JAL-3033 updated classlist for loading the example file (jim's kitchensink corefile)
authorJim Procter <jprocter@issues.jalview.org>
Mon, 8 Apr 2019 13:23:29 +0000 (14:23 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Mon, 8 Apr 2019 13:23:29 +0000 (14:23 +0100)
classlists/jvexamplefile.txt

index e706bb0..444b0bf 100644 (file)
@@ -1,7 +1,9 @@
-com/stevesoft/pat/Boundary.js
+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
@@ -52,76 +54,542 @@ 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/AlignmentUtils.js
+jalview/analysis/AnnotationSorter.js
+jalview/analysis/Conservation.js
+jalview/analysis/CrossRef.js
 jalview/analysis/GeneticCodeI.js
 jalview/analysis/GeneticCodes.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/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/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/AnnotatedCollectionI.js
+jalview/datamodel/Annotation.js
+jalview/datamodel/BinaryNode.js
+jalview/datamodel/ColumnSelection.js
+jalview/datamodel/ContiguousI.js
 jalview/datamodel/DBRefEntry.js
+jalview/datamodel/DBRefSource.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/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/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
+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/AnnotationLabels.js
+jalview/gui/AnnotationPanel.js
 jalview/gui/AppJmol.js
 jalview/gui/AppJmolBinding.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/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/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/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/AppletFormatAdapter.js
+jalview/io/DataSourceType.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/JalviewFileChooser.js
 jalview/io/JalviewFileFilter.js
 jalview/io/JalviewFileView.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/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/GPreferences.js
 jalview/jbgui/GSliderPanel.js
 jalview/jbgui/GStructureViewer.js
+jalview/jbgui/GTreePanel.js
+jalview/jbgui/IntKeyStringValueEntry.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/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/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/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/awt/AWTKeyStroke.js
+java/awt/AlphaComposite.js
+java/awt/CardLayout.js
+java/awt/Composite.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/FocusTraversalPolicy.js
+java/awt/GridBagConstraints.js
+java/awt/GridBagLayout.js
+java/awt/GridBagLayoutInfo.js
+java/awt/GridLayout.js
+java/awt/Image.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/KeyboardFocusManager.js
+java/awt/SentEvent.js
+java/awt/TextComponent.js
+java/awt/VKCollection.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/ActionEvent.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/ContainerEvent.js
+java/awt/event/FocusAdapter.js
+java/awt/event/KeyAdapter.js
+java/awt/event/KeyEvent.js
+java/awt/event/MouseAdapter.js
+java/awt/event/MouseMotionAdapter.js
+java/awt/event/MouseWheelEvent.js
 java/awt/font/TextAttribute.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/RectIterator.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/ImageProducer.js
+java/awt/image/PackedColorModel.js
 java/awt/image/PixelGrabber.js
+java/awt/image/Raster.js
+java/awt/image/RenderedImage.js
+java/awt/image/SampleModel.js
+java/awt/image/SinglePixelPackedSampleModel.js
+java/awt/image/WritableRaster.js
+java/awt/peer/DialogPeer.js
+java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/print/Printable.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/File.js
+java/io/FileDescriptor.js
+java/io/FileInputStream.js
 java/io/FileOutputStream.js
+java/io/FileReader.js
+java/io/FileSystem.js
 java/io/FilenameFilter.js
+java/io/FilterInputStream.js
 java/io/FilterOutputStream.js
+java/io/InputStream.js
+java/io/InputStreamReader.js
+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/AutoCloseable.js
+java/lang/Iterable.js
+java/lang/Readable.js
+java/lang/Runtime.js
+java/lang/StringBuilder.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/HttpURLConnection.js
+java/net/HttpsURLConnection.js
+java/net/URI.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/security/AccessController.js
+java/security/PrivilegedAction.js
+java/security/PrivilegedExceptionAction.js
+java/text/AttributedCharacterIterator.js
+java/text/CharacterIterator.js
+java/text/DateFormat.js
+java/text/DateFormatSymbols.js
+java/text/DecimalFormat.js
+java/text/DecimalFormatSymbols.js
+java/text/DigitList.js
+java/text/FieldPosition.js
+java/text/Format.js
+java/text/MessageFormat.js
+java/text/NumberFormat.js
+java/text/SimpleDateFormat.js
+java/util/AbstractQueue.js
+java/util/AbstractSequentialList.js
+java/util/ArrayDeque.js
+java/util/BitSet.js
+java/util/Calendar.js
+java/util/Collection.js
+java/util/ComparableTimSort.js
+java/util/Comparator.js
+java/util/Deque.js
+java/util/DualPivotQuicksort.js
+java/util/Enumeration.js
+java/util/GregorianCalendar.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/Map.js
+java/util/NavigableMap.js
+java/util/NavigableSet.js
+java/util/Objects.js
+java/util/Properties.js
+java/util/PropertyResourceBundle.js
+java/util/Queue.js
+java/util/RandomAccess.js
+java/util/ResourceBundle.js
+java/util/Set.js
+java/util/SortedMap.js
+java/util/SortedSet.js
+java/util/StringTokenizer.js
+java/util/TimSort.js
+java/util/TimeZone.js
+java/util/TreeMap.js
+java/util/TreeSet.js
+java/util/concurrent/AbstractExecutorService.js
+java/util/concurrent/BlockingQueue.js
+java/util/concurrent/ConcurrentHashMap.js
+java/util/concurrent/ConcurrentMap.js
+java/util/concurrent/Executor.js
+java/util/concurrent/ExecutorService.js
+java/util/concurrent/Executors.js
+java/util/concurrent/LinkedBlockingQueue.js
+java/util/concurrent/RejectedExecutionHandler.js
+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
+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/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/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/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/AjaxURLStreamHandler.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/LimitedLineReader.js
 javajs/util/M3.js
 javajs/util/M34.js
@@ -130,27 +598,183 @@ javajs/util/OC.js
 javajs/util/P3.js
 javajs/util/P3i.js
 javajs/util/P4.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/swing/AbstractAction.js
+javax/swing/AbstractCellEditor.js
+javax/swing/AbstractSpinnerModel.js
+javax/swing/Action.js
+javax/swing/Autoscroller.js
+javax/swing/CellEditor.js
 javax/swing/CellRendererPane.js
+javax/swing/ColorChooserDialog.js
+javax/swing/ComponentInputMap.js
+javax/swing/DefaultCellEditor.js
+javax/swing/DefaultDesktopManager.js
+javax/swing/DefaultListCellRenderer.js
 javax/swing/DefaultListSelectionModel.js
+javax/swing/DefaultRowSorter.js
+javax/swing/DesktopManager.js
 javax/swing/DropMode.js
+javax/swing/Icon.js
+javax/swing/ImageIcon.js
+javax/swing/InputMap.js
+javax/swing/JColorChooser.js
+javax/swing/JDesktopPane.js
+javax/swing/JDialog.js
 javax/swing/JFileChooser.js
+javax/swing/JFormattedTextField.js
+javax/swing/JInternalFrame.js
 javax/swing/JList.js
+javax/swing/JOptionPane.js
+javax/swing/JProgressBar.js
+javax/swing/JRadioButton.js
+javax/swing/JScrollPane.js
+javax/swing/JSlider.js
+javax/swing/JSpinner.js
+javax/swing/JTabbedPane.js
+javax/swing/JTable.js
+javax/swing/JTextArea.js
+javax/swing/JTextField.js
+javax/swing/JToolTip.js
+javax/swing/JViewport.js
+javax/swing/JWindow.js
+javax/swing/KeyStroke.js
+javax/swing/ListCellRenderer.js
 javax/swing/ListSelectionModel.js
+javax/swing/MenuSelectionManager.js
+javax/swing/Popup.js
+javax/swing/PopupFactory.js
+javax/swing/RowFilter.js
+javax/swing/RowSorter.js
+javax/swing/ScrollPaneConstants.js
+javax/swing/ScrollPaneLayout.js
+javax/swing/Scrollable.js
+javax/swing/SortOrder.js
+javax/swing/SpinnerModel.js
+javax/swing/SpinnerNumberModel.js
 javax/swing/Spring.js
 javax/swing/SpringLayout.js
+javax/swing/Timer.js
+javax/swing/ToolTipManager.js
+javax/swing/ViewportLayout.js
+javax/swing/border/CompoundBorder.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/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/CellEditorListener.js
+javax/swing/event/DocumentEvent.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/InternalFrameAdapter.js
+javax/swing/event/InternalFrameEvent.js
+javax/swing/event/InternalFrameListener.js
+javax/swing/event/ListSelectionEvent.js
 javax/swing/event/ListSelectionListener.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/ComponentInputMapUIResource.js
 javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/basic/BasicBorders.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/Caret.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
+javax/swing/text/Segment.js
+javax/swing/text/SegmentCache.js
+javax/swing/text/SimpleAttributeSet.js
+javax/swing/text/Style.js
+javax/swing/text/StyleConstants.js
+javax/swing/text/StyleContext.js
+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/tree/TreeNode.js
+javax/swing/undo/AbstractUndoableEdit.js
+javax/swing/undo/CompoundEdit.js
+javax/swing/undo/UndoableEdit.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/XMLGregorianCalendar.js
+javax/xml/namespace/QName.js
+javax/xml/stream/XMLInputFactory.js
+javax/xml/stream/XMLStreamReader.js
 mc_view/Atom.js
 mc_view/Bond.js
 mc_view/PDBChain.js
 mc_view/Residue.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
@@ -163,6 +787,7 @@ 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/GenericFileInterface.js
@@ -253,6 +878,10 @@ 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/render/BallsRenderer.js
@@ -356,13 +985,110 @@ org/jmol/viewer/TransformManager.js
 org/jmol/viewer/Viewer.js
 org/jmol/viewer/binding/Binding.js
 org/jmol/viewer/binding/JmolBinding.js
+org/xml/sax/AttributeList.js
+org/xml/sax/Attributes.js
+org/xml/sax/ContentHandler.js
+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/CausedFocusEvent.js
+sun/awt/EventQueueItem.js
+sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/SunGraphicsCallback.js
+sun/awt/image/DataStealer.js
+sun/awt/image/IntegerComponentRaster.js
+sun/awt/image/IntegerInterleavedRaster.js
 sun/awt/image/OffScreenImageSource.js
+sun/awt/image/SunWritableRaster.js
 sun/font/AttributeValues.js
 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/swing/DefaultLookup.js
 sun/swing/StringUIClientPropertyKey.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/util/calendar/AbstractCalendar.js
+sun/util/calendar/BaseCalendar.js
+sun/util/calendar/CalendarDate.js
+sun/util/calendar/CalendarSystem.js
+sun/util/calendar/CalendarUtils.js
+sun/util/calendar/Gregorian.js
+sun/util/calendar/ZoneInfo.js
+sun/util/resources/LocaleData.js
+swingjs/JSAbstractDocument.js
+swingjs/JSCharSet.js
 swingjs/JSDnD.js
+swingjs/JSDocumentEvent.js
+swingjs/JSFocusPeer.js
+swingjs/JSGraphicsCompositor.js
+swingjs/JSImage.js
+swingjs/JSImagekit.js
+swingjs/JSKeyEvent.js
+swingjs/JSMenuManager.js
+swingjs/JSPlainDocument.js
 swingjs/JSTempFile.js
+swingjs/a2s/A2SContainer.js
+swingjs/a2s/Dialog.js
+swingjs/api/JSMinimalAbstractDocument.js
+swingjs/json/JSON.js
+swingjs/jzlib/Adler32.js
+swingjs/jzlib/CRC32.js
+swingjs/jzlib/Checksum.js
+swingjs/jzlib/InfBlocks.js
+swingjs/jzlib/InfCodes.js
+swingjs/jzlib/InfTree.js
+swingjs/jzlib/Inflate.js
+swingjs/jzlib/Inflater.js
+swingjs/jzlib/InflaterInputStream.js
+swingjs/jzlib/ZStream.js
+swingjs/plaf/BasicArrowButton.js
 swingjs/plaf/BasicHTML.js
+swingjs/plaf/CellHolder.js
+swingjs/plaf/CenterLayout.js
+swingjs/plaf/JSAppletUI.js
+swingjs/plaf/JSColorChooserUI.js
+swingjs/plaf/JSDesktopIconUI.js
+swingjs/plaf/JSDesktopPaneUI.js
+swingjs/plaf/JSDialogUI.js
+swingjs/plaf/JSFormattedTextFieldUI.js
+swingjs/plaf/JSGraphicsUtils.js
+swingjs/plaf/JSInternalFrameUI.js
 swingjs/plaf/JSListUI.js
+swingjs/plaf/JSPopupUI.js
+swingjs/plaf/JSProgressBarUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSSpinnerUI.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/TextListener.js
+swingjs/xml/JSJAXBClass.js
+swingjs/xml/JSJAXBContext.js
+swingjs/xml/JSJAXBContextFactory.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/Boundary.js