
src2/fr/orsay/lri/varna/models/naView/Region.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/DrawRNATemplate.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/Mapping.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModelBaseStyle.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBP.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBPStyle.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBackbone.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBackboneElement.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBase.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBaseNucleotide.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleBasesComparison.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleColorMap.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/ModeleStrand.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/RNA.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/StructureTemp.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/VARNAPoint.java [deleted file]
src2/fr/orsay/lri/varna/models/rna/VARNASecDraw.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/BatchBenchmark.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/Benchmark.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/DrawRNATemplateCurveMethod.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/DrawRNATemplateMethod.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNANodeValue2TemplateDistance.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNANodeValueTemplate.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBasePair.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateBrokenBasePair.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNANodeValueTemplateSequence.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNATemplate.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNATemplateAlign.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNATemplateDrawingAlgorithmException.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNATemplateMapping.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/RNATemplateMappingException.java [deleted file]
src2/fr/orsay/lri/varna/models/templates/TODO.txt [deleted file]
src2/fr/orsay/lri/varna/models/treealign/AlignedNode.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/ExampleDistance2.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/ExampleDistance3.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/GraphvizDrawableNodeValue.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNANodeValue.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNANodeValue2WrongTypeException.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNATree.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNATree2.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/RNATree2Exception.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/Tree.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeAlign.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeAlignException.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeAlignLabelDistanceAsymmetric.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeAlignLabelDistanceSymmetric.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeAlignResult.java [deleted file]
src2/fr/orsay/lri/varna/models/treealign/TreeGraphviz.java [deleted file]
src2/fr/orsay/lri/varna/utils/RNAMLParser.java [deleted file]
src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java [deleted file]
src2/fr/orsay/lri/varna/utils/VARNASessionParser.java [deleted file]
src2/fr/orsay/lri/varna/utils/XMLUtils.java [deleted file]
src2/fr/orsay/lri/varna/views/Imprimer.java [deleted file]
src2/fr/orsay/lri/varna/views/PrintTest.java [deleted file]
src2/fr/orsay/lri/varna/views/VueAboutPanel.java [deleted file]
src2/fr/orsay/lri/varna/views/VueAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBPHeightIncrement.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBPList.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBPThickness.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBPType.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBaseValues.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBases.java [deleted file]
src2/fr/orsay/lri/varna/views/VueBorder.java [deleted file]
src2/fr/orsay/lri/varna/views/VueChemProbAnnotation.java [deleted file]
src2/fr/orsay/lri/varna/views/VueColorMapStyle.java [deleted file]
src2/fr/orsay/lri/varna/views/VueFont.java [deleted file]
src2/fr/orsay/lri/varna/views/VueGlobalRescale.java [deleted file]
src2/fr/orsay/lri/varna/views/VueGlobalRotation.java [deleted file]
src2/fr/orsay/lri/varna/views/VueHighlightRegionEdit.java [deleted file]
src2/fr/orsay/lri/varna/views/VueJPEG.java [deleted file]
src2/fr/orsay/lri/varna/views/VueListeAnnotations.java [deleted file]
src2/fr/orsay/lri/varna/views/VueLoadColorMapValues.java [deleted file]
src2/fr/orsay/lri/varna/views/VueManualInput.java [deleted file]
src2/fr/orsay/lri/varna/views/VueMenu.java [deleted file]
src2/fr/orsay/lri/varna/views/VueNumPeriod.java [deleted file]
src2/fr/orsay/lri/varna/views/VueRNAList.java [deleted file]
src2/fr/orsay/lri/varna/views/VueSpaceBetweenBases.java [deleted file]
src2/fr/orsay/lri/varna/views/VueStyleBP.java [deleted file]
src2/fr/orsay/lri/varna/views/VueUI.java [deleted file]
src2/fr/orsay/lri/varna/views/VueZoom.java [deleted file]
src2/javajs/J2SIgnoreImport.java [deleted file]
src2/javajs/J2SRequireImport.java [deleted file]
src2/javajs/_README.txt [deleted file]
src2/javajs/api/BytePoster.java [deleted file]
src2/javajs/api/EigenInterface.java [deleted file]
src2/javajs/api/GenericBinaryDocument.java [deleted file]
src2/javajs/api/GenericBinaryDocumentReader.java [deleted file]
src2/javajs/api/GenericCifDataParser.java [deleted file]
src2/javajs/api/GenericColor.java [deleted file]
src2/javajs/api/GenericImageDialog.java [deleted file]
src2/javajs/api/GenericImageEncoder.java [deleted file]
src2/javajs/api/GenericLineReader.java [deleted file]
src2/javajs/api/GenericOutputChannel.java [deleted file]
src2/javajs/api/GenericZipInputStream.java [deleted file]
src2/javajs/api/GenericZipTools.java [deleted file]
src2/javajs/api/Interface.java [deleted file]
src2/javajs/api/JSFunction.java [deleted file]
src2/javajs/api/JSInterface.java [deleted file]
src2/javajs/api/JSONEncodable.java [deleted file]
src2/javajs/api/ResettableStream.java [deleted file]
src2/javajs/api/ZInputStream.java [deleted file]
src2/javajs/api/js/J2SObjectInterface.java [deleted file]
src2/javajs/api/js/JSInterface.java [deleted file]
src2/javajs/export/PDFCreator.java [deleted file]
src2/javajs/export/PDFObject.java [deleted file]
src2/javajs/img/BMPDecoder.java [deleted file]
src2/javajs/img/CRCEncoder.java [deleted file]
src2/javajs/img/GifEncoder.java [deleted file]
src2/javajs/img/ImageEncoder.java [deleted file]
src2/javajs/img/Jpg64Encoder.java [deleted file]
src2/javajs/img/JpgEncoder.java [deleted file]
src2/javajs/img/PdfEncoder.java [deleted file]
src2/javajs/img/PngEncoder.java [deleted file]
src2/javajs/img/PpmEncoder.java [deleted file]
src2/javajs/util/A4.java [deleted file]
src2/javajs/util/AU.java [deleted file]
src2/javajs/util/AjaxURLConnection.java [deleted file]
src2/javajs/util/AjaxURLStreamHandler.java [deleted file]
src2/javajs/util/AjaxURLStreamHandlerFactory.java [deleted file]
src2/javajs/util/ArrayDataReader.java [deleted file]
src2/javajs/util/BArray.java [deleted file]
src2/javajs/util/BC.java [deleted file]
src2/javajs/util/BS.java [deleted file]
src2/javajs/util/Base64.java [deleted file]
src2/javajs/util/BinaryDocument.java [deleted file]
src2/javajs/util/CU.java [deleted file]
src2/javajs/util/CifDataParser.java [deleted file]
src2/javajs/util/CompoundDocDirEntry.java [deleted file]
src2/javajs/util/CompoundDocHeader.java [deleted file]
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