added _j2sclasslist.txt for buildcore.xml and

jalview_bin_JalviewJS_core.html

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
index 27ab6a6..5d60006 100644 (file)
--- a/_j2sclasslist.txt
+++ b/_j2sclasslist.txt
@@ -1,13 +1,20 @@
 jalview/analysis/AAFrequency.js
 jalview/analysis/AlignSeq.js
+jalview/analysis/AlignmentAnnotationUtils.js
+jalview/analysis/AlignmentUtils.js
 jalview/analysis/AnnotationSorter.js
 jalview/analysis/Conservation.js
 jalview/analysis/CrossRef.js
+jalview/analysis/NJTree.js
+jalview/analysis/SeqsetUtils.js
+jalview/analysis/TreeBuilder.js
+jalview/analysis/TreeModel.js
 jalview/analysis/scoremodels/DistanceScoreModel.js
 jalview/analysis/scoremodels/FeatureDistanceModel.js
 jalview/analysis/scoremodels/PIDModel.js
 jalview/analysis/scoremodels/ScoreMatrix.js
 jalview/analysis/scoremodels/ScoreModels.js
+jalview/analysis/scoremodels/SimilarityParams.js
 jalview/analysis/scoremodels/SimilarityScoreModel.js
 jalview/api/AlignCalcManagerI.js
 jalview/api/AlignCalcWorkerI.js
@@ -25,6 +32,7 @@ jalview/api/StructureSelectionManagerProvider.js
 jalview/api/ViewStyleI.js
 jalview/api/analysis/PairwiseScoreModelI.js
 jalview/api/analysis/ScoreModelI.js
+jalview/api/analysis/SimilarityParamsI.js
 jalview/bin/ArgsParser.js
 jalview/bin/BuildDetails.js
 jalview/bin/Cache.js
@@ -36,8 +44,13 @@ jalview/datamodel/ASequenceI.js
 jalview/datamodel/Alignment.js
 jalview/datamodel/AlignmentAnnotation.js
 jalview/datamodel/AlignmentI.js
+jalview/datamodel/AlignmentView.js
 jalview/datamodel/AnnotatedCollectionI.js
 jalview/datamodel/Annotation.js
+jalview/datamodel/BinaryNode.js
+jalview/datamodel/CigarArray.js
+jalview/datamodel/CigarBase.js
+jalview/datamodel/CigarSimple.js
 jalview/datamodel/ColumnSelection.js
 jalview/datamodel/ContiguousI.js
 jalview/datamodel/DBRefSource.js
@@ -51,15 +64,18 @@ jalview/datamodel/ProfileI.js
 jalview/datamodel/Profiles.js
 jalview/datamodel/ProfilesI.js
 jalview/datamodel/Range.js
+jalview/datamodel/RangeIterator.js
 jalview/datamodel/ResidueCount.js
 jalview/datamodel/SearchResults.js
 jalview/datamodel/SearchResultsI.js
+jalview/datamodel/SeqCigar.js
 jalview/datamodel/Sequence.js
 jalview/datamodel/SequenceCollectionI.js
 jalview/datamodel/SequenceCursor.js
 jalview/datamodel/SequenceFeature.js
 jalview/datamodel/SequenceGroup.js
 jalview/datamodel/SequenceI.js
+jalview/datamodel/SequenceNode.js
 jalview/datamodel/features/FeatureLocationI.js
 jalview/datamodel/features/FeatureMatcher.js
 jalview/datamodel/features/FeatureMatcherI.js
@@ -74,7 +90,9 @@ jalview/gui/AlignViewport.js
 jalview/gui/AlignmentPanel.js
 jalview/gui/AnnotationLabels.js
 jalview/gui/AnnotationPanel.js
+jalview/gui/CalculationChooser.js
 jalview/gui/ColourMenuHelper.js
+jalview/gui/ComboBoxTooltipRenderer.js
 jalview/gui/Desktop.js
 jalview/gui/FeatureRenderer.js
 jalview/gui/IProgressIndicator.js
@@ -84,11 +102,15 @@ jalview/gui/IdwidthAdjuster.js
 jalview/gui/JalviewChangeSupport.js
 jalview/gui/JvSwingUtils.js
 jalview/gui/PaintRefresher.js
+jalview/gui/PopupMenu.js
+jalview/gui/Preferences.js
 jalview/gui/ProgressBar.js
 jalview/gui/ScalePanel.js
 jalview/gui/SeqCanvas.js
 jalview/gui/SeqPanel.js
 jalview/gui/SequenceRenderer.js
+jalview/gui/TreeCanvas.js
+jalview/gui/TreePanel.js
 jalview/gui/ViewSelectionMenu.js
 jalview/io/AlignFile.js
 jalview/io/AlignmentFileReaderI.js
@@ -114,6 +136,10 @@ jalview/javascript/log4j/spi/OptionHandler.js
 jalview/jbgui/GAlignFrame.js
 jalview/jbgui/GAlignmentPanel.js
 jalview/jbgui/GDesktop.js
+jalview/jbgui/GPreferences.js
+jalview/jbgui/GTreePanel.js
+jalview/math/Matrix.js
+jalview/math/MatrixI.js
 jalview/project/Jalview2XML.js
 jalview/renderer/AnnotationRenderer.js
 jalview/renderer/AwtRenderPanelI.js
@@ -152,7 +178,16 @@ jalview/structure/SequenceListener.js
 jalview/structure/StructureImportSettings.js
 jalview/structure/StructureSelectionManager.js
 jalview/structure/VamsasSource.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/ColorUtils.js
 jalview/util/Comparison.js
 jalview/util/DBRefUtils.js
@@ -160,6 +195,8 @@ jalview/util/Format.js
 jalview/util/MessageManager.js
 jalview/util/Platform.js
 jalview/util/QuickSort.js
+jalview/util/StringUtils.js
+jalview/util/UrlLink.js
 jalview/util/jarInputStreamProvider.js
 jalview/util/matcher/Condition.js
 jalview/util/matcher/Matcher.js
@@ -191,19 +228,67 @@ 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/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/awt/AWTEvent.js
+java/awt/AWTEventMulticaster.js
 java/awt/AWTKeyStroke.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
 java/awt/AlphaComposite.js
+java/awt/BasicStroke.js
+java/awt/BorderLayout.js
+java/awt/Color.js
+java/awt/Component.js
+java/awt/ComponentOrientation.js
 java/awt/Composite.js
+java/awt/Container.js
 java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Cursor.js
 java/awt/DefaultFocusTraversalPolicy.js
 java/awt/DefaultKeyboardFocusManager.js
+java/awt/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/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/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/FlavorMap.js
 java/awt/datatransfer/FlavorTable.js
@@ -212,28 +297,73 @@ java/awt/dnd/DropTarget.js
 java/awt/dnd/DropTargetContext.js
 java/awt/dnd/DropTargetListener.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/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/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/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/ImageObserver.js
 java/awt/image/PackedColorModel.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/ComponentPeer.js
+java/awt/peer/ContainerPeer.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/ByteArrayInputStream.js
@@ -241,17 +371,24 @@ java/io/Closeable.js
 java/io/File.js
 java/io/FileDescriptor.js
 java/io/FileInputStream.js
+java/io/FileReader.js
 java/io/FileSystem.js
 java/io/FilterInputStream.js
 java/io/InputStream.js
 java/io/InputStreamReader.js
 java/io/PushbackInputStream.js
 java/io/Reader.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/reflect/Constructor.js
 java/lang/reflect/Method.js
 java/math/BigDecimal.js
@@ -260,9 +397,22 @@ java/math/MathContext.js
 java/math/RoundingMode.js
 java/net/HttpURLConnection.js
 java/net/MalformedURLException.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/AccessControlContext.js
 java/security/AccessController.js
 java/security/PrivilegedAction.js
@@ -279,22 +429,38 @@ java/text/Format.js
 java/text/MessageFormat.js
 java/text/NumberFormat.js
 java/text/SimpleDateFormat.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/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/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/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
@@ -311,6 +477,8 @@ java/util/StringTokenizer.js
 java/util/TimSort.js
 java/util/TimeZone.js
 java/util/TreeMap.js
+java/util/TreeSet.js
+java/util/Vector.js
 java/util/concurrent/AbstractExecutorService.js
 java/util/concurrent/BlockingQueue.js
 java/util/concurrent/ConcurrentHashMap.js
@@ -337,6 +505,8 @@ 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
@@ -345,38 +515,127 @@ java/util/zip/ZipConstants.js
 java/util/zip/ZipEntry.js
 java/util/zip/ZipInputStream.js
 javajs/api/GenericLineReader.js
+javajs/api/JSFunction.js
 javajs/api/JSONEncodable.js
+javajs/util/AU.js
+javajs/util/AjaxURLConnection.js
 javajs/util/AjaxURLStreamHandler.js
+javajs/util/AjaxURLStreamHandlerFactory.js
 javajs/util/Encoding.js
+javajs/util/JSThread.js
+javajs/util/Lst.js
+javajs/util/PT.js
 javajs/util/Rdr.js
 javajs/util/SB.js
 javax/swing/AbstractAction.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/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxModel.js
 javax/swing/ComponentInputMap.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
 javax/swing/DefaultDesktopManager.js
+javax/swing/DefaultListCellRenderer.js
+javax/swing/DefaultSingleSelectionModel.js
 javax/swing/DesktopManager.js
 javax/swing/InputMap.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/JFrame.js
 javax/swing/JInternalFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.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/JSeparator.js
 javax/swing/JTabbedPane.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/ListCellRenderer.js
+javax/swing/ListModel.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/RepaintManager.js
+javax/swing/RootPaneContainer.js
 javax/swing/ScrollPaneConstants.js
 javax/swing/ScrollPaneLayout.js
 javax/swing/Scrollable.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
+javax/swing/SwingConstants.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
 javax/swing/Timer.js
 javax/swing/ToolTipManager.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/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
 javax/swing/border/LineBorder.js
+javax/swing/border/TitledBorder.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
+javax/swing/event/EventListenerList.js
 javax/swing/event/InternalFrameAdapter.js
 javax/swing/event/InternalFrameEvent.js
 javax/swing/event/InternalFrameListener.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/MenuKeyListener.js
 javax/swing/event/MenuListener.js
+javax/swing/event/TableModelListener.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/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/table/AbstractTableModel.js
+javax/swing/table/TableModel.js
 javax/xml/bind/ContextFinder.js
 javax/xml/bind/GetPropertyAction.js
 javax/xml/bind/JAXBContext.js
@@ -395,6 +654,9 @@ javax/xml/namespace/QName.js
 javax/xml/stream/XMLInputFactory.js
 javax/xml/stream/XMLStreamReader.js
 org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js
+org/json/simple/parser/JSONParser.js
+org/json/simple/parser/ParseException.js
+org/json/simple/parser/Yylex.js
 org/xml/sax/AttributeList.js
 org/xml/sax/Attributes.js
 org/xml/sax/ContentHandler.js
@@ -403,9 +665,21 @@ 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/WindowClosingListener.js
+sun/awt/WindowClosingSupport.js
 sun/awt/image/DataStealer.js
 sun/awt/image/IntegerComponentRaster.js
 sun/awt/image/IntegerInterleavedRaster.js
@@ -413,7 +687,15 @@ sun/awt/image/SunWritableRaster.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/SwingLazyValue.js
+sun/swing/UIAction.js
 sun/text/resources/FormatData.js
 sun/text/resources/FormatData_en.js
 sun/util/calendar/AbstractCalendar.js
@@ -424,8 +706,30 @@ sun/util/calendar/CalendarUtils.js
 sun/util/calendar/Gregorian.js
 sun/util/calendar/ZoneInfo.js
 sun/util/resources/LocaleData.js
-swingjs/JSFocusManager.js
+swingjs/JSApp.js
+swingjs/JSApplet.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSCharSet.js
+swingjs/JSFocusPeer.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
+swingjs/JSKeyEvent.js
+swingjs/JSMenuManager.js
+swingjs/JSMouse.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
 swingjs/a2s/Dialog.js
+swingjs/api/Interface.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSInterface.js
+swingjs/jquery/JQueryUI.js
 swingjs/jzlib/Adler32.js
 swingjs/jzlib/CRC32.js
 swingjs/jzlib/Checksum.js
@@ -436,16 +740,45 @@ swingjs/jzlib/Inflate.js
 swingjs/jzlib/Inflater.js
 swingjs/jzlib/InflaterInputStream.js
 swingjs/jzlib/ZStream.js
+swingjs/plaf/ButtonListener.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/JSComboBoxUI.js
+swingjs/plaf/JSComponentUI.js
 swingjs/plaf/JSDesktopIconUI.js
 swingjs/plaf/JSDesktopPaneUI.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/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.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/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
 swingjs/plaf/JSTabbedPaneUI.js
 swingjs/plaf/JSToolTipUI.js
 swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
 swingjs/xml/JSJAXBClass.js
 swingjs/xml/JSJAXBContext.js
 swingjs/xml/JSJAXBContextFactory.js
@@ -455,4 +788,4 @@ swingjs/xml/JSSAXAttributes.js
 swingjs/xml/JSSAXParser.js
 swingjs/xml/JSXMLGregorianCalendarImpl.js
 swingjs/xml/JSXMLInputFactory.js
-swingjs/xml/JSXMLStreamReader.js
\ No newline at end of file
+swingjs/xml/JSXMLStreamReader.js

diff --git a/site-resources/jalview_bin_JalviewJS_core.html b/site-resources/jalview_bin_JalviewJS_core.html
index b883409..abc7b7f 100644 (file)
--- a/site-resources/jalview_bin_JalviewJS_core.html
+++ b/site-resources/jalview_bin_JalviewJS_core.html
@@ -26,7 +26,7 @@ SwingJS.getApplet('testApplet', Info)
 getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
 </script>
 <div style="position:absolute;left:900px;top:30px;width:600px;height:300px;">
-<div id="sysoutdiv" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
+<div id="sysoutdiv" contenteditable="true" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
 This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
 </div>
 </body>