JAL-3066 update classlist for jalviewjs

diff --git a/utils/jalviewjs/classlists/jalview.txt b/utils/jalviewjs/classlists/jalview.txt
index 739f070..8b37728 100644 (file)
--- a/utils/jalviewjs/classlists/jalview.txt
+++ b/utils/jalviewjs/classlists/jalview.txt
@@ -10,41 +10,50 @@ jalview/analysis/AlignmentAnnotationUtils.js
 jalview/analysis/AlignmentSorter.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/NJTree.js
+jalview/analysis/PCA.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/AlignCalcManagerI2.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/FeatureSettingsModelI.js
+jalview/api/FeatureSettingsControllerI.js
 jalview/api/FeaturesDisplayedI.js
-jalview/api/FeaturesSourceI.js
 jalview/api/JalviewJSApi.js
 jalview/api/OOMHandlerI.js
 jalview/api/PollableAlignCalcWorkerI.js
+jalview/api/RendererListenerI.js
+jalview/api/RotatableCanvasI.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/AppletParams.js
 jalview/bin/ApplicationSingletonProvider.js
@@ -52,16 +61,23 @@ jalview/bin/ArgsParser.js
 jalview/bin/BuildDetails.js
 jalview/bin/Cache.js
 jalview/bin/Jalview.js
+jalview/bin/JalviewJS2.js
 jalview/bin/JalviewJSApp.js
 jalview/bin/JalviewTaskbar.js
+jalview/commands/CommandI.js
+jalview/commands/OrderCommand.js
 jalview/controller/AlignViewController.js
+jalview/controller/FeatureSettingsControllerGuiI.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/AllColsCollection.js
+jalview/datamodel/AllColsIterator.js
+jalview/datamodel/AllRowsCollection.js
+jalview/datamodel/AllRowsIterator.js
 jalview/datamodel/AnnotatedCollectionI.js
 jalview/datamodel/Annotation.js
 jalview/datamodel/BinaryNode.js
@@ -72,18 +88,19 @@ 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/Point.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
@@ -97,9 +114,17 @@ jalview/datamodel/SequenceFeature.js
 jalview/datamodel/SequenceGroup.js
 jalview/datamodel/SequenceI.js
 jalview/datamodel/SequenceNode.js
+jalview/datamodel/SequencePoint.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/FeatureStore.js
 jalview/datamodel/features/SequenceFeatures.js
 jalview/datamodel/features/SequenceFeaturesI.js
@@ -108,6 +133,9 @@ jalview/ext/ensembl/EnsemblGene.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
@@ -121,73 +149,72 @@ jalview/gui/APQHandlers.js
 jalview/gui/AlignFrame.js
 jalview/gui/AlignViewport.js
 jalview/gui/AlignmentPanel.js
-jalview/gui/AnnotationColumnChooser.js
+jalview/gui/AnnotationExporter.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/CutAndPasteTransfer.js
 jalview/gui/Desktop.js
 jalview/gui/FeatureRenderer.js
+jalview/gui/FeatureSettings.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/OverviewCanvas.js
+jalview/gui/OverviewPanel.js
+jalview/gui/PCAPanel.js
 jalview/gui/PaintRefresher.js
+jalview/gui/PairwiseAlignPanel.js
 jalview/gui/PopupMenu.js
 jalview/gui/Preferences.js
 jalview/gui/ProgressBar.js
+jalview/gui/ProgressPanel.js
+jalview/gui/RotatableCanvas.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/StructureViewerBase.js
+jalview/gui/TextColourChooser.js
 jalview/gui/TreeCanvas.js
 jalview/gui/TreePanel.js
+jalview/gui/UserDefinedColours.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/FileFormatException.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/io/StructureFile.js
 jalview/javascript/json/JSON.js
 jalview/javascript/log4j/ConsoleAppender.js
 jalview/javascript/log4j/Layout.js
@@ -201,20 +228,29 @@ jalview/javascript/web/ClientResponse.js
 jalview/javascript/web/WebResource.js
 jalview/jbgui/GAlignFrame.js
 jalview/jbgui/GAlignmentPanel.js
+jalview/jbgui/GCutAndPasteTransfer.js
 jalview/jbgui/GDesktop.js
+jalview/jbgui/GPCAPanel.js
+jalview/jbgui/GPairwiseAlignPanel.js
 jalview/jbgui/GPreferences.js
 jalview/jbgui/GSliderPanel.js
 jalview/jbgui/GStructureChooser.js
+jalview/jbgui/GStructureViewer.js
 jalview/jbgui/GTreePanel.js
+jalview/jbgui/GUserDefinedColours.js
 jalview/jbgui/GWebserviceInfo.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
@@ -224,7 +260,6 @@ 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
@@ -244,6 +279,7 @@ jalview/schemes/StrandColourScheme.js
 jalview/schemes/TCoffeeColourScheme.js
 jalview/schemes/TaylorColourScheme.js
 jalview/schemes/TurnColourScheme.js
+jalview/schemes/UserColourScheme.js
 jalview/schemes/ZappoColourScheme.js
 jalview/structure/AtomSpec.js
 jalview/structure/CommandListener.js
@@ -251,8 +287,13 @@ 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
@@ -263,7 +304,7 @@ 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/CaseInsensitiveString.js
 jalview/util/ColorUtils.js
 jalview/util/Comparison.js
 jalview/util/DBRefUtils.js
@@ -272,18 +313,21 @@ 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/ShiftList.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/OverviewDimensionsShowHidden.js
+jalview/viewmodel/PCAModel.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
@@ -297,6 +341,7 @@ jalview/workers/InformationThread.js
 jalview/workers/StrucConsensusThread.js
 jalview/ws/AWSThread.js
 jalview/ws/AWsJob.js
+jalview/ws/DBRefFetcher.js
 jalview/ws/JobStateSummary.js
 jalview/ws/SequenceFetcher.js
 jalview/ws/ServiceChangeListener.js
@@ -305,6 +350,7 @@ jalview/ws/WSClientI.js
 jalview/ws/WSDiscovererI.js
 jalview/ws/WSMenuEntryProviderI.js
 jalview/ws/api/CancellableI.js
+jalview/ws/api/JPredServiceI.js
 jalview/ws/api/JalviewServiceEndpointProviderI.js
 jalview/ws/api/JalviewWebServiceI.js
 jalview/ws/api/JobId.js
@@ -327,10 +373,12 @@ 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/gui/AnnotationWsJob.js
 jalview/ws/gui/MsaWSJob.js
 jalview/ws/gui/MsaWSThread.js
 jalview/ws/gui/WsJob.js
+jalview/ws/jws2/JPredClient.js
 jalview/ws/jws2/Jws2Client.js
 jalview/ws/jws2/Jws2ClientFactory.js
 jalview/ws/jws2/Jws2Discoverer.js
@@ -344,9 +392,7 @@ 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
@@ -357,8 +403,10 @@ jalview/ws/seqfetcher/ASequenceFetcher.js
 jalview/ws/seqfetcher/DbSourceProxy.js
 jalview/ws/seqfetcher/DbSourceProxyImpl.js
 jalview/ws/sifts/SiftsSettings.js
+jalview/ws/slivkaws/RNAalifoldServiceInstance.js
 jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.js
 jalview/ws/slivkaws/SlivkaDatastore.js
+jalview/ws/slivkaws/SlivkaJPredServiceInstance.js
 jalview/ws/slivkaws/SlivkaMsaServiceInstance.js
 jalview/ws/slivkaws/SlivkaParamSet.js
 jalview/ws/slivkaws/SlivkaWSDiscoverer.js
@@ -369,13 +417,39 @@ 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/CofactorType.js
+jalview/xml/binding/uniprot/CommentType.js
+jalview/xml/binding/uniprot/DbReferenceType.js
+jalview/xml/binding/uniprot/Entry.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/InteractantType.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
 java/applet/AppletContext.js
 java/applet/AppletStub.js
 java/applet/JSApplet.js
@@ -565,6 +639,7 @@ java/lang/Iterable.js
 java/lang/Readable.js
 java/lang/Runtime.js
 java/lang/RuntimePermission.js
+java/lang/Shutdown.js
 java/lang/StringBuffer.js
 java/lang/StringBuilder.js
 java/lang/Thread.js
@@ -587,8 +662,20 @@ java/net/HttpURLConnection.js
 java/net/URI.js
 java/net/URL.js
 java/net/URLConnection.js
+java/net/URLDecoder.js
 java/net/URLStreamHandler.js
 java/net/URLStreamHandlerFactory.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/AccessController.js
 java/security/BasicPermission.js
 java/security/Guard.js
@@ -654,6 +741,7 @@ java/util/Map.js
 java/util/NavigableMap.js
 java/util/NavigableSet.js
 java/util/Objects.js
+java/util/Optional.js
 java/util/PriorityQueue.js
 java/util/Properties.js
 java/util/PropertyResourceBundle.js
@@ -666,6 +754,7 @@ java/util/Set.js
 java/util/SortedMap.js
 java/util/SortedSet.js
 java/util/Spliterator.js
+java/util/Stack.js
 java/util/StringTokenizer.js
 java/util/TimSort.js
 java/util/TimeZone.js
@@ -712,7 +801,6 @@ 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
@@ -743,11 +831,13 @@ java/util/zip/ZipConstants.js
 java/util/zip/ZipEntry.js
 java/util/zip/ZipInputStream.js
 javajs/api/BytePoster.js
+javajs/api/EigenInterface.js
+javajs/api/GenericCifDataParser.js
 javajs/api/GenericLineReader.js
 javajs/api/GenericOutputChannel.js
+javajs/api/Interface.js
 javajs/api/JSONEncodable.js
 javajs/async/SwingJSUtils.js
-javajs/http/ClientProtocolException.js
 javajs/http/HttpClient.js
 javajs/http/HttpClientFactory.js
 javajs/http/SimpleHttpClient.js
@@ -759,7 +849,9 @@ 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/Eigen.js
 javajs/util/Encoding.js
 javajs/util/JSThread.js
 javajs/util/LimitedLineReader.js
@@ -767,11 +859,13 @@ javajs/util/Lst.js
 javajs/util/M3.js
 javajs/util/M34.js
 javajs/util/M4.js
+javajs/util/Measure.js
 javajs/util/OC.js
 javajs/util/P3.js
 javajs/util/P3i.js
 javajs/util/P4.js
 javajs/util/PT.js
+javajs/util/Quat.js
 javajs/util/Rdr.js
 javajs/util/SB.js
 javajs/util/T3.js
@@ -791,7 +885,6 @@ javax/swing/ArrayTable.js
 javax/swing/Autoscroller.js
 javax/swing/BorderFactory.js
 javax/swing/BoundedRangeModel.js
-javax/swing/Box.js
 javax/swing/BoxLayout.js
 javax/swing/ButtonGroup.js
 javax/swing/ButtonModel.js
@@ -803,6 +896,7 @@ javax/swing/ComboBoxModel.js
 javax/swing/ComponentInputMap.js
 javax/swing/DefaultBoundedRangeModel.js
 javax/swing/DefaultButtonModel.js
+javax/swing/DefaultCellEditor.js
 javax/swing/DefaultComboBoxModel.js
 javax/swing/DefaultDesktopManager.js
 javax/swing/DefaultListCellRenderer.js
@@ -820,11 +914,12 @@ javax/swing/JApplet.js
 javax/swing/JButton.js
 javax/swing/JCheckBox.js
 javax/swing/JCheckBoxMenuItem.js
+javax/swing/JColorChooser.js
 javax/swing/JComboBox.js
 javax/swing/JComponent.js
 javax/swing/JDesktopPane.js
 javax/swing/JDialog.js
-javax/swing/JFileChooser.js
+javax/swing/JEditorPane.js
 javax/swing/JFormattedTextField.js
 javax/swing/JFrame.js
 javax/swing/JInternalFrame.js
@@ -846,10 +941,12 @@ javax/swing/JScrollPane.js
 javax/swing/JSeparator.js
 javax/swing/JSlider.js
 javax/swing/JSpinner.js
+javax/swing/JSplitPane.js
 javax/swing/JTabbedPane.js
 javax/swing/JTable.js
 javax/swing/JTextArea.js
 javax/swing/JTextField.js
+javax/swing/JTextPane.js
 javax/swing/JToggleButton.js
 javax/swing/JToolTip.js
 javax/swing/JViewport.js
@@ -869,7 +966,6 @@ javax/swing/Popup.js
 javax/swing/PopupFactory.js
 javax/swing/RepaintManager.js
 javax/swing/RootPaneContainer.js
-javax/swing/RowFilter.js
 javax/swing/RowSorter.js
 javax/swing/ScrollPaneConstants.js
 javax/swing/ScrollPaneLayout.js
@@ -880,8 +976,6 @@ javax/swing/SortOrder.js
 javax/swing/SortingFocusTraversalPolicy.js
 javax/swing/SpinnerModel.js
 javax/swing/SpinnerNumberModel.js
-javax/swing/Spring.js
-javax/swing/SpringLayout.js
 javax/swing/SwingConstants.js
 javax/swing/SwingContainerOrderFocusTraversalPolicy.js
 javax/swing/SwingDefaultFocusTraversalPolicy.js
@@ -901,7 +995,20 @@ 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
@@ -933,8 +1040,6 @@ 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
@@ -967,6 +1072,7 @@ javax/swing/text/DefaultCaret.js
 javax/swing/text/DefaultEditorKit.js
 javax/swing/text/DefaultFormatter.js
 javax/swing/text/DefaultFormatterFactory.js
+javax/swing/text/DefaultStyledDocument.js
 javax/swing/text/Document.js
 javax/swing/text/DocumentFilter.js
 javax/swing/text/EditorKit.js
@@ -975,6 +1081,7 @@ javax/swing/text/GapContent.js
 javax/swing/text/GapVector.js
 javax/swing/text/InternationalFormatter.js
 javax/swing/text/JTextComponent.js
+javax/swing/text/Keymap.js
 javax/swing/text/MutableAttributeSet.js
 javax/swing/text/NumberFormatter.js
 javax/swing/text/PlainDocument.js
@@ -986,11 +1093,15 @@ javax/swing/text/SimpleAttributeSet.js
 javax/swing/text/Style.js
 javax/swing/text/StyleConstants.js
 javax/swing/text/StyleContext.js
+javax/swing/text/StyledDocument.js
+javax/swing/text/StyledEditorKit.js
 javax/swing/text/TabExpander.js
 javax/swing/text/TextAction.js
 javax/swing/text/Utilities.js
 javax/swing/text/View.js
+javax/swing/text/ViewFactory.js
 javax/swing/text/WrappedPlainView.js
+javax/swing/tree/TreeCellEditor.js
 javax/swing/tree/TreeNode.js
 javax/swing/undo/AbstractUndoableEdit.js
 javax/swing/undo/CompoundEdit.js
@@ -1008,14 +1119,16 @@ 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
+mc_view/Atom.js
+mc_view/Bond.js
+mc_view/PDBChain.js
+mc_view/PDBfile.js
+mc_view/Residue.js
 net/miginfocom/layout/AC.js
 net/miginfocom/layout/AnimSpec.js
 net/miginfocom/layout/BoundSize.js
@@ -1034,8 +1147,9 @@ 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
 org/jmol/adapter/readers/pdb/PdbReader.js
 org/jmol/adapter/smarter/Atom.js
 org/jmol/adapter/smarter/AtomIterator.js
@@ -1048,18 +1162,24 @@ 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/GenericMenuInterface.js
 org/jmol/api/GenericMouseInterface.js
 org/jmol/api/GenericPlatform.js
 org/jmol/api/Interface.js
+org/jmol/api/JmolAbstractButton.js
 org/jmol/api/JmolAdapter.js
 org/jmol/api/JmolAdapterAtomIterator.js
 org/jmol/api/JmolAdapterBondIterator.js
 org/jmol/api/JmolAdapterStructureIterator.js
+org/jmol/api/JmolAppConsoleInterface.js
 org/jmol/api/JmolCallbackListener.js
+org/jmol/api/JmolDropEditor.js
+org/jmol/api/JmolFilesReaderInterface.js
 org/jmol/api/JmolGraphicsInterface.js
 org/jmol/api/JmolMeasurementClient.js
 org/jmol/api/JmolPropertyManager.js
@@ -1072,13 +1192,18 @@ org/jmol/api/JmolSelectionListener.js
 org/jmol/api/JmolStatusListener.js
 org/jmol/api/JmolViewer.js
 org/jmol/api/PlatformViewer.js
+org/jmol/api/SC.js
 org/jmol/api/SymmetryInterface.js
 org/jmol/api/Translator.js
 org/jmol/atomdata/AtomDataServer.js
 org/jmol/atomdata/RadiusData.js
 org/jmol/awt/AwtFile.js
 org/jmol/awt/AwtFont.js
+org/jmol/awt/AwtJmolPopup.js
+org/jmol/awt/AwtPopupHelper.js
+org/jmol/awt/AwtSwingComponent.js
 org/jmol/awt/Display.js
+org/jmol/awt/FileDropper.js
 org/jmol/awt/Image.js
 org/jmol/awt/Mouse.js
 org/jmol/awt/Platform.js
@@ -1094,6 +1219,9 @@ org/jmol/c/PAL.js
 org/jmol/c/STER.js
 org/jmol/c/STR.js
 org/jmol/c/VDW.js
+org/jmol/console/GenericConsole.js
+org/jmol/console/JmolButton.js
+org/jmol/console/JmolConsole.js
 org/jmol/g3d/CylinderRenderer.js
 org/jmol/g3d/G3DRenderer.js
 org/jmol/g3d/Graphics3D.js
@@ -1110,6 +1238,7 @@ 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
@@ -1140,8 +1269,16 @@ 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/PhosphorusMonomer.js
 org/jmol/modelsetbio/ProteinStructure.js
 org/jmol/modelsetbio/Sheet.js
+org/jmol/popup/GenericPopup.js
+org/jmol/popup/JmolGenericPopup.js
+org/jmol/popup/JmolPopup.js
+org/jmol/popup/MainPopupResourceBundle.js
+org/jmol/popup/PopupHelper.js
+org/jmol/popup/PopupResource.js
 org/jmol/render/BallsRenderer.js
 org/jmol/render/BbcageRenderer.js
 org/jmol/render/CageRenderer.js
@@ -1155,6 +1292,7 @@ org/jmol/render/ShapeRenderer.js
 org/jmol/render/SticksRenderer.js
 org/jmol/render/TextRenderer.js
 org/jmol/render/UccageRenderer.js
+org/jmol/renderbio/BackboneRenderer.js
 org/jmol/renderbio/BioShapeRenderer.js
 org/jmol/renderbio/CartoonRenderer.js
 org/jmol/renderbio/RocketsRenderer.js
@@ -1171,6 +1309,7 @@ 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
@@ -1189,6 +1328,7 @@ org/jmol/shape/Shape.js
 org/jmol/shape/Sticks.js
 org/jmol/shape/TextShape.js
 org/jmol/shape/Uccage.js
+org/jmol/shapebio/Backbone.js
 org/jmol/shapebio/BioShape.js
 org/jmol/shapebio/BioShapeCollection.js
 org/jmol/shapebio/Cartoon.js
@@ -1198,6 +1338,7 @@ org/jmol/symmetry/SymmetryInfo.js
 org/jmol/symmetry/UnitCell.js
 org/jmol/thread/HoverWatcherThread.js
 org/jmol/thread/JmolThread.js
+org/jmol/thread/SpinThread.js
 org/jmol/thread/TimeoutThread.js
 org/jmol/util/BSUtil.js
 org/jmol/util/BoxInfo.js
@@ -1206,6 +1347,7 @@ org/jmol/util/ColorEncoder.js
 org/jmol/util/CommandHistory.js
 org/jmol/util/DefaultLogger.js
 org/jmol/util/Edge.js
+org/jmol/util/EigenSort.js
 org/jmol/util/Elements.js
 org/jmol/util/Escape.js
 org/jmol/util/Font.js
@@ -1226,6 +1368,8 @@ org/jmol/util/SimpleEdge.js
 org/jmol/util/SimpleNode.js
 org/jmol/util/SimpleUnitCell.js
 org/jmol/util/TempArray.js
+org/jmol/util/Tensor.js
+org/jmol/util/Txt.js
 org/jmol/viewer/ActionManager.js
 org/jmol/viewer/AnimationManager.js
 org/jmol/viewer/ColorManager.js
@@ -1246,9 +1390,10 @@ org/jmol/viewer/Viewer.js
 org/jmol/viewer/binding/Binding.js
 org/jmol/viewer/binding/JmolBinding.js
 org/json/JSONArray.js
-org/json/JSONException.js
 org/json/JSONObject.js
 org/json/JSONTokener.js
+org/openscience/jmol/app/jmolpanel/console/AppConsole.js
+org/openscience/jmol/app/jmolpanel/console/EnterListener.js
 org/xml/sax/AttributeList.js
 org/xml/sax/Attributes.js
 org/xml/sax/ContentHandler.js
@@ -1279,6 +1424,12 @@ sun/font/FontDesignMetrics.js
 sun/java2d/StateTrackable.js
 sun/java2d/StateTrackableDelegate.js
 sun/misc/Unsafe.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/swing/DefaultLookup.js
 sun/swing/StringUIClientPropertyKey.js
 sun/swing/SwingLazyValue.js
@@ -1320,6 +1471,7 @@ sun/util/spi/CalendarProvider.js
 swingjs/JSApp.js
 swingjs/JSAppletThread.js
 swingjs/JSAppletViewer.js
+swingjs/JSCharSet.js
 swingjs/JSDummyApplet.js
 swingjs/JSFocusPeer.js
 swingjs/JSFontMetrics.js
@@ -1364,18 +1516,21 @@ 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/JSButtonUI.js
 swingjs/plaf/JSCheckBoxMenuItemUI.js
 swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSColorChooserUI.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/JSEditorPaneUI.js
 swingjs/plaf/JSEventHandler.js
 swingjs/plaf/JSFormattedTextFieldUI.js
 swingjs/plaf/JSFrameUI.js
@@ -1402,11 +1557,13 @@ swingjs/plaf/JSScrollPaneUI.js
 swingjs/plaf/JSSeparatorUI.js
 swingjs/plaf/JSSliderUI.js
 swingjs/plaf/JSSpinnerUI.js
+swingjs/plaf/JSSplitPaneUI.js
 swingjs/plaf/JSTabbedPaneUI.js
 swingjs/plaf/JSTableHeaderUI.js
 swingjs/plaf/JSTableUI.js
 swingjs/plaf/JSTextAreaUI.js
 swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextPaneUI.js
 swingjs/plaf/JSTextUI.js
 swingjs/plaf/JSToolTipUI.js
 swingjs/plaf/JSViewportUI.js
@@ -1417,7 +1574,6 @@ 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