JAL-3848 update jalview core with slivka classes, example file import and structure...
authorJim Procter <j.procter@dundee.ac.uk>
Sun, 25 Jul 2021 14:45:28 +0000 (15:45 +0100)
committerJim Procter <j.procter@dundee.ac.uk>
Sun, 25 Jul 2021 14:53:48 +0000 (15:53 +0100)
utils/jalviewjs/classlists/jalview.txt

index e60fe60..739f070 100644 (file)
-java/applet/Applet.js
+intervalstore/api/IntervalI.js
+intervalstore/api/IntervalStoreI.js
+intervalstore/impl/BinarySearcher.js
+intervalstore/impl/IntervalStore.js
+intervalstore/impl/NCList.js
+intervalstore/impl/NCNode.js
+jalview/analysis/AAFrequency.js
+jalview/analysis/AlignSeq.js
+jalview/analysis/AlignmentAnnotationUtils.js
+jalview/analysis/AlignmentSorter.js
+jalview/analysis/AlignmentUtils.js
+jalview/analysis/AnnotationSorter.js
+jalview/analysis/Conservation.js
+jalview/analysis/CrossRef.js
+jalview/analysis/GeneticCodeI.js
+jalview/analysis/GeneticCodes.js
+jalview/analysis/SeqsetUtils.js
+jalview/analysis/SequenceIdMatcher.js
+jalview/analysis/TreeModel.js
+jalview/analysis/scoremodels/DistanceScoreModel.js
+jalview/analysis/scoremodels/FeatureDistanceModel.js
+jalview/analysis/scoremodels/PIDModel.js
+jalview/analysis/scoremodels/ScoreMatrix.js
+jalview/analysis/scoremodels/ScoreModels.js
+jalview/analysis/scoremodels/SimilarityScoreModel.js
+jalview/api/AlignCalcManagerI2.js
+jalview/api/AlignCalcWorkerI.js
+jalview/api/AlignViewControllerGuiI.js
+jalview/api/AlignViewControllerI.js
+jalview/api/AlignViewportI.js
+jalview/api/AlignmentViewPanel.js
+jalview/api/BuildDetailsI.js
+jalview/api/DBRefEntryI.js
+jalview/api/FeatureColourI.js
+jalview/api/FeatureRenderer.js
+jalview/api/FeatureSettingsModelI.js
+jalview/api/FeaturesDisplayedI.js
+jalview/api/FeaturesSourceI.js
+jalview/api/JalviewJSApi.js
+jalview/api/OOMHandlerI.js
+jalview/api/PollableAlignCalcWorkerI.js
+jalview/api/SequenceRenderer.js
+jalview/api/SequenceStructureBinding.js
+jalview/api/StructureSelectionManagerProvider.js
+jalview/api/ViewStyleI.js
+jalview/api/analysis/PairwiseScoreModelI.js
+jalview/api/analysis/ScoreModelI.js
+jalview/api/structures/JalviewStructureDisplayI.js
+jalview/bin/AppletParams.js
+jalview/bin/ApplicationSingletonProvider.js
+jalview/bin/ArgsParser.js
+jalview/bin/BuildDetails.js
+jalview/bin/Cache.js
+jalview/bin/Jalview.js
+jalview/bin/JalviewJSApp.js
+jalview/bin/JalviewTaskbar.js
+jalview/controller/AlignViewController.js
+jalview/datamodel/ASequence.js
+jalview/datamodel/ASequenceI.js
+jalview/datamodel/Alignment.js
+jalview/datamodel/AlignmentAnnotation.js
+jalview/datamodel/AlignmentI.js
+jalview/datamodel/AlignmentOrder.js
+jalview/datamodel/AlignmentView.js
+jalview/datamodel/AnnotatedCollectionI.js
+jalview/datamodel/Annotation.js
+jalview/datamodel/BinaryNode.js
+jalview/datamodel/CigarArray.js
+jalview/datamodel/CigarBase.js
+jalview/datamodel/CigarSimple.js
+jalview/datamodel/ColumnSelection.js
+jalview/datamodel/ContiguousI.js
+jalview/datamodel/DBRefEntry.js
+jalview/datamodel/DBRefSource.js
+jalview/datamodel/GraphLine.js
+jalview/datamodel/HiddenColumns.js
+jalview/datamodel/HiddenColumnsCursor.js
+jalview/datamodel/HiddenCursorPosition.js
+jalview/datamodel/HiddenSequences.js
+jalview/datamodel/Mapping.js
+jalview/datamodel/PDBEntry.js
+jalview/datamodel/Profile.js
+jalview/datamodel/ProfileI.js
+jalview/datamodel/Profiles.js
+jalview/datamodel/ProfilesI.js
+jalview/datamodel/Range.js
+jalview/datamodel/RangeIterator.js
+jalview/datamodel/ResidueCount.js
+jalview/datamodel/SearchResultMatchI.js
+jalview/datamodel/SearchResults.js
+jalview/datamodel/SearchResultsI.js
+jalview/datamodel/SeqCigar.js
+jalview/datamodel/Sequence.js
+jalview/datamodel/SequenceCollectionI.js
+jalview/datamodel/SequenceCursor.js
+jalview/datamodel/SequenceFeature.js
+jalview/datamodel/SequenceGroup.js
+jalview/datamodel/SequenceI.js
+jalview/datamodel/SequenceNode.js
+jalview/datamodel/StructureViewerModel.js
+jalview/datamodel/features/FeatureAttributes.js
+jalview/datamodel/features/FeatureLocationI.js
+jalview/datamodel/features/FeatureStore.js
+jalview/datamodel/features/SequenceFeatures.js
+jalview/datamodel/features/SequenceFeaturesI.js
+jalview/ext/ensembl/EnsemblData.js
+jalview/ext/ensembl/EnsemblGene.js
+jalview/ext/ensembl/EnsemblRestClient.js
+jalview/ext/ensembl/EnsemblSeqProxy.js
+jalview/ext/ensembl/EnsemblSequenceFetcher.js
+jalview/fts/api/FTSData.js
+jalview/fts/api/FTSDataColumnI.js
+jalview/fts/api/FTSRestClientI.js
+jalview/fts/core/DecimalFormatTableCellRenderer.js
+jalview/fts/core/FTSDataColumnPreferences.js
+jalview/fts/core/FTSRestClient.js
+jalview/fts/core/FTSRestRequest.js
+jalview/fts/core/FTSRestResponse.js
+jalview/fts/service/pdb/PDBFTSRestClient.js
+jalview/gui/APQHandlers.js
+jalview/gui/AlignFrame.js
+jalview/gui/AlignViewport.js
+jalview/gui/AlignmentPanel.js
+jalview/gui/AnnotationColumnChooser.js
+jalview/gui/AnnotationLabels.js
+jalview/gui/AnnotationPanel.js
+jalview/gui/AnnotationRowFilter.js
+jalview/gui/ColourMenuHelper.js
+jalview/gui/ComboBoxTooltipRenderer.js
+jalview/gui/Desktop.js
+jalview/gui/FeatureRenderer.js
+jalview/gui/IProgressIndicator.js
+jalview/gui/IProgressIndicatorHandler.js
+jalview/gui/IdCanvas.js
+jalview/gui/IdPanel.js
+jalview/gui/IdwidthAdjuster.js
+jalview/gui/JalviewBooleanRadioButtons.js
+jalview/gui/JalviewChangeSupport.js
+jalview/gui/JvOptionPane.js
+jalview/gui/JvSwingUtils.js
+jalview/gui/OptsAndParamsPage.js
+jalview/gui/OptsParametersContainerI.js
+jalview/gui/PaintRefresher.js
+jalview/gui/PopupMenu.js
+jalview/gui/Preferences.js
+jalview/gui/ProgressBar.js
+jalview/gui/ScalePanel.js
+jalview/gui/SeqCanvas.js
+jalview/gui/SeqPanel.js
+jalview/gui/SequenceFetcher.js
+jalview/gui/SequenceRenderer.js
+jalview/gui/SliderPanel.js
+jalview/gui/SlivkaPreferences.js
+jalview/gui/StructureChooser.js
+jalview/gui/StructureViewer.js
+jalview/gui/TreeCanvas.js
+jalview/gui/TreePanel.js
+jalview/gui/ViewSelectionMenu.js
+jalview/gui/WebserviceInfo.js
+jalview/gui/WsJobParameters.js
+jalview/gui/WsParamSetManager.js
+jalview/hmmer/HmmerCommand.js
+jalview/io/AlignFile.js
+jalview/io/AlignmentFileReaderI.js
+jalview/io/AlignmentFileWriterI.js
+jalview/io/AnnotationFile.js
+jalview/io/AppletFormatAdapter.js
+jalview/io/BackupFilenameParts.js
+jalview/io/BackupFiles.js
+jalview/io/BackupFilesPresetEntry.js
+jalview/io/DataSourceType.js
+jalview/io/FastaFile.js
+jalview/io/FeaturesFile.js
+jalview/io/FileFormat.js
+jalview/io/FileFormatI.js
+jalview/io/FileFormats.js
+jalview/io/FileLoader.js
+jalview/io/FileParse.js
+jalview/io/FormatAdapter.js
+jalview/io/IdentifyFile.js
+jalview/io/IntKeyStringValueEntry.js
+jalview/io/JalviewFileChooser.js
+jalview/io/JalviewFileFilter.js
+jalview/io/JalviewFileView.js
+jalview/io/NewickFile.js
+jalview/io/PIRFile.js
+jalview/io/ScoreMatrixFile.js
+jalview/io/SequenceAnnotationReport.js
+jalview/io/StockholmFile.js
+jalview/io/cache/JvCacheableInputBox.js
+jalview/javascript/json/JSON.js
+jalview/javascript/log4j/ConsoleAppender.js
+jalview/javascript/log4j/Layout.js
+jalview/javascript/log4j/Level.js
+jalview/javascript/log4j/Logger.js
+jalview/javascript/log4j/Priority.js
+jalview/javascript/log4j/SimpleLayout.js
+jalview/javascript/log4j/spi/OptionHandler.js
+jalview/javascript/web/Client.js
+jalview/javascript/web/ClientResponse.js
+jalview/javascript/web/WebResource.js
+jalview/jbgui/GAlignFrame.js
+jalview/jbgui/GAlignmentPanel.js
+jalview/jbgui/GDesktop.js
+jalview/jbgui/GPreferences.js
+jalview/jbgui/GSliderPanel.js
+jalview/jbgui/GStructureChooser.js
+jalview/jbgui/GTreePanel.js
+jalview/jbgui/GWebserviceInfo.js
+jalview/project/Jalview2XML.js
+jalview/renderer/AnnotationRenderer.js
+jalview/renderer/AwtRenderPanelI.js
+jalview/renderer/OverviewResColourFinder.js
+jalview/renderer/ResidueColourFinder.js
+jalview/renderer/ResidueShader.js
+jalview/renderer/ResidueShaderI.js
+jalview/renderer/ScaleRenderer.js
+jalview/renderer/seqfeatures/FeatureRenderer.js
+jalview/schemes/Blosum62ColourScheme.js
+jalview/schemes/BuriedColourScheme.js
+jalview/schemes/ClustalxColourScheme.js
+jalview/schemes/ColourSchemeI.js
+jalview/schemes/ColourSchemeProperty.js
+jalview/schemes/ColourSchemes.js
+jalview/schemes/Consensus.js
+jalview/schemes/FeatureColour.js
+jalview/schemes/FeatureSettingsAdapter.js
+jalview/schemes/HMMMatchScoreColourScheme.js
+jalview/schemes/HelixColourScheme.js
+jalview/schemes/HmmerColourScheme.js
+jalview/schemes/HmmerGlobalBackground.js
+jalview/schemes/HmmerLocalBackground.js
+jalview/schemes/HydrophobicColourScheme.js
+jalview/schemes/IdColourScheme.js
+jalview/schemes/JalviewColourScheme.js
+jalview/schemes/NucleotideColourScheme.js
+jalview/schemes/PIDColourScheme.js
+jalview/schemes/PurinePyrimidineColourScheme.js
+jalview/schemes/RNAHelicesColour.js
+jalview/schemes/ResidueColourScheme.js
+jalview/schemes/ResidueProperties.js
+jalview/schemes/ScoreColourScheme.js
+jalview/schemes/StrandColourScheme.js
+jalview/schemes/TCoffeeColourScheme.js
+jalview/schemes/TaylorColourScheme.js
+jalview/schemes/TurnColourScheme.js
+jalview/schemes/ZappoColourScheme.js
+jalview/structure/AtomSpec.js
+jalview/structure/CommandListener.js
+jalview/structure/SelectionListener.js
+jalview/structure/SelectionSource.js
+jalview/structure/SequenceListener.js
+jalview/structure/StructureImportSettings.js
+jalview/structure/StructureSelectionManager.js
+jalview/structure/VamsasSource.js
+jalview/urls/CustomUrlProvider.js
+jalview/urls/IdOrgSettings.js
+jalview/urls/IdentifiersUrlProvider.js
+jalview/urls/UrlLinkDisplay.js
+jalview/urls/UrlLinkTableModel.js
+jalview/urls/UrlProvider.js
+jalview/urls/UrlProviderImpl.js
+jalview/urls/api/UrlProviderFactoryI.js
+jalview/urls/api/UrlProviderI.js
+jalview/urls/desktop/DesktopUrlProviderFactory.js
+jalview/util/BrowserLauncher.js
+jalview/util/ColorUtils.js
+jalview/util/Comparison.js
+jalview/util/DBRefUtils.js
+jalview/util/FileUtils.js
+jalview/util/Format.js
+jalview/util/LinkedIdentityHashSet.js
+jalview/util/MapList.js
+jalview/util/MessageManager.js
+jalview/util/ParseHtmlBodyAndLinks.js
+jalview/util/Platform.js
+jalview/util/QuickSort.js
+jalview/util/StringUtils.js
+jalview/util/UrlLink.js
+jalview/util/dialogrunner/DialogRunnerI.js
+jalview/util/jarInputStreamProvider.js
+jalview/viewmodel/AlignmentViewport.js
+jalview/viewmodel/ViewportListenerI.js
+jalview/viewmodel/ViewportProperties.js
+jalview/viewmodel/ViewportRanges.js
+jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js
+jalview/viewmodel/seqfeatures/FeatureRendererModel.js
+jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
+jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
+jalview/viewmodel/styles/ViewStyle.js
+jalview/workers/AlignCalcManager2.js
+jalview/workers/AlignCalcWorker.js
+jalview/workers/ComplementConsensusThread.js
+jalview/workers/ConsensusThread.js
+jalview/workers/ConservationThread.js
+jalview/workers/InformationThread.js
+jalview/workers/StrucConsensusThread.js
+jalview/ws/AWSThread.js
+jalview/ws/AWsJob.js
+jalview/ws/JobStateSummary.js
+jalview/ws/SequenceFetcher.js
+jalview/ws/ServiceChangeListener.js
+jalview/ws/WSClient.js
+jalview/ws/WSClientI.js
+jalview/ws/WSDiscovererI.js
+jalview/ws/WSMenuEntryProviderI.js
+jalview/ws/api/CancellableI.js
+jalview/ws/api/JalviewServiceEndpointProviderI.js
+jalview/ws/api/JalviewWebServiceI.js
+jalview/ws/api/JobId.js
+jalview/ws/api/MsaI.js
+jalview/ws/api/MsaResultI.js
+jalview/ws/api/MultipleSequenceAlignmentI.js
+jalview/ws/api/SequenceAnnotationServiceI.js
+jalview/ws/api/ServiceWithParameters.js
+jalview/ws/api/UIinfo.js
+jalview/ws/api/WSAnnotationCalcManagerI.js
+jalview/ws/dbsources/EbiFileRetrievedProxy.js
+jalview/ws/dbsources/EmblCdsSource.js
+jalview/ws/dbsources/EmblSource.js
+jalview/ws/dbsources/EmblXmlSource.js
+jalview/ws/dbsources/Pdb.js
+jalview/ws/dbsources/Pfam.js
+jalview/ws/dbsources/PfamFull.js
+jalview/ws/dbsources/PfamSeed.js
+jalview/ws/dbsources/Rfam.js
+jalview/ws/dbsources/RfamSeed.js
+jalview/ws/dbsources/Uniprot.js
+jalview/ws/dbsources/Xfam.js
+jalview/ws/gui/AnnotationWsJob.js
+jalview/ws/gui/MsaWSJob.js
+jalview/ws/gui/MsaWSThread.js
+jalview/ws/gui/WsJob.js
+jalview/ws/jws2/Jws2Client.js
+jalview/ws/jws2/Jws2ClientFactory.js
+jalview/ws/jws2/Jws2Discoverer.js
+jalview/ws/jws2/MsaWSClient.js
+jalview/ws/jws2/PreferredServiceChangeListener.js
+jalview/ws/jws2/PreferredServiceRegistry.js
+jalview/ws/jws2/SeqAnnotationServiceCalcWorker.js
+jalview/ws/jws2/SequenceAnnotationWSClient.js
+jalview/ws/jws2/dm/AAConSettings.js
+jalview/ws/params/ArgumentI.js
+jalview/ws/params/AutoCalcSetting.js
+jalview/ws/params/OptionI.js
+jalview/ws/params/ParamDatastoreI.js
+jalview/ws/params/ParamManager.js
+jalview/ws/params/ParameterI.js
+jalview/ws/params/ValueConstrainI.js
+jalview/ws/params/WsParamSetI.js
+jalview/ws/params/simple/BooleanOption.js
+jalview/ws/params/simple/DoubleParameter.js
+jalview/ws/params/simple/IntegerParameter.js
+jalview/ws/params/simple/Option.js
+jalview/ws/params/simple/StringParameter.js
+jalview/ws/seqfetcher/ASequenceFetcher.js
+jalview/ws/seqfetcher/DbSourceProxy.js
+jalview/ws/seqfetcher/DbSourceProxyImpl.js
+jalview/ws/sifts/SiftsSettings.js
+jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.js
+jalview/ws/slivkaws/SlivkaDatastore.js
+jalview/ws/slivkaws/SlivkaMsaServiceInstance.js
+jalview/ws/slivkaws/SlivkaParamSet.js
+jalview/ws/slivkaws/SlivkaWSDiscoverer.js
+jalview/ws/slivkaws/SlivkaWSInstance.js
+jalview/ws/uimodel/AlignAnalysisUIText.js
+jalview/ws/utils/UrlDownloadClient.js
+jalview/xml/binding/jalview/Annotation.js
+jalview/xml/binding/jalview/AnnotationElement.js
+jalview/xml/binding/jalview/Feature.js
+jalview/xml/binding/jalview/JalviewModel.js
+jalview/xml/binding/jalview/ObjectFactory.js
+jalview/xml/binding/jalview/Pdbentry.js
+jalview/xml/binding/jalview/Sequence.js
+jalview/xml/binding/jalview/SequenceSet.js
+jalview/xml/binding/jalview/SequenceType.js
+jalview/xml/binding/jalview/VAMSAS.js
+jalview/xml/binding/jalview/WebServiceParameterSet.js
 java/applet/AppletContext.js
 java/applet/AppletStub.js
 java/applet/JSApplet.js
-java/awt/ActiveEvent.js
-java/awt/Adjustable.js
 java/awt/AWTEvent.js
 java/awt/AWTEventMulticaster.js
 java/awt/AWTKeyStroke.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
+java/awt/AlphaComposite.js
 java/awt/BasicStroke.js
 java/awt/BorderLayout.js
-java/awt/Button.js
+java/awt/CardLayout.js
 java/awt/Color.js
-java/awt/color/ColorSpace.js
 java/awt/Component.js
 java/awt/ComponentOrientation.js
-java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Composite.js
 java/awt/Container.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
 java/awt/Cursor.js
 java/awt/DefaultFocusTraversalPolicy.js
 java/awt/DefaultKeyboardFocusManager.js
+java/awt/Desktop.js
 java/awt/Dialog.js
 java/awt/Dimension.js
+java/awt/EventDispatchThread.js
+java/awt/EventFilter.js
+java/awt/EventQueue.js
+java/awt/EventQueueItem.js
+java/awt/FlowLayout.js
+java/awt/FocusTraversalPolicy.js
+java/awt/Font.js
+java/awt/FontMetrics.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.js
+java/awt/GridBagConstraints.js
+java/awt/GridBagLayout.js
+java/awt/GridBagLayoutInfo.js
+java/awt/GridLayout.js
+java/awt/Image.js
+java/awt/ImageMediaEntry.js
+java/awt/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/KeyboardFocusManager.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/MediaEntry.js
+java/awt/MediaTracker.js
+java/awt/Paint.js
+java/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/SentEvent.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/Taskbar.js
+java/awt/TextComponent.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/VKCollection.js
+java/awt/Window.js
+java/awt/color/ColorSpace.js
+java/awt/datatransfer/ClipboardOwner.js
+java/awt/datatransfer/FlavorMap.js
+java/awt/datatransfer/FlavorTable.js
+java/awt/datatransfer/SystemFlavorMap.js
+java/awt/dnd/DropTarget.js
+java/awt/dnd/DropTargetContext.js
+java/awt/dnd/DropTargetListener.js
 java/awt/dnd/peer/DropTargetPeer.js
+java/awt/event/AWTEventListener.js
+java/awt/event/ActionEvent.js
 java/awt/event/ActionListener.js
 java/awt/event/AdjustmentEvent.js
 java/awt/event/AdjustmentListener.js
-java/awt/event/AWTEventListener.js
 java/awt/event/ComponentAdapter.js
 java/awt/event/ComponentEvent.js
 java/awt/event/ComponentListener.js
+java/awt/event/ContainerEvent.js
 java/awt/event/ContainerListener.js
+java/awt/event/FocusAdapter.js
 java/awt/event/FocusEvent.js
 java/awt/event/FocusListener.js
 java/awt/event/HierarchyBoundsListener.js
+java/awt/event/HierarchyEvent.js
 java/awt/event/HierarchyListener.js
 java/awt/event/InputEvent.js
 java/awt/event/InputMethodListener.js
 java/awt/event/InvocationEvent.js
 java/awt/event/ItemEvent.js
 java/awt/event/ItemListener.js
+java/awt/event/KeyAdapter.js
+java/awt/event/KeyEvent.js
 java/awt/event/KeyListener.js
+java/awt/event/MouseAdapter.js
 java/awt/event/MouseEvent.js
 java/awt/event/MouseListener.js
+java/awt/event/MouseMotionAdapter.js
 java/awt/event/MouseMotionListener.js
+java/awt/event/MouseWheelEvent.js
 java/awt/event/MouseWheelListener.js
 java/awt/event/TextListener.js
 java/awt/event/WindowAdapter.js
@@ -50,239 +492,491 @@ java/awt/event/WindowEvent.js
 java/awt/event/WindowFocusListener.js
 java/awt/event/WindowListener.js
 java/awt/event/WindowStateListener.js
-java/awt/EventDispatchThread.js
-java/awt/EventFilter.js
-java/awt/EventQueue.js
-java/awt/EventQueueItem.js
-java/awt/FlowLayout.js
-java/awt/FocusTraversalPolicy.js
-java/awt/Font.js
 java/awt/font/FontRenderContext.js
-java/awt/FontMetrics.js
-java/awt/Frame.js
+java/awt/font/TextAttribute.js
 java/awt/geom/AffineTransform.js
 java/awt/geom/Dimension2D.js
 java/awt/geom/Path2D.js
 java/awt/geom/PathIterator.js
 java/awt/geom/Point2D.js
+java/awt/geom/RectIterator.js
 java/awt/geom/Rectangle2D.js
 java/awt/geom/RectangularShape.js
-java/awt/geom/RectIterator.js
-java/awt/GraphicsCallback.js
-java/awt/GraphicsConfiguration.js
-java/awt/GraphicsDevice.js
-java/awt/GraphicsEnvironment.js
+java/awt/image/BufferedImage.js
+java/awt/image/ColorModel.js
+java/awt/image/DataBuffer.js
+java/awt/image/DataBufferInt.js
+java/awt/image/DirectColorModel.js
+java/awt/image/ImageConsumer.js
 java/awt/image/ImageObserver.js
-java/awt/Insets.js
-java/awt/ItemSelectable.js
-java/awt/JSComponent.js
-java/awt/JSDialog.js
-java/awt/JSFrame.js
-java/awt/JSPanel.js
-java/awt/KeyboardFocusManager.js
-java/awt/KeyEventDispatcher.js
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-java/awt/Panel.js
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 java/awt/peer/ComponentPeer.js
 java/awt/peer/ContainerPeer.js
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 java/awt/peer/FramePeer.js
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 java/awt/peer/LightweightPeer.js
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-java/awt/Point.js
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-java/awt/Scrollbar.js
-java/awt/ScrollPane.js
-java/awt/Shape.js
-java/awt/Stroke.js
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-java/awt/TextComponent.js
-java/awt/TextField.js
-java/awt/Toolkit.js
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-java/awt/Window.js
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 java/beans/ChangeListenerMap.js
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 java/beans/PropertyChangeListener.js
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 java/lang/AbstractStringBuilder.js
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 java/lang/Class.js
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 java/math/RoundingMode.js
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 java/net/URL.js
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 java/net/URLStreamHandlerFactory.js
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+java/security/Guard.js
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+java/text/AttributedCharacterIterator.js
 java/text/CharacterIterator.js
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 java/text/DecimalFormat.js
 java/text/DecimalFormatSymbols.js
 java/text/DigitList.js
 java/text/FieldPosition.js
 java/text/Format.js
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 java/text/NumberFormat.js
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 java/util/AbstractCollection.js
 java/util/AbstractList.js
 java/util/AbstractMap.js
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 java/util/AbstractSequentialList.js
 java/util/AbstractSet.js
+java/util/ArrayDeque.js
 java/util/ArrayList.js
 java/util/Arrays.js
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 java/util/Collection.js
 java/util/Collections.js
+java/util/ComparableTimSort.js
 java/util/Comparator.js
 java/util/Deque.js
 java/util/Dictionary.js
+java/util/DualPivotQuicksort.js
+java/util/EnumMap.js
 java/util/Enumeration.js
 java/util/EventListener.js
 java/util/EventObject.js
+java/util/Formatter.js
+java/util/GregorianCalendar.js
 java/util/HashMap.js
 java/util/HashSet.js
 java/util/Hashtable.js
 java/util/IdentityHashMap.js
+java/util/ImmutableCollections.js
 java/util/Iterator.js
 java/util/LinkedHashMap.js
+java/util/LinkedHashSet.js
 java/util/LinkedList.js
 java/util/List.js
-java/util/ListResourceBundle.js
+java/util/ListIterator.js
 java/util/Locale.js
 java/util/Map.js
+java/util/NavigableMap.js
+java/util/NavigableSet.js
 java/util/Objects.js
+java/util/PriorityQueue.js
+java/util/Properties.js
+java/util/PropertyResourceBundle.js
 java/util/Queue.js
 java/util/Random.js
 java/util/RandomAccess.js
 java/util/ResourceBundle.js
+java/util/ServiceLoader.js
 java/util/Set.js
+java/util/SortedMap.js
+java/util/SortedSet.js
+java/util/Spliterator.js
+java/util/StringTokenizer.js
 java/util/TimSort.js
+java/util/TimeZone.js
+java/util/TreeMap.js
+java/util/TreeSet.js
 java/util/Vector.js
-javajs/api/JSFunction.js
+java/util/WeakHashMap.js
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+java/util/concurrent/CompletableFuture.js
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+java/util/concurrent/ConcurrentMap.js
+java/util/concurrent/CopyOnWriteArrayList.js
+java/util/concurrent/CopyOnWriteArraySet.js
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+java/util/concurrent/ForkJoinTask.js
+java/util/concurrent/Future.js
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+java/util/concurrent/LinkedBlockingQueue.js
+java/util/concurrent/RejectedExecutionHandler.js
+java/util/concurrent/RunnableFuture.js
+java/util/concurrent/RunnableScheduledFuture.js
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+java/util/concurrent/ScheduledFuture.js
+java/util/concurrent/ScheduledThreadPoolExecutor.js
+java/util/concurrent/Semaphore.js
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+java/util/concurrent/atomic/AtomicInteger.js
+java/util/concurrent/atomic/AtomicLong.js
+java/util/concurrent/locks/AbstractOwnableSynchronizer.js
+java/util/concurrent/locks/AbstractQueuedSynchronizer.js
+java/util/concurrent/locks/Condition.js
+java/util/concurrent/locks/Lock.js
+java/util/concurrent/locks/ReadWriteLock.js
+java/util/concurrent/locks/ReentrantLock.js
+java/util/concurrent/locks/ReentrantReadWriteLock.js
+java/util/function/Consumer.js
+java/util/function/Function.js
+java/util/function/Predicate.js
+java/util/function/Supplier.js
+java/util/jar/JarEntry.js
+java/util/jar/JarInputStream.js
+java/util/regex/MatchResult.js
+java/util/regex/Matcher.js
+java/util/regex/Pattern.js
+java/util/spi/CalendarDataProvider.js
+java/util/spi/CurrencyNameProvider.js
+java/util/spi/LocaleNameProvider.js
+java/util/spi/LocaleServiceProvider.js
+java/util/spi/TimeZoneNameProvider.js
+java/util/stream/AbstractPipeline.js
+java/util/stream/BaseStream.js
+java/util/stream/MatchOps.js
+java/util/stream/PipelineHelper.js
+java/util/stream/ReferencePipeline.js
+java/util/stream/Sink.js
+java/util/stream/Stream.js
+java/util/stream/StreamOpFlag.js
+java/util/stream/StreamShape.js
+java/util/stream/StreamSupport.js
+java/util/stream/TerminalOp.js
+java/util/zip/CRC32.js
+java/util/zip/Inflater.js
+java/util/zip/InflaterInputStream.js
+java/util/zip/ZipConstants.js
+java/util/zip/ZipEntry.js
+java/util/zip/ZipInputStream.js
+javajs/api/BytePoster.js
+javajs/api/GenericLineReader.js
+javajs/api/GenericOutputChannel.js
+javajs/api/JSONEncodable.js
+javajs/async/SwingJSUtils.js
+javajs/http/ClientProtocolException.js
+javajs/http/HttpClient.js
+javajs/http/HttpClientFactory.js
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+javajs/util/A4.js
+javajs/util/AU.js
 javajs/util/AjaxURLConnection.js
+javajs/util/AjaxURLStreamHandler.js
 javajs/util/AjaxURLStreamHandlerFactory.js
-javajs/util/AU.js
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+javajs/util/Base64.js
+javajs/util/CU.js
+javajs/util/DF.js
+javajs/util/Encoding.js
 javajs/util/JSThread.js
+javajs/util/LimitedLineReader.js
 javajs/util/Lst.js
+javajs/util/M3.js
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 javajs/util/PT.js
+javajs/util/Rdr.js
 javajs/util/SB.js
-javax/net/ssl/HttpsUrlConnection.js
+javajs/util/T3.js
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+javax/net/ssl/HttpsURLConnection.js
 javax/swing/AbstractAction.js
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+javax/swing/AbstractCellEditor.js
 javax/swing/AbstractListModel.js
+javax/swing/AbstractSpinnerModel.js
 javax/swing/Action.js
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 javax/swing/AncestorNotifier.js
 javax/swing/ArrayTable.js
-javax/swing/border/AbstractBorder.js
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-javax/swing/border/Border.js
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-javax/swing/border/EtchedBorder.js
-javax/swing/border/LineBorder.js
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+javax/swing/Box.js
 javax/swing/BoxLayout.js
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 javax/swing/ClientPropertyKey.js
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 javax/swing/DefaultBoundedRangeModel.js
 javax/swing/DefaultButtonModel.js
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+javax/swing/DefaultDesktopManager.js
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 javax/swing/DefaultSingleSelectionModel.js
+javax/swing/DesktopManager.js
 javax/swing/DropMode.js
-javax/swing/event/AncestorEvent.js
-javax/swing/event/AncestorListener.js
-javax/swing/event/CaretEvent.js
-javax/swing/event/CaretListener.js
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-javax/swing/event/ChangeListener.js
-javax/swing/event/DocumentEvent.js
-javax/swing/event/DocumentListener.js
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-javax/swing/event/ListDataListener.js
-javax/swing/event/UndoableEditEvent.js
-javax/swing/event/UndoableEditListener.js
 javax/swing/FocusManager.js
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-javax/swing/LayoutComparator.js
-javax/swing/LayoutFocusTraversalPolicy.js
-javax/swing/SortingFocusTraversalPolicy.js
-javax/swing/SwingContainerOrderFocusTraversalPolicy.js
-javax/swing/SwingDefaultFocusTraversalPolicy.js
+javax/swing/Icon.js
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+javax/swing/InternalFrameFocusTraversalPolicy.js
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 javax/swing/JCheckBoxMenuItem.js
 javax/swing/JComboBox.js
 javax/swing/JComponent.js
+javax/swing/JDesktopPane.js
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 javax/swing/JFrame.js
+javax/swing/JInternalFrame.js
 javax/swing/JLabel.js
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+javax/swing/JList.js
 javax/swing/JMenu.js
 javax/swing/JMenuBar.js
 javax/swing/JMenuItem.js
+javax/swing/JOptionPane.js
 javax/swing/JPanel.js
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+javax/swing/JProgressBar.js
+javax/swing/JRadioButton.js
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 javax/swing/JRootPane.js
 javax/swing/JScrollBar.js
 javax/swing/JScrollPane.js
 javax/swing/JSeparator.js
+javax/swing/JSlider.js
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+javax/swing/JTabbedPane.js
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 javax/swing/JToggleButton.js
+javax/swing/JToolTip.js
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-javax/swing/KeyboardManager.js
+javax/swing/JWindow.js
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+javax/swing/ListCellRenderer.js
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+javax/swing/ListSelectionModel.js
 javax/swing/LookAndFeel.js
 javax/swing/MenuElement.js
+javax/swing/MenuSelectionManager.js
 javax/swing/MutableComboBoxModel.js
-javax/swing/plaf/ActionMapUIResource.js
-javax/swing/plaf/basic/BasicBorders.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/ColorUIResource.js
-javax/swing/plaf/ComponentUI.js
-javax/swing/plaf/DimensionUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/InputMapUIResource.js
-javax/swing/plaf/InsetsUIResource.js
-javax/swing/plaf/UIResource.js
+javax/swing/Popup.js
+javax/swing/PopupFactory.js
 javax/swing/RepaintManager.js
 javax/swing/RootPaneContainer.js
-javax/swing/Scrollable.js
+javax/swing/RowFilter.js
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 javax/swing/SingleSelectionModel.js
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+javax/swing/SortOrder.js
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+javax/swing/SpinnerModel.js
+javax/swing/SpinnerNumberModel.js
+javax/swing/Spring.js
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+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
 javax/swing/SwingPaintEventDispatcher.js
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+javax/swing/Timer.js
+javax/swing/ToolTipManager.js
+javax/swing/TransferHandler.js
+javax/swing/UIDefaults.js
+javax/swing/UIManager.js
+javax/swing/ViewportLayout.js
+javax/swing/WindowConstants.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
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+javax/swing/event/AncestorEvent.js
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+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/ListSelectionEvent.js
+javax/swing/event/ListSelectionListener.js
+javax/swing/event/MenuEvent.js
+javax/swing/event/MenuKeyListener.js
+javax/swing/event/MenuListener.js
+javax/swing/event/MouseInputListener.js
+javax/swing/event/RowSorterEvent.js
+javax/swing/event/RowSorterListener.js
+javax/swing/event/SwingPropertyChangeSupport.js
+javax/swing/event/TableColumnModelEvent.js
+javax/swing/event/TableColumnModelListener.js
+javax/swing/event/TableModelEvent.js
+javax/swing/event/TableModelListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.js
+javax/swing/filechooser/FileFilter.js
+javax/swing/filechooser/FileView.js
+javax/swing/plaf/ActionMapUIResource.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.js
+javax/swing/plaf/ComponentInputMapUIResource.js
+javax/swing/plaf/ComponentUI.js
+javax/swing/plaf/DimensionUIResource.js
+javax/swing/plaf/FontUIResource.js
+javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/basic/BasicGraphicsUtils.js
+javax/swing/table/AbstractTableModel.js
+javax/swing/table/DefaultTableCellRenderer.js
+javax/swing/table/DefaultTableColumnModel.js
+javax/swing/table/DefaultTableModel.js
+javax/swing/table/JTableHeader.js
+javax/swing/table/TableCellEditor.js
+javax/swing/table/TableCellRenderer.js
+javax/swing/table/TableColumn.js
+javax/swing/table/TableColumnModel.js
+javax/swing/table/TableModel.js
+javax/swing/table/TableRowSorter.js
 javax/swing/text/AbstractDocument.js
 javax/swing/text/AttributeSet.js
+javax/swing/text/BoxView.js
 javax/swing/text/Caret.js
+javax/swing/text/CompositeView.js
 javax/swing/text/DefaultCaret.js
 javax/swing/text/DefaultEditorKit.js
+javax/swing/text/DefaultFormatter.js
+javax/swing/text/DefaultFormatterFactory.js
 javax/swing/text/Document.js
+javax/swing/text/DocumentFilter.js
 javax/swing/text/EditorKit.js
 javax/swing/text/Element.js
 javax/swing/text/GapContent.js
 javax/swing/text/GapVector.js
+javax/swing/text/InternationalFormatter.js
 javax/swing/text/JTextComponent.js
 javax/swing/text/MutableAttributeSet.js
+javax/swing/text/NumberFormatter.js
 javax/swing/text/PlainDocument.js
 javax/swing/text/PlainView.js
 javax/swing/text/Position.js
@@ -296,65 +990,380 @@ javax/swing/text/TabExpander.js
 javax/swing/text/TextAction.js
 javax/swing/text/Utilities.js
 javax/swing/text/View.js
+javax/swing/text/WrappedPlainView.js
 javax/swing/tree/TreeNode.js
-javax/swing/UIDefaults.js
-javax/swing/UIManager.js
 javax/swing/undo/AbstractUndoableEdit.js
 javax/swing/undo/CompoundEdit.js
 javax/swing/undo/UndoableEdit.js
-javax/swing/ViewportLayout.js
-javax/swing/WindowConstants.js
-sun/awt/AppContext.js
+javax/xml/bind/ContextFinder.js
+javax/xml/bind/GetPropertyAction.js
+javax/xml/bind/JAXBContext.js
+javax/xml/bind/JAXBContextFactory.js
+javax/xml/bind/JAXBElement.js
+javax/xml/bind/ModuleUtil.js
+javax/xml/bind/ServiceLoaderUtil.js
+javax/xml/bind/Unmarshaller.js
+javax/xml/bind/ValidationEventHandler.js
+javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js
+javax/xml/bind/annotation/adapters/XmlAdapter.js
+javax/xml/bind/helpers/AbstractUnmarshallerImpl.js
+javax/xml/bind/helpers/DefaultValidationEventHandler.js
+javax/xml/datatype/DatatypeFactory.js
+javax/xml/datatype/FactoryFinder.js
+javax/xml/datatype/SecuritySupport.js
+javax/xml/datatype/XMLGregorianCalendar.js
+javax/xml/namespace/QName.js
+javax/xml/stream/XMLInputFactory.js
+javax/xml/stream/XMLStreamConstants.js
+javax/xml/stream/XMLStreamReader.js
+net/miginfocom/layout/AC.js
+net/miginfocom/layout/AnimSpec.js
+net/miginfocom/layout/BoundSize.js
+net/miginfocom/layout/CC.js
+net/miginfocom/layout/ComponentWrapper.js
+net/miginfocom/layout/ConstraintParser.js
+net/miginfocom/layout/ContainerWrapper.js
+net/miginfocom/layout/DimConstraint.js
+net/miginfocom/layout/Grid.js
+net/miginfocom/layout/LC.js
+net/miginfocom/layout/LayoutUtil.js
+net/miginfocom/layout/LinkHandler.js
+net/miginfocom/layout/PlatformDefaults.js
+net/miginfocom/layout/ResizeConstraint.js
+net/miginfocom/layout/UnitValue.js
+net/miginfocom/swing/MigLayout.js
+net/miginfocom/swing/SwingComponentWrapper.js
+net/miginfocom/swing/SwingContainerWrapper.js
+org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js
+org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
+org/jmol/adapter/readers/pdb/PdbReader.js
+org/jmol/adapter/smarter/Atom.js
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+org/jmol/adapter/smarter/AtomSetCollection.js
+org/jmol/adapter/smarter/AtomSetCollectionReader.js
+org/jmol/adapter/smarter/AtomSetObject.js
+org/jmol/adapter/smarter/Bond.js
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+org/jmol/adapter/smarter/Resolver.js
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@@ -362,19 +1371,29 @@ swingjs/plaf/JSButtonUI.js
 swingjs/plaf/JSCheckBoxMenuItemUI.js
 swingjs/plaf/JSCheckBoxUI.js
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+swingjs/plaf/JSComboPopupList.js
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@@ -382,14 +1401,33 @@ swingjs/plaf/JSScrollBarUI.js
 swingjs/plaf/JSScrollPaneUI.js
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+swingjs/plaf/JSToolTipUI.js
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-
-
+swingjs/xml/JSJAXBClass.js
+swingjs/xml/JSJAXBContext.js
+swingjs/xml/JSJAXBContextFactory.js
+swingjs/xml/JSJAXBDatatypeFactory.js
+swingjs/xml/JSJAXBField.js
+swingjs/xml/JSJAXBUnmarshaller.js
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