JAL-3746 update the example corefile for jalviewjs
authorJim Procter <j.procter@dundee.ac.uk>
Mon, 27 Sep 2021 13:29:48 +0000 (14:29 +0100)
committerJim Procter <j.procter@dundee.ac.uk>
Mon, 27 Sep 2021 13:29:48 +0000 (14:29 +0100)
utils/jalviewjs/classlists/jvexamplefile.txt

index ae01fe1..fd38213 100644 (file)
-
-com/stevesoft/pat/Any.js
-com/stevesoft/pat/Bracket.js
-com/stevesoft/pat/Branch.js
-com/stevesoft/pat/CaseMgr.js
-com/stevesoft/pat/DotMulti.js
-com/stevesoft/pat/End.js
-com/stevesoft/pat/FastBracket.js
-com/stevesoft/pat/FastChar.js
-com/stevesoft/pat/FastMulti.js
-com/stevesoft/pat/NUnicodeAlpha.js
-com/stevesoft/pat/NUnicodeCurrency.js
-com/stevesoft/pat/NUnicodeDigit.js
-com/stevesoft/pat/NUnicodeMath.js
-com/stevesoft/pat/NUnicodePunct.js
-com/stevesoft/pat/NUnicodeW.js
-com/stevesoft/pat/NUnicodeWhite.js
-com/stevesoft/pat/NoPattern.js
-com/stevesoft/pat/NullPattern.js
-com/stevesoft/pat/Or.js
-com/stevesoft/pat/OrMark.js
-com/stevesoft/pat/Pattern.js
-com/stevesoft/pat/PatternSub.js
-com/stevesoft/pat/Pthings.js
-com/stevesoft/pat/Range.js
-com/stevesoft/pat/RegHolder.js
-com/stevesoft/pat/RegOpt.js
-com/stevesoft/pat/RegRes.js
-com/stevesoft/pat/Regex.js
-com/stevesoft/pat/ReplaceRule.js
-com/stevesoft/pat/Replacer.js
-com/stevesoft/pat/Rthings.js
-com/stevesoft/pat/Skip.js
-com/stevesoft/pat/StrPos.js
-com/stevesoft/pat/StringLike.js
-com/stevesoft/pat/StringRule.js
-com/stevesoft/pat/SubMark.js
-com/stevesoft/pat/UniValidator.js
-com/stevesoft/pat/UnicodeAlpha.js
-com/stevesoft/pat/UnicodeCurrency.js
-com/stevesoft/pat/UnicodeDigit.js
-com/stevesoft/pat/UnicodeLower.js
-com/stevesoft/pat/UnicodeMath.js
-com/stevesoft/pat/UnicodePunct.js
-com/stevesoft/pat/UnicodeUpper.js
-com/stevesoft/pat/UnicodeW.js
-com/stevesoft/pat/UnicodeWhite.js
-com/stevesoft/pat/Validator.js
-com/stevesoft/pat/oneChar.js
-com/stevesoft/pat/parsePerl.js
-com/stevesoft/pat/patInf.js
-com/stevesoft/pat/patInt.js
-com/stevesoft/pat/wrap/StringWrap.js
+com/stevesoft/pat/Boundary.js
+com/stevesoft/pat/Start.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/AlignmentUtils.js
-jalview/analysis/AnnotationSorter.js
-jalview/analysis/AverageDistanceTree.js
-jalview/analysis/Conservation.js
-jalview/analysis/CrossRef.js
-jalview/analysis/GeneticCodeI.js
-jalview/analysis/GeneticCodes.js
-jalview/analysis/Grouping.js
-jalview/analysis/NJTree.js
-jalview/analysis/SeqsetUtils.js
-jalview/analysis/SequenceIdMatcher.js
-jalview/analysis/TreeBuilder.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/SimilarityParams.js
-jalview/analysis/scoremodels/SimilarityScoreModel.js
-jalview/api/AlignCalcManagerI.js
-jalview/api/AlignCalcWorkerI.js
-jalview/api/AlignViewControllerGuiI.js
-jalview/api/AlignViewControllerI.js
-jalview/api/AlignViewportI.js
-jalview/api/AlignmentColsCollectionI.js
-jalview/api/AlignmentRowsCollectionI.js
-jalview/api/AlignmentViewPanel.js
-jalview/api/BuildDetailsI.js
-jalview/api/DBRefEntryI.js
-jalview/api/FeatureColourI.js
-jalview/api/FeatureRenderer.js
-jalview/api/FeatureSettingsControllerI.js
-jalview/api/FeatureSettingsModelI.js
-jalview/api/FeaturesDisplayedI.js
-jalview/api/OOMHandlerI.js
-jalview/api/RendererListenerI.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/analysis/SimilarityParamsI.js
-jalview/api/structures/JalviewStructureDisplayI.js
-jalview/bin/ArgsParser.js
-jalview/bin/BuildDetails.js
-jalview/bin/Cache.js
-jalview/bin/Jalview.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/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/RangeElementsIterator.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/StartRegionIterator.js
-jalview/datamodel/StructureViewerModel.js
-jalview/datamodel/VisibleColsCollection.js
-jalview/datamodel/VisibleContigsIterator.js
-jalview/datamodel/VisibleRowsCollection.js
-jalview/datamodel/VisibleRowsIterator.js
-jalview/datamodel/features/FeatureAttributes.js
-jalview/datamodel/features/FeatureLocationI.js
-jalview/datamodel/features/FeatureMatcherSet.js
-jalview/datamodel/features/FeatureMatcherSetI.js
-jalview/datamodel/features/FeatureSources.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/EnsemblGenomes.js
-jalview/ext/ensembl/EnsemblRestClient.js
-jalview/ext/ensembl/EnsemblSeqProxy.js
-jalview/ext/ensembl/EnsemblSequenceFetcher.js
-jalview/ext/jmol/JalviewJmolBinding.js
-jalview/ext/jmol/JmolCommands.js
-jalview/ext/jmol/JmolParser.js
-jalview/fts/api/FTSData.js
-jalview/fts/api/FTSDataColumnI.js
-jalview/fts/api/FTSRestClientI.js
-jalview/fts/api/GFTSPanelI.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/core/GFTSPanel.js
-jalview/fts/service/pdb/PDBFTSPanel.js
-jalview/fts/service/pdb/PDBFTSRestClient.js
-jalview/fts/service/uniprot/UniProtFTSRestClient.js
-jalview/fts/service/uniprot/UniprotFTSPanel.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/AppJmol.js
-jalview/gui/AppJmolBinding.js
-jalview/gui/CalculationChooser.js
-jalview/gui/ColourMenuHelper.js
-jalview/gui/ComboBoxTooltipRenderer.js
-jalview/gui/Desktop.js
-jalview/gui/FeatureRenderer.js
-jalview/gui/FeatureSettings.js
-jalview/gui/FeatureTypeSettings.js
-jalview/gui/FontChooser.js
-jalview/gui/IProgressIndicator.js
-jalview/gui/IdCanvas.js
-jalview/gui/IdPanel.js
-jalview/gui/IdwidthAdjuster.js
-jalview/gui/JalviewBooleanRadioButtons.js
-jalview/gui/JalviewChangeSupport.js
-jalview/gui/JalviewColourChooser.js
-jalview/gui/JalviewDialog.js
-jalview/gui/JvSwingUtils.js
-jalview/gui/OverviewCanvas.js
-jalview/gui/OverviewPanel.js
-jalview/gui/PaintRefresher.js
-jalview/gui/PopupMenu.js
-jalview/gui/Preferences.js
-jalview/gui/ProgressBar.js
-jalview/gui/ProgressPanel.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/StructureChooser.js
-jalview/gui/StructureViewer.js
-jalview/gui/StructureViewerBase.js
-jalview/gui/TreeCanvas.js
-jalview/gui/TreePanel.js
-jalview/gui/ViewSelectionMenu.js
-jalview/io/AlignFile.js
-jalview/io/AlignmentFileReaderI.js
-jalview/io/AlignmentFileWriterI.js
-jalview/io/AnnotationFile.js
-jalview/io/AppletFormatAdapter.js
-jalview/io/DataSourceType.js
-jalview/io/FastaFile.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/JPredFile.js
-jalview/io/JalviewFileChooser.js
-jalview/io/JalviewFileFilter.js
-jalview/io/JalviewFileView.js
-jalview/io/JnetAnnotationMaker.js
-jalview/io/NewickFile.js
-jalview/io/PDBFeatureSettings.js
-jalview/io/PIRFile.js
-jalview/io/ScoreMatrixFile.js
-jalview/io/SequenceAnnotationReport.js
-jalview/io/StructureFile.js
-jalview/io/TCoffeeScoreFile.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/BackupFilesPresetEntry.js
-jalview/jbgui/GAlignFrame.js
-jalview/jbgui/GAlignmentPanel.js
-jalview/jbgui/GDesktop.js
-jalview/jbgui/GFontChooser.js
-jalview/jbgui/GPreferences.js
-jalview/jbgui/GSliderPanel.js
-jalview/jbgui/GStructureChooser.js
-jalview/jbgui/GStructureViewer.js
-jalview/jbgui/GTreePanel.js
-jalview/jbgui/IntKeyStringValueEntry.js
-jalview/math/Matrix.js
-jalview/math/MatrixI.js
-jalview/project/Jalview2XML.js
-jalview/renderer/AnnotationRenderer.js
-jalview/renderer/AwtRenderPanelI.js
-jalview/renderer/OverviewRenderer.js
-jalview/renderer/OverviewResColourFinder.js
-jalview/renderer/ResidueColourFinder.js
-jalview/renderer/ResidueShader.js
-jalview/renderer/ResidueShaderI.js
-jalview/renderer/ScaleRenderer.js
-jalview/renderer/seqfeatures/FeatureColourFinder.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/HelixColourScheme.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/StructureListener.js
-jalview/structure/StructureMapping.js
-jalview/structure/StructureMappingcommandSet.js
-jalview/structure/StructureSelectionManager.js
-jalview/structure/VamsasSource.js
-jalview/structures/models/AAStructureBindingModel.js
-jalview/structures/models/SequenceStructureBindingModel.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/CaseInsensitiveString.js
-jalview/util/ColorUtils.js
-jalview/util/Comparison.js
-jalview/util/DBRefUtils.js
-jalview/util/Format.js
-jalview/util/LinkedIdentityHashSet.js
-jalview/util/MapList.js
-jalview/util/MessageManager.js
-jalview/util/Platform.js
-jalview/util/QuickSort.js
-jalview/util/SetUtils.js
-jalview/util/StringUtils.js
-jalview/util/UrlLink.js
-jalview/util/dialogrunner/DialogRunnerI.js
-jalview/util/jarInputStreamProvider.js
-jalview/viewmodel/AlignmentViewport.js
-jalview/viewmodel/OverviewDimensions.js
-jalview/viewmodel/OverviewDimensionsHideHidden.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/AlignCalcManager.js
-jalview/workers/AlignCalcWorker.js
-jalview/workers/ComplementConsensusThread.js
-jalview/workers/ConsensusThread.js
-jalview/workers/ConservationThread.js
-jalview/workers/StrucConsensusThread.js
-jalview/ws/SequenceFetcher.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/ebi/EBIFetchClient.js
-jalview/ws/seqfetcher/ASequenceFetcher.js
-jalview/ws/seqfetcher/DbSourceProxy.js
-jalview/ws/seqfetcher/DbSourceProxyImpl.js
-jalview/ws/sifts/SiftsSettings.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
-jalview/xml/binding/uniprot/CitationType.js
-jalview/xml/binding/uniprot/CommentType.js
-jalview/xml/binding/uniprot/ConsortiumType.js
-jalview/xml/binding/uniprot/DbReferenceType.js
-jalview/xml/binding/uniprot/Entry.js
-jalview/xml/binding/uniprot/EventType.js
-jalview/xml/binding/uniprot/EvidenceType.js
-jalview/xml/binding/uniprot/EvidencedStringType.js
-jalview/xml/binding/uniprot/FeatureType.js
-jalview/xml/binding/uniprot/GeneNameType.js
-jalview/xml/binding/uniprot/GeneType.js
-jalview/xml/binding/uniprot/IsoformType.js
-jalview/xml/binding/uniprot/KeywordType.js
-jalview/xml/binding/uniprot/LocationType.js
-jalview/xml/binding/uniprot/NameListType.js
-jalview/xml/binding/uniprot/OrganismNameType.js
-jalview/xml/binding/uniprot/OrganismType.js
-jalview/xml/binding/uniprot/PersonType.js
-jalview/xml/binding/uniprot/PositionType.js
-jalview/xml/binding/uniprot/PropertyType.js
-jalview/xml/binding/uniprot/ProteinExistenceType.js
-jalview/xml/binding/uniprot/ProteinType.js
-jalview/xml/binding/uniprot/ReferenceType.js
-jalview/xml/binding/uniprot/SequenceType.js
-jalview/xml/binding/uniprot/SourceDataType.js
-jalview/xml/binding/uniprot/SourceType.js
-jalview/xml/binding/uniprot/SubcellularLocationType.js
-jalview/xml/binding/uniprot/Uniprot.js
+jalview/bin/JalviewTaskbar.js
+jalview/datamodel/AlignedCodonFrame.js
+jalview/ext/ensembl/EnsemblFeatures.js
+jalview/ext/ensembl/EnsemblLookup.js
+jalview/ext/ensembl/EnsemblSymbol.js
+jalview/ext/ensembl/EnsemblXref.js
+jalview/ext/ensembl/Species.js
+jalview/fts/api/StructureFTSRestClientI.js
+jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.js
+jalview/gui/APQHandlers.js
+jalview/gui/CrossRefAction.js
+jalview/gui/CutAndPasteTransfer.js
+jalview/gui/JvOptionPane.js
+jalview/gui/SplashScreen.js
+jalview/gui/structurechooser/PDBStructureChooserQuerySource.js
+jalview/gui/structurechooser/StructureChooserQuerySource.js
+jalview/gui/structurechooser/TDBResultAnalyser.js
+jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.js
+jalview/io/gff/SequenceOntologyFactory.js
+jalview/io/gff/SequenceOntologyI.js
+jalview/io/gff/SequenceOntologyLite.js
+jalview/jbgui/FilterOption.js
+jalview/jbgui/GCutAndPasteTransfer.js
+jalview/structure/AtomSpecModel.js
+jalview/structure/StructureCommand.js
+jalview/structure/StructureCommandI.js
+jalview/structure/StructureCommandsBase.js
+jalview/structure/StructureCommandsI.js
+jalview/util/ChannelProperties.js
+jalview/util/HttpUtils.js
+jalview/util/IntRangeComparator.js
+jalview/util/JSONUtils.js
+jalview/util/ShortcutKeyMaskExWrapper.js
+jalview/util/ShortcutKeyMaskExWrapper8.js
+jalview/util/ShortcutKeyMaskExWrapperI.js
+jalview/ws/SequenceFetcherFactory.js
+jalview/ws/dbsources/EBIAlfaFold.js
+jalview/ws/dbsources/EmblFlatfileSource.js
+jalview/ws/utils/UrlDownloadClient.js
+jalview/xml/binding/uniprot/InteractantType.js
+jalview/xml/binding/uniprot/MoleculeType.js
+jalview/xml/binding/uniprot/ReactionType.js
+java/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.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/CardLayout.js
+java/awt/Color.js
+java/awt/Component.js
+java/awt/ComponentOrientation.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/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/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/DataFlavor.js
 java/awt/datatransfer/FlavorMap.js
 java/awt/datatransfer/FlavorTable.js
-java/awt/datatransfer/MimeType.js
-java/awt/datatransfer/MimeTypeParameterList.js
 java/awt/datatransfer/SystemFlavorMap.js
-java/awt/datatransfer/Transferable.js
 java/awt/dnd/DropTarget.js
 java/awt/dnd/DropTargetContext.js
-java/awt/dnd/DropTargetDropEvent.js
-java/awt/dnd/DropTargetEvent.js
 java/awt/dnd/DropTargetListener.js
-java/awt/dnd/peer/DropTargetContextPeer.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/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
+java/awt/event/WindowEvent.js
+java/awt/event/WindowFocusListener.js
+java/awt/event/WindowListener.js
+java/awt/event/WindowStateListener.js
+java/awt/font/FontRenderContext.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/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/image/ImageProducer.js
 java/awt/image/PackedColorModel.js
 java/awt/image/PixelGrabber.js
@@ -494,15 +186,26 @@ java/awt/image/RenderedImage.js
 java/awt/image/SampleModel.js
 java/awt/image/SinglePixelPackedSampleModel.js
 java/awt/image/WritableRaster.js
+java/awt/peer/ComponentPeer.js
+java/awt/peer/ContainerPeer.js
 java/awt/peer/DialogPeer.js
+java/awt/peer/FramePeer.js
 java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/peer/LightweightPeer.js
+java/awt/peer/WindowPeer.js
 java/awt/print/Printable.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyChangeEvent.js
+java/beans/PropertyChangeListener.js
+java/beans/PropertyChangeSupport.js
 java/io/BufferedInputStream.js
 java/io/BufferedReader.js
 java/io/BufferedWriter.js
 java/io/ByteArrayInputStream.js
 java/io/ByteArrayOutputStream.js
 java/io/Closeable.js
+java/io/DataInput.js
+java/io/DataInputStream.js
 java/io/File.js
 java/io/FileDescriptor.js
 java/io/FileInputStream.js
@@ -518,41 +221,44 @@ java/io/ObjectStreamField.js
 java/io/OutputStream.js
 java/io/OutputStreamWriter.js
 java/io/PrintStream.js
-java/io/PrintWriter.js
-java/io/PushbackInputStream.js
 java/io/Reader.js
 java/io/StringReader.js
 java/io/StringWriter.js
 java/io/Writer.js
+java/lang/AbstractStringBuilder.js
 java/lang/AutoCloseable.js
+java/lang/Class.js
+java/lang/Enum.js
 java/lang/Iterable.js
 java/lang/Readable.js
 java/lang/Runtime.js
+java/lang/StringBuffer.js
 java/lang/StringBuilder.js
+java/lang/Thread.js
+java/lang/ThreadGroup.js
+java/lang/ThreadLocal.js
+java/lang/ref/ReferenceQueue.js
+java/lang/reflect/AccessibleObject.js
+java/lang/reflect/AnnotatedElement.js
 java/lang/reflect/Constructor.js
 java/lang/reflect/Method.js
 java/math/BigDecimal.js
 java/math/BigInteger.js
 java/math/MathContext.js
 java/math/RoundingMode.js
+java/net/ContentHandler.js
 java/net/HttpURLConnection.js
-java/net/HttpsURLConnection.js
 java/net/URI.js
+java/net/URL.js
 java/net/URLConnection.js
-java/net/URLDecoder.js
 java/net/URLStreamHandler.js
-java/nio/Bits.js
-java/nio/Buffer.js
-java/nio/ByteBuffer.js
-java/nio/ByteOrder.js
-java/nio/CharBuffer.js
-java/nio/HeapByteBuffer.js
-java/nio/HeapCharBuffer.js
-java/nio/charset/Charset.js
-java/nio/charset/CharsetDecoder.js
-java/nio/charset/CoderResult.js
-java/nio/charset/CodingErrorAction.js
-java/security/AccessControlContext.js
+java/net/URLStreamHandlerFactory.js
+java/net/UnknownHostException.js
+java/nio/file/FileSystem.js
+java/nio/file/FileSystems.js
+java/nio/file/Path.js
+java/nio/file/Watchable.js
+java/nio/file/spi/FileSystemProvider.js
 java/security/AccessController.js
 java/security/PrivilegedAction.js
 java/security/PrivilegedExceptionAction.js
@@ -568,26 +274,46 @@ java/text/Format.js
 java/text/MessageFormat.js
 java/text/NumberFormat.js
 java/text/SimpleDateFormat.js
+java/text/spi/BreakIteratorProvider.js
+java/text/spi/CollatorProvider.js
+java/text/spi/DateFormatProvider.js
+java/text/spi/DateFormatSymbolsProvider.js
+java/text/spi/DecimalFormatSymbolsProvider.js
+java/text/spi/NumberFormatProvider.js
+java/util/AbstractCollection.js
+java/util/AbstractList.js
+java/util/AbstractMap.js
 java/util/AbstractQueue.js
 java/util/AbstractSequentialList.js
+java/util/AbstractSet.js
 java/util/ArrayDeque.js
+java/util/ArrayList.js
+java/util/Arrays.js
 java/util/BitSet.js
 java/util/Calendar.js
 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/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/Iterator.js
 java/util/LinkedHashMap.js
 java/util/LinkedHashSet.js
 java/util/LinkedList.js
 java/util/List.js
 java/util/ListIterator.js
-java/util/ListResourceBundle.js
+java/util/Locale.js
 java/util/Map.js
 java/util/NavigableMap.js
 java/util/NavigableSet.js
@@ -595,16 +321,22 @@ java/util/Objects.js
 java/util/Properties.js
 java/util/PropertyResourceBundle.js
 java/util/Queue.js
+java/util/Random.js
 java/util/RandomAccess.js
+java/util/RandomAccessSubList.js
 java/util/ResourceBundle.js
+java/util/ServiceLoader.js
 java/util/Set.js
 java/util/SortedMap.js
 java/util/SortedSet.js
+java/util/Stack.js
 java/util/StringTokenizer.js
+java/util/SubList.js
 java/util/TimSort.js
 java/util/TimeZone.js
 java/util/TreeMap.js
 java/util/TreeSet.js
+java/util/Vector.js
 java/util/WeakHashMap.js
 java/util/concurrent/AbstractExecutorService.js
 java/util/concurrent/BlockingQueue.js
@@ -619,7 +351,6 @@ java/util/concurrent/Semaphore.js
 java/util/concurrent/ThreadFactory.js
 java/util/concurrent/ThreadPoolExecutor.js
 java/util/concurrent/TimeUnit.js
-java/util/concurrent/atomic/AtomicBoolean.js
 java/util/concurrent/atomic/AtomicInteger.js
 java/util/concurrent/locks/AbstractOwnableSynchronizer.js
 java/util/concurrent/locks/AbstractQueuedSynchronizer.js
@@ -628,14 +359,16 @@ 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/Function.js
 java/util/jar/JarEntry.js
 java/util/jar/JarInputStream.js
-java/util/logging/Level.js
-java/util/logging/Logger.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/zip/CRC32.js
 java/util/zip/Inflater.js
 java/util/zip/InflaterInputStream.js
@@ -647,17 +380,20 @@ javajs/api/GenericCifDataParser.js
 javajs/api/GenericLineReader.js
 javajs/api/GenericOutputChannel.js
 javajs/api/JSONEncodable.js
-javajs/awt/Font.js
-javajs/awt/FontManager.js
 javajs/util/A4.js
+javajs/util/AU.js
+javajs/util/AjaxURLConnection.js
 javajs/util/AjaxURLStreamHandler.js
+javajs/util/AjaxURLStreamHandlerFactory.js
 javajs/util/BS.js
 javajs/util/Base64.js
 javajs/util/CU.js
 javajs/util/CifDataParser.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
 javajs/util/M34.js
 javajs/util/M4.js
@@ -665,96 +401,141 @@ javajs/util/OC.js
 javajs/util/P3.js
 javajs/util/P3i.js
 javajs/util/P4.js
+javajs/util/PT.js
 javajs/util/Rdr.js
 javajs/util/SB.js
 javajs/util/T3.js
 javajs/util/T3i.js
 javajs/util/T4.js
 javajs/util/V3.js
+javax/net/ssl/HttpsURLConnection.js
 javax/swing/AbstractAction.js
-javax/swing/AbstractCellEditor.js
-javax/swing/AbstractSpinnerModel.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
 javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
 javax/swing/Autoscroller.js
-javax/swing/CellEditor.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
 javax/swing/CellRendererPane.js
-javax/swing/ColorChooserDialog.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxEditor.js
+javax/swing/ComboBoxModel.js
 javax/swing/ComponentInputMap.js
-javax/swing/DefaultCellEditor.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
 javax/swing/DefaultDesktopManager.js
 javax/swing/DefaultListCellRenderer.js
 javax/swing/DefaultListSelectionModel.js
 javax/swing/DefaultRowSorter.js
+javax/swing/DefaultSingleSelectionModel.js
 javax/swing/DesktopManager.js
 javax/swing/DropMode.js
+javax/swing/FocusManager.js
 javax/swing/Icon.js
 javax/swing/ImageIcon.js
 javax/swing/InputMap.js
-javax/swing/JColorChooser.js
+javax/swing/InternalFrameFocusTraversalPolicy.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
+javax/swing/JComboBox.js
+javax/swing/JComponent.js
 javax/swing/JDesktopPane.js
 javax/swing/JDialog.js
-javax/swing/JFileChooser.js
-javax/swing/JFormattedTextField.js
+javax/swing/JFrame.js
 javax/swing/JInternalFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
 javax/swing/JList.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.js
 javax/swing/JOptionPane.js
+javax/swing/JPanel.js
+javax/swing/JPopupMenu.js
 javax/swing/JProgressBar.js
-javax/swing/JRadioButton.js
+javax/swing/JRadioButtonMenuItem.js
+javax/swing/JRootPane.js
+javax/swing/JScrollBar.js
 javax/swing/JScrollPane.js
-javax/swing/JSlider.js
-javax/swing/JSpinner.js
+javax/swing/JSeparator.js
 javax/swing/JTabbedPane.js
 javax/swing/JTable.js
 javax/swing/JTextArea.js
 javax/swing/JTextField.js
+javax/swing/JToggleButton.js
 javax/swing/JToolTip.js
 javax/swing/JViewport.js
 javax/swing/JWindow.js
 javax/swing/KeyStroke.js
+javax/swing/KeyboardManager.js
+javax/swing/LayoutComparator.js
+javax/swing/LayoutFocusTraversalPolicy.js
 javax/swing/ListCellRenderer.js
+javax/swing/ListModel.js
 javax/swing/ListSelectionModel.js
+javax/swing/LookAndFeel.js
+javax/swing/MenuElement.js
 javax/swing/MenuSelectionManager.js
+javax/swing/MutableComboBoxModel.js
 javax/swing/Popup.js
 javax/swing/PopupFactory.js
-javax/swing/RowFilter.js
+javax/swing/RepaintManager.js
+javax/swing/RootPaneContainer.js
 javax/swing/RowSorter.js
 javax/swing/ScrollPaneConstants.js
 javax/swing/ScrollPaneLayout.js
 javax/swing/Scrollable.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
 javax/swing/SortOrder.js
-javax/swing/SpinnerModel.js
-javax/swing/SpinnerNumberModel.js
-javax/swing/Spring.js
-javax/swing/SpringLayout.js
+javax/swing/SortingFocusTraversalPolicy.js
+javax/swing/SwingConstants.js
+javax/swing/SwingContainerOrderFocusTraversalPolicy.js
+javax/swing/SwingDefaultFocusTraversalPolicy.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
 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
+javax/swing/border/Border.js
 javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
 javax/swing/border/LineBorder.js
-javax/swing/border/MatteBorder.js
-javax/swing/border/TitledBorder.js
-javax/swing/colorchooser/AbstractColorChooserPanel.js
-javax/swing/colorchooser/CenterLayout.js
-javax/swing/colorchooser/ColorChooserComponentFactory.js
-javax/swing/colorchooser/ColorSelectionModel.js
-javax/swing/colorchooser/DefaultColorSelectionModel.js
-javax/swing/colorchooser/DefaultPreviewPanel.js
-javax/swing/colorchooser/DefaultRGBChooserPanel.js
-javax/swing/colorchooser/DefaultSwatchChooserPanel.js
-javax/swing/colorchooser/MainSwatchPanel.js
-javax/swing/colorchooser/RecentSwatchPanel.js
-javax/swing/colorchooser/SmartGridLayout.js
-javax/swing/colorchooser/SwatchPanel.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
 javax/swing/event/CaretEvent.js
 javax/swing/event/CaretListener.js
 javax/swing/event/CellEditorListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
 javax/swing/event/DocumentEvent.js
 javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/HyperlinkListener.js
 javax/swing/event/InternalFrameAdapter.js
 javax/swing/event/InternalFrameEvent.js
 javax/swing/event/InternalFrameListener.js
+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
@@ -767,17 +548,23 @@ 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
@@ -785,21 +572,18 @@ 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
@@ -813,7 +597,7 @@ javax/swing/text/TabExpander.js
 javax/swing/text/TextAction.js
 javax/swing/text/Utilities.js
 javax/swing/text/View.js
-javax/swing/tree/TreeCellEditor.js
+javax/swing/text/WrappedPlainView.js
 javax/swing/tree/TreeNode.js
 javax/swing/undo/AbstractUndoableEdit.js
 javax/swing/undo/CompoundEdit.js
@@ -831,15 +615,11 @@ 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/XMLGregorianCalendar.js
 javax/xml/namespace/QName.js
 javax/xml/stream/XMLInputFactory.js
+javax/xml/stream/XMLStreamConstants.js
 javax/xml/stream/XMLStreamReader.js
-mc_view/Atom.js
-mc_view/Bond.js
-mc_view/PDBChain.js
-mc_view/Residue.js
 net/miginfocom/layout/AC.js
 net/miginfocom/layout/AnimSpec.js
 net/miginfocom/layout/BoundSize.js
@@ -858,7 +638,6 @@ 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/cif/CifReader.js
 org/jmol/adapter/readers/cif/MMCifReader.js
@@ -874,9 +653,9 @@ org/jmol/adapter/smarter/Resolver.js
 org/jmol/adapter/smarter/SmarterJmolAdapter.js
 org/jmol/adapter/smarter/Structure.js
 org/jmol/adapter/smarter/StructureIterator.js
-org/jmol/adapter/smarter/XtalSymmetry.js
 org/jmol/api/AtomIndexIterator.js
 org/jmol/api/EventManager.js
+org/jmol/api/FontManager.js
 org/jmol/api/GenericFileInterface.js
 org/jmol/api/GenericMouseInterface.js
 org/jmol/api/GenericPlatform.js
@@ -886,9 +665,9 @@ org/jmol/api/JmolAdapterAtomIterator.js
 org/jmol/api/JmolAdapterBondIterator.js
 org/jmol/api/JmolAdapterStructureIterator.js
 org/jmol/api/JmolCallbackListener.js
+org/jmol/api/JmolFilesReaderInterface.js
 org/jmol/api/JmolGraphicsInterface.js
 org/jmol/api/JmolMeasurementClient.js
-org/jmol/api/JmolPropertyManager.js
 org/jmol/api/JmolRendererInterface.js
 org/jmol/api/JmolRepaintManager.js
 org/jmol/api/JmolScriptEvaluator.js
@@ -920,6 +699,8 @@ org/jmol/c/PAL.js
 org/jmol/c/STER.js
 org/jmol/c/STR.js
 org/jmol/c/VDW.js
+org/jmol/dssx/Bridge.js
+org/jmol/dssx/DSSP.js
 org/jmol/g3d/CylinderRenderer.js
 org/jmol/g3d/G3DRenderer.js
 org/jmol/g3d/Graphics3D.js
@@ -936,6 +717,7 @@ org/jmol/i18n/GT.js
 org/jmol/i18n/Language.js
 org/jmol/i18n/Resource.js
 org/jmol/io/FileReader.js
+org/jmol/io/FilesReader.js
 org/jmol/modelset/Atom.js
 org/jmol/modelset/AtomCollection.js
 org/jmol/modelset/AtomIteratorWithinModel.js
@@ -945,9 +727,11 @@ org/jmol/modelset/BondIterator.js
 org/jmol/modelset/BondIteratorSelected.js
 org/jmol/modelset/Chain.js
 org/jmol/modelset/Group.js
+org/jmol/modelset/HBond.js
 org/jmol/modelset/LabelToken.js
 org/jmol/modelset/Measurement.js
 org/jmol/modelset/MeasurementData.js
+org/jmol/modelset/MeasurementPending.js
 org/jmol/modelset/Model.js
 org/jmol/modelset/ModelLoader.js
 org/jmol/modelset/ModelSet.js
@@ -965,12 +749,9 @@ org/jmol/modelsetbio/BioPolymer.js
 org/jmol/modelsetbio/BioResolver.js
 org/jmol/modelsetbio/Helix.js
 org/jmol/modelsetbio/Monomer.js
-org/jmol/modelsetbio/NucleicMonomer.js
-org/jmol/modelsetbio/NucleicPolymer.js
-org/jmol/modelsetbio/PhosphorusMonomer.js
-org/jmol/modelsetbio/PhosphorusPolymer.js
 org/jmol/modelsetbio/ProteinStructure.js
 org/jmol/modelsetbio/Sheet.js
+org/jmol/modelsetbio/Turn.js
 org/jmol/render/BallsRenderer.js
 org/jmol/render/BbcageRenderer.js
 org/jmol/render/CageRenderer.js
@@ -1000,6 +781,7 @@ org/jmol/script/ScriptFunction.js
 org/jmol/script/ScriptManager.js
 org/jmol/script/ScriptMathProcessor.js
 org/jmol/script/ScriptParam.js
+org/jmol/script/ScriptQueueThread.js
 org/jmol/script/ScriptTokenParser.js
 org/jmol/script/T.js
 org/jmol/scriptext/CmdExt.js
@@ -1008,6 +790,7 @@ org/jmol/scriptext/ScriptExt.js
 org/jmol/shape/AtomShape.js
 org/jmol/shape/Balls.js
 org/jmol/shape/Bbcage.js
+org/jmol/shape/Echo.js
 org/jmol/shape/FontLineShape.js
 org/jmol/shape/Frank.js
 org/jmol/shape/Hover.js
@@ -1027,6 +810,7 @@ org/jmol/symmetry/SymmetryInfo.js
 org/jmol/symmetry/UnitCell.js
 org/jmol/thread/HoverWatcherThread.js
 org/jmol/thread/JmolThread.js
+org/jmol/thread/TimeoutThread.js
 org/jmol/util/BSUtil.js
 org/jmol/util/BoxInfo.js
 org/jmol/util/C.js
@@ -1036,6 +820,7 @@ org/jmol/util/DefaultLogger.js
 org/jmol/util/Edge.js
 org/jmol/util/Elements.js
 org/jmol/util/Escape.js
+org/jmol/util/Font.js
 org/jmol/util/GData.js
 org/jmol/util/Geodesic.js
 org/jmol/util/Int2IntHash.js
@@ -1063,7 +848,6 @@ org/jmol/viewer/JC.js
 org/jmol/viewer/ModelManager.js
 org/jmol/viewer/MotionPoint.js
 org/jmol/viewer/MouseState.js
-org/jmol/viewer/PropertyManager.js
 org/jmol/viewer/SelectionManager.js
 org/jmol/viewer/ShapeManager.js
 org/jmol/viewer/StateManager.js
@@ -1072,6 +856,7 @@ org/jmol/viewer/TransformManager.js
 org/jmol/viewer/Viewer.js
 org/jmol/viewer/binding/Binding.js
 org/jmol/viewer/binding/JmolBinding.js
+org/json/simple/parser/ParseException.js
 org/xml/sax/AttributeList.js
 org/xml/sax/Attributes.js
 org/xml/sax/ContentHandler.js
@@ -1079,11 +864,18 @@ org/xml/sax/InputSource.js
 org/xml/sax/Parser.js
 org/xml/sax/XMLReader.js
 org/xml/sax/ext/Attributes2.js
-sun/awt/AWTAccessor.js
+sun/awt/AWTAutoShutdown.js
+sun/awt/AppContext.js
 sun/awt/CausedFocusEvent.js
+sun/awt/ComponentFactory.js
 sun/awt/EventQueueItem.js
-sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/MostRecentKeyValue.js
+sun/awt/MostRecentThreadAppContext.js
+sun/awt/PaintEventDispatcher.js
+sun/awt/PostEventQueue.js
+sun/awt/RequestFocusController.js
 sun/awt/SunGraphicsCallback.js
+sun/awt/SunToolkit.js
 sun/awt/image/DataStealer.js
 sun/awt/image/IntegerComponentRaster.js
 sun/awt/image/IntegerInterleavedRaster.js
@@ -1094,20 +886,18 @@ sun/font/EAttribute.js
 sun/font/FontDesignMetrics.js
 sun/java2d/StateTrackable.js
 sun/java2d/StateTrackableDelegate.js
-sun/nio/cs/ArrayDecoder.js
-sun/nio/cs/HistoricallyNamedCharset.js
-sun/nio/cs/StandardCharsets.js
-sun/nio/cs/ThreadLocalCoders.js
-sun/nio/cs/UTF_8.js
-sun/nio/cs/Unicode.js
+sun/net/www/MessageHeader.js
 sun/swing/DefaultLookup.js
 sun/swing/StringUIClientPropertyKey.js
+sun/swing/SwingLazyValue.js
 sun/swing/SwingUtilities2.js
 sun/swing/UIAction.js
 sun/swing/UIClientPropertyKey.js
 sun/swing/table/DefaultTableCellHeaderRenderer.js
 sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.js
+sun/text/resources/en/FormatData_en.js
+sun/text/resources/en/FormatData_en_GB.js
+sun/text/resources/en/FormatData_en_US.js
 sun/util/calendar/AbstractCalendar.js
 sun/util/calendar/BaseCalendar.js
 sun/util/calendar/CalendarDate.js
@@ -1115,22 +905,56 @@ sun/util/calendar/CalendarSystem.js
 sun/util/calendar/CalendarUtils.js
 sun/util/calendar/Gregorian.js
 sun/util/calendar/ZoneInfo.js
+sun/util/calendar/ZoneInfoFile.js
+sun/util/locale/BaseLocale.js
+sun/util/locale/LanguageTag.js
+sun/util/locale/LocaleUtils.js
+sun/util/locale/provider/AuxLocaleProviderAdapter.js
+sun/util/locale/provider/AvailableLanguageTags.js
+sun/util/locale/provider/CalendarDataProviderImpl.js
+sun/util/locale/provider/CalendarDataUtility.js
+sun/util/locale/provider/CalendarProviderImpl.js
+sun/util/locale/provider/DateFormatProviderImpl.js
+sun/util/locale/provider/JRELocaleProviderAdapter.js
+sun/util/locale/provider/LocaleDataMetaInfo.js
+sun/util/locale/provider/LocaleProviderAdapter.js
+sun/util/locale/provider/LocaleResources.js
+sun/util/locale/provider/LocaleServiceProviderPool.js
+sun/util/locale/provider/ResourceBundleBasedAdapter.js
+sun/util/locale/provider/SPILocaleProviderAdapter.js
 sun/util/resources/LocaleData.js
-swingjs/JSAbstractDocument.js
-swingjs/JSCharSet.js
-swingjs/JSDnD.js
-swingjs/JSDocumentEvent.js
+sun/util/resources/ParallelListResourceBundle.js
+sun/util/spi/CalendarProvider.js
+swingjs/JSApp.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSDummyApplet.js
+swingjs/JSFileSystem.js
 swingjs/JSFocusPeer.js
-swingjs/JSGraphicsCompositor.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
 swingjs/JSImage.js
 swingjs/JSImagekit.js
 swingjs/JSKeyEvent.js
 swingjs/JSMenuManager.js
-swingjs/JSPlainDocument.js
-swingjs/JSTempFile.js
+swingjs/JSMouse.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
 swingjs/a2s/A2SContainer.js
 swingjs/a2s/Dialog.js
-swingjs/api/JSMinimalAbstractDocument.js
+swingjs/api/Interface.js
+swingjs/api/JSUtilI.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5Canvas.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSFunction.js
+swingjs/api/js/JSInterface.js
+swingjs/jquery/JQueryUI.js
 swingjs/json/JSON.js
 swingjs/jzlib/Adler32.js
 swingjs/jzlib/CRC32.js
@@ -1142,42 +966,66 @@ swingjs/jzlib/Inflate.js
 swingjs/jzlib/Inflater.js
 swingjs/jzlib/InflaterInputStream.js
 swingjs/jzlib/ZStream.js
-swingjs/plaf/BasicArrowButton.js
+swingjs/plaf/BasicComboBoxEditor.js
+swingjs/plaf/BasicComboBoxRenderer.js
 swingjs/plaf/BasicHTML.js
+swingjs/plaf/ButtonListener.js
 swingjs/plaf/CellHolder.js
-swingjs/plaf/CenterLayout.js
+swingjs/plaf/DefaultMenuLayout.js
+swingjs/plaf/HTML5LookAndFeel.js
 swingjs/plaf/JSAppletUI.js
-swingjs/plaf/JSColorChooserUI.js
+swingjs/plaf/JSButtonUI.js
+swingjs/plaf/JSCheckBoxMenuItemUI.js
+swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSComboBoxUI.js
+swingjs/plaf/JSComboPopupList.js
+swingjs/plaf/JSComponentUI.js
 swingjs/plaf/JSDesktopIconUI.js
 swingjs/plaf/JSDesktopPaneUI.js
 swingjs/plaf/JSDialogUI.js
-swingjs/plaf/JSFormattedTextFieldUI.js
+swingjs/plaf/JSEventHandler.js
+swingjs/plaf/JSFrameUI.js
 swingjs/plaf/JSGraphicsUtils.js
 swingjs/plaf/JSInternalFrameUI.js
+swingjs/plaf/JSLabelUI.js
+swingjs/plaf/JSLayeredPaneUI.js
+swingjs/plaf/JSLightweightUI.js
 swingjs/plaf/JSListUI.js
+swingjs/plaf/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.js
+swingjs/plaf/JSOptionPaneUI.js
+swingjs/plaf/JSPanelUI.js
+swingjs/plaf/JSPopupMenuSeparatorUI.js
+swingjs/plaf/JSPopupMenuUI.js
 swingjs/plaf/JSPopupUI.js
 swingjs/plaf/JSProgressBarUI.js
+swingjs/plaf/JSRadioButtonMenuItemUI.js
+swingjs/plaf/JSRadioButtonUI.js
+swingjs/plaf/JSRootPaneUI.js
+swingjs/plaf/JSScrollBarUI.js
 swingjs/plaf/JSScrollPaneUI.js
-swingjs/plaf/JSSpinnerUI.js
+swingjs/plaf/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
 swingjs/plaf/JSTabbedPaneUI.js
 swingjs/plaf/JSTableHeaderUI.js
 swingjs/plaf/JSTableUI.js
 swingjs/plaf/JSTextAreaUI.js
 swingjs/plaf/JSTextFieldUI.js
 swingjs/plaf/JSTextUI.js
-swingjs/plaf/JSTextViewUI.js
 swingjs/plaf/JSToolTipUI.js
 swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
 swingjs/plaf/TextListener.js
 swingjs/xml/JSJAXBClass.js
 swingjs/xml/JSJAXBContext.js
 swingjs/xml/JSJAXBContextFactory.js
-swingjs/xml/JSJAXBDatatypeFactory.js
 swingjs/xml/JSJAXBField.js
 swingjs/xml/JSJAXBUnmarshaller.js
 swingjs/xml/JSSAXAttributes.js
 swingjs/xml/JSSAXParser.js
 swingjs/xml/JSXMLGregorianCalendarImpl.js
 swingjs/xml/JSXMLInputFactory.js
-swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Any.js
-swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Boundary.js
+swingjs/xml/JSXMLStreamReader.js