JAL-1807 j2s/develop-bh-2
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 21 Jul 2015 21:56:20 +0000 (22:56 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 21 Jul 2015 21:56:20 +0000 (22:56 +0100)
commit4231d40261fef32ce4570a6bbad0d35df44e8baf
tree07aabf2ea5ae2017071961035997a21aeea186a8
parentc07eb2c5794833bd0241000d6844d783fe10cb82
JAL-1807
first version showing alignment;
off-screen images working);
mouse-action roughed in;
no threads;
3175 files changed:
buildSite.xml [new file with mode: 0644]
site/j2s/JU/A4.js [new file with mode: 0644]
site/j2s/JU/AU.js [new file with mode: 0644]
site/j2s/JU/Adler32.js [new file with mode: 0644]
site/j2s/JU/AjaxURLConnection.js [new file with mode: 0644]
site/j2s/JU/AjaxURLStreamHandler.js [new file with mode: 0644]
site/j2s/JU/AjaxURLStreamHandlerFactory.js [new file with mode: 0644]
site/j2s/JU/ArrayDataReader.js [new file with mode: 0644]
site/j2s/JU/BArray.js [new file with mode: 0644]
site/j2s/JU/BC.js [new file with mode: 0644]
site/j2s/JU/BS.js [new file with mode: 0644]
site/j2s/JU/Base64.js [new file with mode: 0644]
site/j2s/JU/BinaryDocument.js [new file with mode: 0644]
site/j2s/JU/CRC32.js [new file with mode: 0644]
site/j2s/JU/CU.js [new file with mode: 0644]
site/j2s/JU/Checksum.js [new file with mode: 0644]
site/j2s/JU/CifDataParser.js [new file with mode: 0644]
site/j2s/JU/CompoundDocDirEntry.js [new file with mode: 0644]
site/j2s/JU/CompoundDocHeader.js [new file with mode: 0644]
site/j2s/JU/CompoundDocument.js [new file with mode: 0644]
site/j2s/JU/DF.js [new file with mode: 0644]
site/j2s/JU/DataReader.js [new file with mode: 0644]
site/j2s/JU/Deflate.js [new file with mode: 0644]
site/j2s/JU/Deflater.js [new file with mode: 0644]
site/j2s/JU/DeflaterOutputStream.js [new file with mode: 0644]
site/j2s/JU/Eigen.js [new file with mode: 0644]
site/j2s/JU/Encoding.js [new file with mode: 0644]
site/j2s/JU/GZIPException.js [new file with mode: 0644]
site/j2s/JU/GZIPHeader.js [new file with mode: 0644]
site/j2s/JU/GZIPInputStream.js [new file with mode: 0644]
site/j2s/JU/GZIPOutputStream.js [new file with mode: 0644]
site/j2s/JU/InfBlocks.js [new file with mode: 0644]
site/j2s/JU/InfCodes.js [new file with mode: 0644]
site/j2s/JU/InfTree.js [new file with mode: 0644]
site/j2s/JU/Inflate.js [new file with mode: 0644]
site/j2s/JU/Inflater.js [new file with mode: 0644]
site/j2s/JU/InflaterInputStream.js [new file with mode: 0644]
site/j2s/JU/JZlib.js [new file with mode: 0644]
site/j2s/JU/LimitedLineReader.js [new file with mode: 0644]
site/j2s/JU/ListDataReader.js [new file with mode: 0644]
site/j2s/JU/Lst.js [new file with mode: 0644]
site/j2s/JU/M3.js [new file with mode: 0644]
site/j2s/JU/M34.js [new file with mode: 0644]
site/j2s/JU/M4.js [new file with mode: 0644]
site/j2s/JU/Matrix.js [new file with mode: 0644]
site/j2s/JU/Measure.js [new file with mode: 0644]
site/j2s/JU/OC.js [new file with mode: 0644]
site/j2s/JU/P3.js [new file with mode: 0644]
site/j2s/JU/P3i.js [new file with mode: 0644]
site/j2s/JU/P4.js [new file with mode: 0644]
site/j2s/JU/PT.js [new file with mode: 0644]
site/j2s/JU/Quat.js [new file with mode: 0644]
site/j2s/JU/Rdr.js [new file with mode: 0644]
site/j2s/JU/SB.js [new file with mode: 0644]
site/j2s/JU/StaticTree.js [new file with mode: 0644]
site/j2s/JU/StringDataReader.js [new file with mode: 0644]
site/j2s/JU/T3.js [new file with mode: 0644]
site/j2s/JU/T3d.js [new file with mode: 0644]
site/j2s/JU/T3i.js [new file with mode: 0644]
site/j2s/JU/T4.js [new file with mode: 0644]
site/j2s/JU/Tree.js [new file with mode: 0644]
site/j2s/JU/V3.js [new file with mode: 0644]
site/j2s/JU/V3d.js [new file with mode: 0644]
site/j2s/JU/XmlUtil.js [new file with mode: 0644]
site/j2s/JU/ZStream.js [new file with mode: 0644]
site/j2s/JU/ZStreamException.js [new file with mode: 0644]
site/j2s/JU/ZipData.js [new file with mode: 0644]
site/j2s/JU/ZipTools.js [new file with mode: 0644]
site/j2s/MCview/Atom.js [new file with mode: 0644]
site/j2s/MCview/Bond.js [new file with mode: 0644]
site/j2s/MCview/PDBChain.js [new file with mode: 0644]
site/j2s/MCview/PDBfile.js [new file with mode: 0644]
site/j2s/MCview/Residue.js [new file with mode: 0644]
site/j2s/awt2swing/Button.js [new file with mode: 0644]
site/j2s/awt2swing/Canvas.js [new file with mode: 0644]
site/j2s/awt2swing/Checkbox.js [new file with mode: 0644]
site/j2s/awt2swing/CheckboxMenuItem.js [new file with mode: 0644]
site/j2s/awt2swing/Choice.js [new file with mode: 0644]
site/j2s/awt2swing/Frame.js [new file with mode: 0644]
site/j2s/awt2swing/Label.js [new file with mode: 0644]
site/j2s/awt2swing/Menu.js [new file with mode: 0644]
site/j2s/awt2swing/MenuBar.js [new file with mode: 0644]
site/j2s/awt2swing/MenuItem.js [new file with mode: 0644]
site/j2s/awt2swing/Panel.js [new file with mode: 0644]
site/j2s/awt2swing/PopupMenu.js [new file with mode: 0644]
site/j2s/awt2swing/ScrollPane.js [new file with mode: 0644]
site/j2s/awt2swing/Scrollbar.js [new file with mode: 0644]
site/j2s/awt2swing/TextArea.js [new file with mode: 0644]
site/j2s/awt2swing/TextField.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/Ctrl.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/FastBracket.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/Group.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/LeftRule.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/MessageManager.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/Multi.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/MultiMin.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/NoPattern.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/NonDirFileRegex.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/NullPattern.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/RuleHolder.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/SpecialRule.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/Start.js [new file with mode: 0644]
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site/j2s/com/stevesoft/pat/SubMark.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/TransPat.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/Transformer.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/UniValidator.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/Util.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/Validator.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/WantMoreTextReplaceRule.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/lookAhead.js [new file with mode: 0644]
site/j2s/com/stevesoft/pat/oneChar.js [new file with mode: 0644]
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site/j2s/core/core.z.js [new file with mode: 0644]
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site/j2s/core/package.js [new file with mode: 0644]
site/j2s/fr/orsay/lri/varna/models/rna/RNA.js [new file with mode: 0644]
site/j2s/jalview/analysis/AAFrequency.js [new file with mode: 0644]
site/j2s/jalview/analysis/AlignSeq.js [new file with mode: 0644]
site/j2s/jalview/analysis/AlignmentAnnotationUtils.js [new file with mode: 0644]
site/j2s/jalview/analysis/AlignmentSorter.js [new file with mode: 0644]
site/j2s/jalview/analysis/AlignmentUtils.js [new file with mode: 0644]
site/j2s/jalview/analysis/AnnotationSorter.js [new file with mode: 0644]
site/j2s/jalview/analysis/CodingUtils.js [new file with mode: 0644]
site/j2s/jalview/analysis/CodonComparator.js [new file with mode: 0644]
site/j2s/jalview/analysis/Conservation.js [new file with mode: 0644]
site/j2s/jalview/analysis/Dna.js [new file with mode: 0644]
site/j2s/jalview/analysis/Finder.js [new file with mode: 0644]
site/j2s/jalview/analysis/Grouping.js [new file with mode: 0644]
site/j2s/jalview/analysis/NJTree.js [new file with mode: 0644]
site/j2s/jalview/analysis/PCA.js [new file with mode: 0644]
site/j2s/jalview/analysis/ParseProperties.js [new file with mode: 0644]
site/j2s/jalview/analysis/Rna.js [new file with mode: 0644]
site/j2s/jalview/analysis/SecStrConsensus.js [new file with mode: 0644]
site/j2s/jalview/analysis/SeqsetUtils.js [new file with mode: 0644]
site/j2s/jalview/analysis/SequenceIdMatcher.js [new file with mode: 0644]
site/j2s/jalview/analysis/StructureFrequency.js [new file with mode: 0644]
site/j2s/jalview/analysis/WUSSParseException.js [new file with mode: 0644]
site/j2s/jalview/analysis/package.js [new file with mode: 0644]
site/j2s/jalview/analysis/scoremodels/FeatureScoreModel.js [new file with mode: 0644]
site/j2s/jalview/analysis/scoremodels/PIDScoreModel.js [new file with mode: 0644]
site/j2s/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js [new file with mode: 0644]
site/j2s/jalview/analysis/scoremodels/SWScoreModel.js [new file with mode: 0644]
site/j2s/jalview/api/AlignCalcManagerI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignCalcWorkerI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignExportSettingI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignViewControllerGuiI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignViewControllerI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignViewportI.js [new file with mode: 0644]
site/j2s/jalview/api/AlignmentViewPanel.js [new file with mode: 0644]
site/j2s/jalview/api/ComplexAlignFile.js [new file with mode: 0644]
site/j2s/jalview/api/FeatureRenderer.js [new file with mode: 0644]
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site/j2s/jalview/api/FeatureSettingsModelI.js [new file with mode: 0644]
site/j2s/jalview/api/FeaturesDisplayedI.js [new file with mode: 0644]
site/j2s/jalview/api/OOMHandlerI.js [new file with mode: 0644]
site/j2s/jalview/api/RotatableCanvasI.js [new file with mode: 0644]
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site/j2s/jalview/api/SequenceStructureBinding.js [new file with mode: 0644]
site/j2s/jalview/api/SplitContainerI.js [new file with mode: 0644]
site/j2s/jalview/api/StructureSelectionManagerProvider.js [new file with mode: 0644]
site/j2s/jalview/api/ViewStyleI.js [new file with mode: 0644]
site/j2s/jalview/api/analysis/ScoreModelI.js [new file with mode: 0644]
site/j2s/jalview/api/analysis/ViewBasedAnalysisI.js [new file with mode: 0644]
site/j2s/jalview/api/structures/JalviewStructureDisplayI.js [new file with mode: 0644]
site/j2s/jalview/appletgui/APopupMenu.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AlignFrame.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AlignViewport.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AlignmentPanel.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AnnotationColourChooser.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/AnnotationLabels.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AnnotationPanel.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AnnotationRowFilter.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AppletJmol.js [new file with mode: 0644]
site/j2s/jalview/appletgui/AppletJmolBinding.js [new file with mode: 0644]
site/j2s/jalview/appletgui/CutAndPasteTransfer.js [new file with mode: 0644]
site/j2s/jalview/appletgui/EditNameDialog.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/ExtJmol.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/Finder.js [new file with mode: 0644]
site/j2s/jalview/appletgui/FontChooser.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/IdwidthAdjuster.js [new file with mode: 0644]
site/j2s/jalview/appletgui/JVDialog.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/PCAPanel.js [new file with mode: 0644]
site/j2s/jalview/appletgui/PaintRefresher.js [new file with mode: 0644]
site/j2s/jalview/appletgui/PairwiseAlignPanel.js [new file with mode: 0644]
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site/j2s/jalview/appletgui/Tooltip.js [new file with mode: 0644]
site/j2s/jalview/appletgui/TreeCanvas.js [new file with mode: 0644]
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site/j2s/jalview/commands/ChangeCaseCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/CommandI.js [new file with mode: 0644]
site/j2s/jalview/commands/EditCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/OrderCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/RemoveGapColCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/RemoveGapsCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/SlideSequencesCommand.js [new file with mode: 0644]
site/j2s/jalview/commands/TrimRegionCommand.js [new file with mode: 0644]
site/j2s/jalview/controller/AlignViewController.js [new file with mode: 0644]
site/j2s/jalview/controller/FeatureSettingsController.js [new file with mode: 0644]
site/j2s/jalview/controller/FeatureSettingsControllerGuiI.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/Container.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Cursor.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Dialog.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/DisplayMode.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Event.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/EventDispatchThread.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/EventFilter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/EventQueue.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/FlowLayout.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/Graphics.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/GraphicsCallback.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/GraphicsDevice.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/GraphicsEnvironment.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/GridBagConstraints.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/GridBagLayoutInfo.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/GridLayout.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/Image.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/ImageCapabilities.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Insets.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/ItemSelectable.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/LayoutManager2.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/ModalEventFilter.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/Polygon.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Rectangle.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/RenderingHints.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/SentEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/SequencedEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Shape.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Stroke.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Toolkit.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/Transparency.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/color/ColorSpace.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/event/ActionEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ActionListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/AdjustmentEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/AdjustmentListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ComponentAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ComponentEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ComponentListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ContainerAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ContainerEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ContainerListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/FocusAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/FocusEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/FocusListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/HierarchyBoundsAdapter.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/event/HierarchyEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/HierarchyListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/InputEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/InputMethodEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/InputMethodListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/InvocationEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ItemEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/ItemListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/KeyAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/KeyEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/KeyListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseMotionAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseMotionListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseWheelEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/MouseWheelListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/NativeLibLoader.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/PaintEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/TextEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/TextListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/WindowAdapter.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/WindowEvent.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/WindowFocusListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/WindowListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/event/WindowStateListener.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/font/FontRenderContext.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/font/GraphicAttribute.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/font/LineMetrics.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/font/TextAttribute.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/AffineTransform.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/Arc2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/ArcIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/Area.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/CubicCurve2D.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/geom/Dimension2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/Ellipse2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/EllipseIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/FlatteningPathIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/IllegalPathStateException.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/Line2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/LineIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/NoninvertibleTransformException.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/geom/PathIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/Point2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/QuadCurve2D.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/geom/RectangularShape.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/RoundRectIterator.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/RoundRectangle2D.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/geom/package.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/image/AffineTransformOp.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/image/Kernel.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/image/Raster.js [new file with mode: 0644]
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site/swingjs/j2s/java/awt/package.js [new file with mode: 0644]
site/swingjs/j2s/java/awt/peer/CanvasPeer.js [new file with mode: 0644]
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site/swingjs/j2s/java/io/Serializable.js [new file with mode: 0644]
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site/swingjs/j2s/swingjs/plaf/JSToolBarSeparatorUI.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/plaf/JSViewportUI.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/plaf/LazyActionMap.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/plaf/TextListener.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/test/BugTest.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/test/FormattedTextFieldDemo.js [new file with mode: 0644]
site/swingjs/j2s/swingjs/test/JumbledImageApplet.js [new file with mode: 0644]
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site/swingjs/j2s/swingjs/test/converter/Unit.js [new file with mode: 0644]
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site/swingjs/jquery/JQuery_UI_Core1.js [new file with mode: 0644]
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site/swingjs/js/JSmol.js [new file with mode: 0644]
site/swingjs/js/JSmolCore.js [new file with mode: 0644]
site/swingjs/js/JSmolJavaExt.js [new file with mode: 0644]
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site/test.htm [new file with mode: 0644]
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site/uniref50.fa [new file with mode: 0644]
src/awt2swing/Button.java [new file with mode: 0644]
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src/awt2swing/Panel.java [new file with mode: 0644]
src/awt2swing/PopupMenu.java [new file with mode: 0644]
src/awt2swing/ScrollPane.java [new file with mode: 0644]
src/awt2swing/Scrollbar.java [new file with mode: 0644]
src/awt2swing/TextArea.java [new file with mode: 0644]
src/awt2swing/TextField.java [new file with mode: 0644]
src/com/stevesoft/pat/BackRefRule.java
src/com/stevesoft/pat/BasicStringBufferLike.java
src/com/stevesoft/pat/CaseMgr.java
src/com/stevesoft/pat/DirFileRegex.java
src/com/stevesoft/pat/FileRegex.java
src/com/stevesoft/pat/MessageManager.java [new file with mode: 0644]
src/com/stevesoft/pat/NonDirFileRegex.java
src/com/stevesoft/pat/Pattern.java
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src/com/stevesoft/pat/Regex.java
src/com/stevesoft/pat/RegexReader.java
src/com/stevesoft/pat/RegexTokenizer.java
src/com/stevesoft/pat/RegexWriter.java
src/com/stevesoft/pat/ReplaceRule.java
src/com/stevesoft/pat/Replacer.java
src/com/stevesoft/pat/Skip.java
src/com/stevesoft/pat/Skip2.java
src/com/stevesoft/pat/SkipBMH.java
src/com/stevesoft/pat/StringBufferLike.java
src/com/stevesoft/pat/Transformer.java
src/com/stevesoft/pat/Util.java [new file with mode: 0644]
src/com/stevesoft/pat/Validator.java
src/com/stevesoft/pat/oneChar.java
src/com/stevesoft/pat/parsePerl.java
src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
src/com/stevesoft/pat/wrap/StringBufferWrap.java
src/com/stevesoft/pat/wrap/WriterWrap.java
src/fr/orsay/lri/varna/models/rna/RNA.java [new file with mode: 0644]
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignmentAnnotationUtils.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Finder.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/ParseProperties.java
src/jalview/analysis/Rna.java
src/jalview/analysis/StructureFrequency.java
src/jalview/api/analysis/ViewBasedAnalysisI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationColumnChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AnnotationRowFilter.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/EditNameDialog.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/IdwidthAdjuster.java
src/jalview/appletgui/JVDialog.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/SplitFrame.java
src/jalview/appletgui/TitledPanel.java
src/jalview/appletgui/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/JalviewLite.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/CigarBase.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/io/AlignmentProperties.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileParse.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/jsdev/Constants.java [new file with mode: 0644]
src/jalview/jsdev/GenericFileAdapter.java [new file with mode: 0644]
src/jalview/jsdev/JSRegex.java [new file with mode: 0644]
src/jalview/jsdev/JavaScriptRegExp.java [new file with mode: 0644]
src/jalview/jsdev/RegExp.java [new file with mode: 0644]
src/jalview/jsdev/api/RegExpInterface.java [new file with mode: 0644]
src/jalview/jsdev/api/VarnaRNA.java [new file with mode: 0644]
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/util/AWTConsole.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/GroupUrlLink.java
src/jalview/util/MessageManager.java
src/jalview/util/QuickSort.java
src/jalview/util/UrlLink.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/workers/AlignCalcWorker.java
src/jalview/workers/ComplementConsensusThread.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/StrucConsensusThread.java
src/javajs/J2SIgnoreImport.java [new file with mode: 0644]
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src/javajs/api/EigenInterface.java [new file with mode: 0644]
src/javajs/api/EventManager.java [new file with mode: 0644]
src/javajs/api/FontManager.java [new file with mode: 0644]
src/javajs/api/GenericBinaryDocument.java [new file with mode: 0644]
src/javajs/api/GenericCifDataParser.java [new file with mode: 0644]
src/javajs/api/GenericColor.java [new file with mode: 0644]
src/javajs/api/GenericFileInterface.java [new file with mode: 0644]
src/javajs/api/GenericImageDialog.java [new file with mode: 0644]
src/javajs/api/GenericImageEncoder.java [new file with mode: 0644]
src/javajs/api/GenericLineReader.java [new file with mode: 0644]
src/javajs/api/GenericMenuInterface.java [new file with mode: 0644]
src/javajs/api/GenericMouseInterface.java [new file with mode: 0644]
src/javajs/api/GenericPlatform.java [new file with mode: 0644]
src/javajs/api/GenericZipInputStream.java [new file with mode: 0644]
src/javajs/api/GenericZipTools.java [new file with mode: 0644]
src/javajs/api/HTMLElement.java [new file with mode: 0644]
src/javajs/api/HTMLWindowEvent.java [new file with mode: 0644]
src/javajs/api/Interface.java [new file with mode: 0644]
src/javajs/api/JSInterface.java [new file with mode: 0644]
src/javajs/api/JSONEncodable.java [new file with mode: 0644]
src/javajs/api/JmolObjectInterface.java [new file with mode: 0644]
src/javajs/api/PlatformViewer.java [new file with mode: 0644]
src/javajs/api/SC.java [new file with mode: 0644]
src/javajs/api/SwingController.java [new file with mode: 0644]
src/javajs/api/ZInputStream.java [new file with mode: 0644]
src/javajs/awt/BorderLayout.java [new file with mode: 0644]
src/javajs/awt/Color.java [new file with mode: 0644]
src/javajs/awt/Component.java [new file with mode: 0644]
src/javajs/awt/Container.java [new file with mode: 0644]
src/javajs/awt/Dimension.java [new file with mode: 0644]
src/javajs/awt/Font.java [new file with mode: 0644]
src/javajs/awt/LayoutManager.java [new file with mode: 0644]
src/javajs/awt/event/ActionEvent.java [new file with mode: 0644]
src/javajs/awt/event/ActionListener.java [new file with mode: 0644]
src/javajs/awt/event/Event.java [new file with mode: 0644]
src/javajs/awt/event/ItemEvent.java [new file with mode: 0644]
src/javajs/awt/event/WindowEvent.java [new file with mode: 0644]
src/javajs/awt/event/WindowListener.java [new file with mode: 0644]
src/javajs/export/PDFCreator.java [new file with mode: 0644]
src/javajs/export/PDFObject.java [new file with mode: 0644]
src/javajs/img/BMPDecoder.java [new file with mode: 0644]
src/javajs/img/CRCEncoder.java [new file with mode: 0644]
src/javajs/img/GifEncoder.java [new file with mode: 0644]
src/javajs/img/ImageEncoder.java [new file with mode: 0644]
src/javajs/img/Jpg64Encoder.java [new file with mode: 0644]
src/javajs/img/JpgEncoder.java [new file with mode: 0644]
src/javajs/img/PdfEncoder.java [new file with mode: 0644]
src/javajs/img/PngEncoder.java [new file with mode: 0644]
src/javajs/img/PpmEncoder.java [new file with mode: 0644]
src/javajs/swing/AbstractButton.java [new file with mode: 0644]
src/javajs/swing/AbstractTableModel.java [new file with mode: 0644]
src/javajs/swing/ButtonGroup.java [new file with mode: 0644]
src/javajs/swing/Cell.java [new file with mode: 0644]
src/javajs/swing/ColumnSelectionModel.java [new file with mode: 0644]
src/javajs/swing/Document.java [new file with mode: 0644]
src/javajs/swing/FlowLayout.java [new file with mode: 0644]
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src/javajs/swing/GridBagConstraints.java [new file with mode: 0644]
src/javajs/swing/GridBagLayout.java [new file with mode: 0644]
src/javajs/swing/Insets.java [new file with mode: 0644]
src/javajs/swing/JButton.java [new file with mode: 0644]
src/javajs/swing/JCheckBox.java [new file with mode: 0644]
src/javajs/swing/JCheckBoxMenuItem.java [new file with mode: 0644]
src/javajs/swing/JComboBox.java [new file with mode: 0644]
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src/javajs/swing/JComponentImp.java [new file with mode: 0644]
src/javajs/swing/JContentPane.java [new file with mode: 0644]
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src/javajs/swing/JEditorPane.java [new file with mode: 0644]
src/javajs/swing/JLabel.java [new file with mode: 0644]
src/javajs/swing/JMenu.java [new file with mode: 0644]
src/javajs/swing/JMenuItem.java [new file with mode: 0644]
src/javajs/swing/JPanel.java [new file with mode: 0644]
src/javajs/swing/JPopupMenu.java [new file with mode: 0644]
src/javajs/swing/JRadioButtonMenuItem.java [new file with mode: 0644]
src/javajs/swing/JScrollPane.java [new file with mode: 0644]
src/javajs/swing/JSplitPane.java [new file with mode: 0644]
src/javajs/swing/JTable.java [new file with mode: 0644]
src/javajs/swing/JTextField.java [new file with mode: 0644]
src/javajs/swing/JTextPane.java [new file with mode: 0644]
src/javajs/swing/ListSelectionModel.java [new file with mode: 0644]
src/javajs/swing/SwingConstants.java [new file with mode: 0644]
src/javajs/swing/TableCellRenderer.java [new file with mode: 0644]
src/javajs/swing/TableColumn.java [new file with mode: 0644]
src/javajs/util/A4.java [new file with mode: 0644]
src/javajs/util/AU.java [new file with mode: 0644]
src/javajs/util/AjaxURLConnection.java [new file with mode: 0644]
src/javajs/util/AjaxURLStreamHandler.java [new file with mode: 0644]
src/javajs/util/AjaxURLStreamHandlerFactory.java [new file with mode: 0644]
src/javajs/util/ArrayDataReader.java [new file with mode: 0644]
src/javajs/util/BArray.java [new file with mode: 0644]
src/javajs/util/BC.java [new file with mode: 0644]
src/javajs/util/BS.java [new file with mode: 0644]
src/javajs/util/Base64.java [new file with mode: 0644]
src/javajs/util/BinaryDocument.java [new file with mode: 0644]
src/javajs/util/CU.java [new file with mode: 0644]
src/javajs/util/CifDataParser.java [new file with mode: 0644]
src/javajs/util/CompoundDocDirEntry.java [new file with mode: 0644]
src/javajs/util/CompoundDocHeader.java [new file with mode: 0644]
src/javajs/util/CompoundDocument.java [new file with mode: 0644]
src/javajs/util/DF.java [new file with mode: 0644]
src/javajs/util/DataReader.java [new file with mode: 0644]
src/javajs/util/Eigen.java [new file with mode: 0644]
src/javajs/util/Encoding.java [new file with mode: 0644]
src/javajs/util/LimitedLineReader.java [new file with mode: 0644]
src/javajs/util/ListDataReader.java [new file with mode: 0644]
src/javajs/util/Lst.java [new file with mode: 0644]
src/javajs/util/M3.java [new file with mode: 0644]
src/javajs/util/M34.java [new file with mode: 0644]
src/javajs/util/M4.java [new file with mode: 0644]
src/javajs/util/Matrix.java [new file with mode: 0644]
src/javajs/util/Measure.java [new file with mode: 0644]
src/javajs/util/OC.java [new file with mode: 0644]
src/javajs/util/P3.java [new file with mode: 0644]
src/javajs/util/P3i.java [new file with mode: 0644]
src/javajs/util/P4.java [new file with mode: 0644]
src/javajs/util/PT.java [new file with mode: 0644]
src/javajs/util/Quat.java [new file with mode: 0644]
src/javajs/util/Rdr.java [new file with mode: 0644]
src/javajs/util/SB.java [new file with mode: 0644]
src/javajs/util/StringDataReader.java [new file with mode: 0644]
src/javajs/util/T3.java [new file with mode: 0644]
src/javajs/util/T3d.java [new file with mode: 0644]
src/javajs/util/T3i.java [new file with mode: 0644]
src/javajs/util/T4.java [new file with mode: 0644]
src/javajs/util/V3.java [new file with mode: 0644]
src/javajs/util/V3d.java [new file with mode: 0644]
src/javajs/util/XmlUtil.java [new file with mode: 0644]
src/javajs/util/ZipData.java [new file with mode: 0644]
src/javajs/util/ZipTools.java [new file with mode: 0644]
src/netscape/javascript/JSException.java [new file with mode: 0644]
src/netscape/javascript/JSObject.java [new file with mode: 0644]
src/org/exolab/castor/mapping/Mapping.java [new file with mode: 0644]
src/org/exolab/castor/xml/Unmarshaller.java [new file with mode: 0644]
src/org/jmol/viewer/Viewer.java [new file with mode: 0644]
src/swingjs/JSImage.java [new file with mode: 0644]
src/swingjs/JSImage.js [new file with mode: 0644]
src/swingjs/JSImagekit.js [new file with mode: 0644]
src/swingjs/JSThread.java [new file with mode: 0644]
src/swingjs/api/DOMNode.java [new file with mode: 0644]
src/swingjs/api/JSFunction.java [new file with mode: 0644]