From: Jim Procter Date: Mon, 8 Apr 2019 13:23:29 +0000 (+0100) Subject: JAL-3033 updated classlist for loading the example file (jim's kitchensink corefile) X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~167^2~1 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2359e3ec0c8ebbd3c62b029453bd77122cdede4f JAL-3033 updated classlist for loading the example file (jim's kitchensink corefile) --- diff --git a/classlists/jvexamplefile.txt b/classlists/jvexamplefile.txt index e706bb0..444b0bf 100644 --- a/classlists/jvexamplefile.txt +++ b/classlists/jvexamplefile.txt @@ -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