From: Jim Procter Date: Mon, 27 Sep 2021 13:29:48 +0000 (+0100) Subject: JAL-3746 update the example corefile for jalviewjs X-Git-Tag: Release_2_11_2_0~30^2~8 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=3722152c0d75e33ba4198cf1fc42fff95800c9ab;p=jalview.git JAL-3746 update the example corefile for jalviewjs --- diff --git a/utils/jalviewjs/classlists/jvexamplefile.txt b/utils/jalviewjs/classlists/jvexamplefile.txt index ae01fe1..fd38213 100644 --- a/utils/jalviewjs/classlists/jvexamplefile.txt +++ b/utils/jalviewjs/classlists/jvexamplefile.txt @@ -1,491 +1,183 @@ - -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 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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