X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=buildSite.xml;h=9d98c85098c70207d15df8295eddad2dfe85ee9c;hp=e5c75c27b94d21a5314118324e0276a895f4fcb6;hb=e34e405ef01487083cc29d8b9a2f96143cbfe6a3;hpb=b9b7a352eee79b7764c3b09c9d19663075061d8c

diff --git a/buildSite.xml b/buildSite.xml
index e5c75c2..9d98c85 100644
--- a/buildSite.xml
+++ b/buildSite.xml
@@ -17,6 +17,13 @@
       </fileset>
     </copy>
    	  	
+  	<echo>...adding package.js from ${project.path}/package</echo>
+   	<copy todir="site/j2s/core">
+  	  <fileset dir="${project.path}/package">
+  	    <include name="package.js" />
+  	  </fileset>
+    </copy>
+
 
   	<echo>...adding to /j2s all src property and css files -- adjust as necessary</echo>
   	<copy todir="site/j2s"  overwrite="true" >
@@ -41,7 +48,7 @@
   	<replace dir="site/j2s" includes="**/*.js" token="Class.forName" value="Clazz._4Name"/>
     <echo>...replacing JavaObject with Clazz._O</echo>
   	<replace dir="site/j2s" includes="**/*.js" token=" JavaObject" value=" Clazz._O"/>
-    <echo>...removing all $fz references for sub/superclass common private function names</echo>
+    <echo>...removing all $fz references for sub/superclass common private function names (not recommended, actually -- see note in Bob's log)</echo>
   	<replace dir="site/j2s" includes="**/*.js" token="($fz =" value=""/>
   	<replace dir="site/j2s" includes="**/*.js" token=", $fz.isPrivate = true, $fz)" value=""/>
   	<echo>...changing Clazz.pu$h() to Clazz.pu$h(self.c$) (only a partial fix)</echo>
@@ -71,394 +78,27 @@
     	
 -->    
 
-   	<!-- 
-
-   	<echo>creating minimal core.z.js</echo>
+   	<echo>creating minimal corejalview.z.js</echo>
   	
     <antcall target="call-core">
-        <param name="call-core.name" value="swingjs" />
+        <param name="call-core.name" value="jalview" />
         <param name="call-core.list" value="
-       		../js/JSmolJavaExt.js
-            java/awt/BasicStroke.js
-            java/awt/Stroke.js
-            java/util/Locale.js
-            java/util/ResourceBundle.js
-            JU/Rdr.js
-            javajs/api/GenericLineReader.js
-            java/io/BufferedInputStream.js
-            java/io/FilterInputStream.js
-            java/io/InputStream.js
-            java/io/BufferedReader.js
-            java/io/ByteArrayInputStream.js
-            java/io/Reader.js	        	
-            java/io/StringReader.js
-            JU/Base64.js
-            JU/Encoding.js
-            java/util/MissingResourceException.js
-        	
-
-            jssun/misc/MessageUtils.js
-            java/awt/Dimension.js
-            java/awt/geom/Dimension2D.js
-            java/awt/Panel.js
-            java/util/ArrayList.js
-            java/util/AbstractList.js
-            java/util/AbstractCollection.js
-            java/awt/ComponentOrientation.js
-            java/security/AccessController.js
-            java/security/AccessControlContext.js
-            java/util/HashMap.js
-            java/util/MapEntry.js
-            java/util/AbstractSet.js
-            java/util/AbstractMap.js
-            java/awt/image/ImageObserver.js
-            java/lang/Enum.js
-            java/applet/AppletStub.js
-            java/applet/AppletContext.js
-            javajs/api/JSInterface.js
-            java/lang/StringBuilder.js
-            java/lang/AbstractStringBuilder.js
-            java/util/Arrays.js
-            java/util/Locale.js
-            java/awt/event/ActionListener.js
-            java/awt/event/AdjustmentListener.js
-            java/awt/event/ComponentListener.js
-            java/awt/event/ContainerListener.js
-            java/awt/event/FocusListener.js
-            java/awt/event/HierarchyBoundsListener.js
-            java/awt/event/HierarchyListener.js
-            java/awt/event/InputMethodListener.js
-            java/awt/event/ItemListener.js
-            java/awt/event/KeyListener.js
-            java/awt/event/MouseListener.js
-            java/awt/event/MouseMotionListener.js
-            java/awt/event/MouseWheelListener.js
-            java/awt/event/TextListener.js
-            java/awt/event/WindowFocusListener.js
-            java/awt/event/WindowListener.js
-            java/awt/event/WindowStateListener.js
-            java/awt/Cursor.js
-            java/awt/AWTError.js
-            java/awt/Insets.js
-            java/awt/RenderingHints.js
-            java/util/Collections.js
-        	java/util/SortedMap.js
-            java/util/SortedSet.js
-            java/util/Random.js
-            java/awt/event/AWTEventListenerProxy.js
-            java/beans/PropertyChangeSupport.js
-            java/beans/ChangeListenerMap.js
-            java/beans/IndexedPropertyChangeEvent.js
-            java/beans/PropertyChangeEvent.js
-            java/beans/PropertyChangeListenerProxy.js
-            java/beans/PropertyChangeListener.js
-            java/security/PrivilegedAction.js
-            java/awt/Point.js
-            jssun/awt/AppContext.js
-            java/lang/StringBuffer.js
-            java/util/IdentityHashMap.js
-            java/util/HashSet.js
-            jssun/awt/ComponentFactory.js
-            jssun/awt/WindowClosingListener.js
-            jssun/awt/WindowClosingSupport.js
-            java/awt/Window.js
-            java/util/Vector.js
-            java/awt/Color.js
-            java/awt/Paint.js
-            java/awt/Transparency.js
-            java/awt/ColorPaintContext.js
-            java/awt/PaintContext.js
-            java/awt/image/ColorModel.js
-            java/awt/color/ColorSpace.js
-            java/util/ResourceBundle.js
-            java/applet/Applet.js
-            java/net/URL.js
-            java/util/Hashtable.js
-            java/util/Dictionary.js
-            java/net/MalformedURLException.js
-            java/awt/GraphicsEnvironment.js
-            java/awt/event/WindowEvent.js
-            javax/swing/JComponent.js
-            javax/swing/Action.js
-            javax/swing/SwingUtilities.js
-            java/awt/Frame.js
-            java/awt/IllegalComponentStateException.js
-            javax/swing/SwingConstants.js
-            java/awt/Rectangle.js
-            java/awt/Shape.js
-            java/awt/geom/Rectangle2D.js
-            java/awt/geom/RectangularShape.js
-            java/awt/geom/FlatteningPathIterator.js
-            java/awt/geom/PathIterator.js
-            java/awt/geom/CubicCurve2D.js
-            java/awt/geom/CubicIterator.js
-            java/awt/geom/Line2D.js
-            java/awt/geom/LineIterator.js
-            java/awt/geom/QuadCurve2D.js
-            java/awt/geom/QuadIterator.js
-            jssun/awt/geom/Curve.js
-            java/awt/geom/IllegalPathStateException.js
-            java/awt/geom/RectIterator.js
-            java/awt/event/ActionEvent.js
-            java/awt/event/KeyEvent.js
-            java/awt/event/MouseWheelEvent.js
-            javax/swing/AbstractAction.js
-            javax/swing/AbstractButton.js
-            javax/swing/ArrayTable.js
-            javax/swing/event/SwingPropertyChangeSupport.js
-            javax/swing/JLayeredPane.js
-            javax/swing/JPanel.js
-            javax/swing/MultiUIDefaults.js
-
-            java/awt/Font.js
-            java/awt/font/TextAttribute.js
-            java/text/AttributedCharacterIterator.js
-            java/text/CharacterIterator.js
-        	java/awt/geom/Point2D.js
-            java/awt/geom/AffineTransform.js
-            java/awt/geom/NoninvertibleTransformException.js
-            java/awt/geom/Path2D.js
-            javax/swing/Icon.js
-            javax/swing/JPasswordField.js
-            javax/swing/JTextField.js
-            javax/swing/ActionPropertyChangeListener.js
-            javax/swing/event/ChangeListener.js
-            javax/swing/ActionMap.js
-            javax/swing/InputMap.js
-            javax/swing/Scrollable.js
-            javax/swing/event/CaretEvent.js
-            javax/swing/event/DocumentListener.js
-            javax/swing/event/EventListenerList.js
-            javax/swing/event/ChangeEvent.js
-            jssun/swing/StringUIClientPropertyKey.js
-            jssun/swing/UIClientPropertyKey.js
-            java/awt/Graphics2D.js
-            java/awt/Graphics.js
-            jssun/font/FontDesignMetrics.js
-            java/awt/FontMetrics.js
-            
-            JU/PT.js
-            javajs/api/JSONEncodable.js
-            JU/AU.js
-            JU/Lst.js
-            JU/DF.js
-            JU/SB.js
-            JU/M34.js
-            JU/M4.js
-            JU/T3.js
-            javax/swing/JRootPane.js
-   	
-            javax/swing/JToggleButton.js
-            javax/swing/ButtonModel.js
-            javax/swing/JRadioButton.js
-
-            javax/swing/JApplet.js
-
-            java/awt/EventQueue.js
-            java/awt/AWTEventMulticaster.js
-            java/awt/AWTEvent.js
-            java/awt/event/AWTEventListener.js
-            java/awt/ActiveEvent.js
-            java/awt/event/InvocationEvent.js
-            java/awt/event/ComponentEvent.js
-            java/awt/event/MouseEvent.js
-            java/awt/event/InputEvent.js
-            java/awt/Toolkit.js
-            java/lang/Thread.js
-            java/lang/ThreadGroup.js
-            java/awt/FlowLayout.js
-            java/awt/BorderLayout.js
-            java/awt/LayoutManager2.js
-            java/awt/LayoutManager.js
-            java/awt/GraphicsCallback.js
-            java/awt/Container.js
-            java/awt/Component.js
-            jssun/awt/SunGraphicsCallback.js
-
-            javax/swing/RepaintManager.js
-            jssun/awt/SunToolkit.js
-
-        	java/awt/Conditional.js
-            java/awt/event/PaintEvent.js
-            java/awt/EventDispatchThread.js
-            java/awt/EventFilter.js
-            java/awt/ModalEventFilter.js
-            java/awt/peer/CanvasPeer.js
-            java/awt/peer/ComponentPeer.js
-            java/awt/peer/ContainerPeer.js
-            java/awt/peer/LightweightPeer.js
-            java/awt/peer/PanelPeer.js
-            java/awt/SentEvent.js
-            java/awt/SequencedEvent.js
-            java/util/AbstractSequentialList.js
-            java/util/LinkedList.js
-            JU/V3.js
-            javax/swing/ButtonGroup.js
-            javax/swing/SwingPaintEventDispatcher.js
-            jssun/awt/AWTAutoShutdown.js
-            jssun/awt/EventQueueItem.js
-            jssun/awt/ModalExclude.js
-            jssun/awt/NullComponentPeer.js
-            jssun/awt/PaintEventDispatcher.js
-            jssun/awt/PostEventQueue.js
-            jssun/java2d/SunGraphics2D.js
-
-        	javax/swing/UIManager.js
-            javax/swing/UIDefaults.js
-            javax/swing/LookAndFeel.js
-            javax/swing/DropMode.js
-            java/awt/font/FontRenderContext.js
-            java/awt/event/InputMethodEvent.js
-            javax/swing/JViewport.js
-            java/awt/event/ComponentAdapter.js
-            javax/swing/CellRendererPane.js
-            jssun/awt/AWTAccessor.js
-            javax/swing/ViewportLayout.js
-            javax/swing/event/CaretListener.js
-            javax/swing/DefaultBoundedRangeModel.js
-            javax/swing/BoundedRangeModel.js
-            javax/swing/KeyStroke.js
-            java/awt/AWTKeyStroke.js
-            java/util/StringTokenizer.js
-            javax/swing/ComponentInputMap.js
-            jssun/swing/DefaultLayoutStyle.js
-            javax/swing/LayoutStyle.js
-            javax/swing/JCheckBox.js
-            java/awt/ItemSelectable.js
-            java/awt/event/ItemEvent.js
-            javax/swing/DefaultButtonModel.js
-            javax/swing/OverlayLayout.js
-            javax/swing/SizeRequirements.js
-            javax/swing/JLabel.js
-            javax/swing/border/Border.js
-            javax/swing/RootPaneContainer.js
-            javax/swing/event/MenuDragMouseEvent.js
-            jssun/swing/UIAction.js
-            jssun/awt/RequestFocusController.js
-            javax/swing/AncestorNotifier.js
-            javax/swing/event/AncestorEvent.js
-            javax/swing/event/AncestorListener.js
-            javax/swing/ClientPropertyKey.js
-            javax/swing/JDialog.js
-            java/awt/Dialog.js
-            javax/swing/WindowConstants.js
-            javax/swing/JFrame.js
-            javax/swing/JWindow.js
-            javax/swing/KeyboardManager.js
-            javax/swing/JMenuBar.js
-            javax/swing/MenuElement.js
-            javax/swing/DefaultSingleSelectionModel.js
-            javax/swing/SingleSelectionModel.js
-            javax/swing/JMenu.js
-            java/awt/event/WindowAdapter.js
-            javax/swing/JMenuItem.js
-            javax/swing/event/MenuDragMouseListener.js
-            javax/swing/event/MenuKeyEvent.js
-            javax/swing/event/MenuKeyListener.js
-            javax/swing/JPopupMenu.js
-            javax/swing/JSeparator.js
-            javax/swing/MenuSelectionManager.js
-            javax/swing/PopupFactory.js
-            javax/swing/Popup.js
-            javax/swing/SwingHeavyWeight.js
-            javax/swing/JToolTip.js
-            javax/swing/event/PopupMenuEvent.js
-            javax/swing/event/PopupMenuListener.js
-            javax/swing/event/MenuEvent.js
-            javax/swing/event/MenuListener.js
-            javax/swing/border/AbstractBorder.js
-            jssun/awt/PeerEvent.js
-            jssun/awt/image/URLImageSource.js
-            jssun/awt/image/InputStreamImageSource.js
-            java/awt/image/ImageProducer.js
-            jssun/awt/image/ImageFetchable.js
-            jssun/awt/image/ImageConsumerQueue.js
-            jssun/awt/image/ImageFetcher.js
-            java/awt/event/FocusEvent.js
-            java/awt/event/HierarchyEvent.js
-            jssun/awt/ConstrainableGraphics.js
-            jssun/awt/Graphics2Delegate.js
-            java/awt/event/ContainerEvent.js
-            jssun/applet/AppletEvent.js
-            jssun/applet/AppletEventMulticaster.js
-            jssun/applet/AppletListener.js
-            jssun/misc/Queue.js
-
-            javax/swing/plaf/UIResource.js
-            javax/swing/plaf/InputMapUIResource.js
-            javax/swing/plaf/ActionMapUIResource.js
-            javax/swing/plaf/ComponentUI.js
-            javax/swing/plaf/FontUIResource.js
-            javax/swing/plaf/ColorUIResource.js
-            javax/swing/plaf/ComponentInputMapUIResource.js
-
-        	swingjs/api/JSFunction.js
-            swingjs/api/JSInterface.js
-            swingjs/api/Interface.js
-            swingjs/api/DOMNode.js
-
-        	swingjs/JSUtil.js
-            swingjs/JSToolkit.js
-        	swingjs/JSEvent.js
-        	swingjs/JSThread.js
-            swingjs/JSThreadGroup.js
-            swingjs/JSAppletPanel.js
-            swingjs/JSGraphics2D.js
-            swingjs/JSAppletThread.js
-            swingjs/JSMouse.js
-            swingjs/JSComponentPeer.js
-
-			swingjs/plaf/HTML5LookAndFeel.js
-            swingjs/plaf/JSComponentUI.js
-            swingjs/plaf/JSPanelUI.js
-            swingjs/plaf/JSRadioButtonUI.js
-            swingjs/plaf/JSRootPaneUI.js
-            swingjs/plaf/JSButtonListener.js
-            swingjs/plaf/JSButtonUI.js
-            swingjs/plaf/JSToggleButtonUI.js
-            swingjs/plaf/LazyActionMap.js
-    
-
-        	"/>
-    </antcall>
-    	-->
-<!--    
-
-   	put classes in here temporarily to exclude them from the 
-   	core load and make them easier to debug
-   	
-        	
-   	minimize additional JSmol JavaScript -->
-
-  </target>
-
-
-  <target name="call-core" id="call-core">
-   	<echo>......Creating core${call-core.name}.js</echo> 	
-   	<concat destfile="site/swingjs/js/core${call-core.name}.js">
-   		<filelist dir="site/swingjs/j2s" files="${call-core.list}" />
-   	</concat> 
-  	<copy file="site/swingjs/js/core${call-core.name}.js" tofile="site/swingjs/js/core2.js" />
-  	<!--
-	   	<echo>...removing unnecessary Clazz.defineStatics blocks</echo>
-  	  This next replacement does not work, because the j2s compiler does not 
-  	  distinguish between final and non-final static variable.
-  	  We will have to do this on a case-by-case basis. 
-  	   
-  	<replaceregexp file="site/swingjs/js/core2.js" match="(Clazz.defineStatics ?\(((?![\[\(]).)*?\);)" flags="gs" replace="/*\1*/" /> 
-  	<copy file="site/swingjs/js/core2.js" tofile="site/swingjs/js/core${call-core.name}3.js" />
-  	
-  	
-  	        java/io/InputStreamReader.js
+            java/io/InputStreamReader.js
             javax/swing/text/JTextComponent.js
+            javax/swing/text/Keymap.js
+            javax/swing/text/DefaultEditorKit.js
+            javax/swing/text/EditorKit.js
+            javax/swing/text/TextAction.js
+            javax/swing/text/BadLocationException.js
             javax/swing/text/DefaultCaret.js
             javax/swing/text/Caret.js
             javax/swing/text/NavigationFilter.js
             javax/swing/text/AbstractDocument.js
             javax/swing/event/DocumentEvent.js
-            javax/swing/text/Document.js
             javax/swing/text/DocumentFilter.js
             javax/swing/text/Element.js
+            javax/swing/text/JSMinimalAbstractDocument.js
+            javax/swing/text/Document.js
             javax/swing/text/MutableAttributeSet.js
             javax/swing/text/AttributeSet.js
             javax/swing/tree/TreeNode.js
@@ -469,55 +109,530 @@
             javax/swing/undo/CompoundEdit.js
             javax/swing/event/UndoableEditEvent.js
             javax/swing/event/UndoableEditListener.js
-            javax/swing/text/BadLocationException.js
             javax/swing/text/SegmentCache.js
             javax/swing/text/Segment.js
-            javax/swing/text/SimpleAttributeSet.js
-            javax/swing/text/StyleConstants.js
             javax/swing/text/StateInvariantError.js
+            javax/swing/text/StyleConstants.js
             javax/swing/text/StyleContext.js
             javax/swing/text/Style.js
+            javax/swing/text/SimpleAttributeSet.js
             javax/swing/text/Utilities.js
             javax/swing/text/CompositeView.js
             javax/swing/text/View.js
             javax/swing/text/Position.js
             javax/swing/text/StyledDocument.js
-        	javax/swing/text/DefaultEditorKit.js
-        	javax/swing/text/EditorKit.js
-            javax/swing/text/TextAction.js
-            javax/swing/text/PlainDocument.js
             javax/swing/text/DefaultHighlighter.js
             javax/swing/text/Highlighter.js
             javax/swing/text/LayeredHighlighter.js
-            javax/swing/text/Keymap.js
-  	
-  	 -->
+            swingjs/JSPlainDocument.js
+            swingjs/JSAbstractDocument.js
+            swingjs/JSDocumentEvent.js
+            swingjs/JSPosition.js
+            swingjs/api/HTML5CanvasContext2D.js
+            javax/swing/DefaultListCellRenderer.js
+            javax/swing/ListCellRenderer.js
+            javax/swing/border/EmptyBorder.js
+            jssun/swing/DefaultLookup.js
+            javax/swing/plaf/DimensionUIResource.js
+            javax/swing/plaf/InsetsUIResource.js
+            swingjs/plaf/JSEventHandler.js
+            JU/AjaxURLStreamHandlerFactory.js
+            java/net/URLStreamHandlerFactory.js
+            JU/AjaxURLStreamHandler.js
+            java/net/URLStreamHandler.js
+            JU/AjaxURLConnection.js
+            java/net/URLConnection.js
+            java/net/UnknownServiceException.js
+            
+            jalview/bin/JalviewLite.js
+            javax/swing/JButton.js
+            jalview/util/MessageManager.js
+            java/util/logging/Logger.js
+            java/util/logging/LogRecord.js
+            java/util/logging/Level.js
+            java/text/MessageFormat.js
+            java/util/PropertyResourceBundle.js
+            jalview/javascript/JalviewLiteJsApi.js
+            jalview/api/StructureSelectionManagerProvider.js
+            awt2swing/Util.js
+            jalview/analysis/SequenceIdMatcher.js
+            jalview/appletgui/AlignFrame.js
+            awt2swing/Canvas.js
+            awt2swing/Panel.js
+            jalview/api/AlignViewControllerGuiI.js
+            jalview/appletgui/EmbmenuFrame.js
+            awt2swing/Frame.js
+            awt2swing/Label.js
+            awt2swing/PopupMenu.js
+            jalview/util/Platform.js
+            awt2swing/CheckboxMenuItem.js
+            awt2swing/Menu.js
+            awt2swing/MenuBar.js
+            awt2swing/MenuItem.js
+            jalview/analysis/AlignmentSorter.js
+            jalview/datamodel/SequenceI.js
+            jalview/datamodel/ASequenceI.js
+            jalview/util/Comparison.js
+            jalview/util/QuickSort.js
+            jalview/analysis/AnnotationSorter.js
+            jalview/analysis/AlignmentUtils.js
+            jalview/analysis/CodonComparator.js
+            jalview/datamodel/AlignedCodonFrame.js
+            jalview/datamodel/Mapping.js
+            jalview/datamodel/AlignedCodon.js
+            jalview/datamodel/IncompleteCodonException.js
+            jalview/datamodel/SequenceFeature.js
+            jalview/util/MapList.js
+            jalview/util/MappingUtils.js
+            jalview/commands/EditCommand.js
+            jalview/commands/CommandI.js
+            jalview/analysis/AlignSeq.js
+            jalview/schemes/ResidueProperties.js
+            jalview/analysis/scoremodels/FeatureScoreModel.js
+            jalview/api/analysis/ScoreModelI.js
+            jalview/api/analysis/ViewBasedAnalysisI.js
+            jalview/analysis/scoremodels/PIDScoreModel.js
+            jalview/schemes/ScoreMatrix.js
+            jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
+            jalview/datamodel/Sequence.js
+            jalview/datamodel/ASequence.js
+            jalview/jsdev/RegExp.js
+            com/stevesoft/pat/Regex.js
+            com/stevesoft/pat/RegRes.js
+            com/stevesoft/pat/UniValidator.js
+            com/stevesoft/pat/Validator.js
+            com/stevesoft/pat/patInf.js
+            com/stevesoft/pat/patInt.js
+            jalview/jsdev/api/RegExpInterface.js
+            com/stevesoft/pat/NoPattern.js
+            com/stevesoft/pat/Pattern.js
+            com/stevesoft/pat/MessageManager.js
+            com/stevesoft/pat/Pthings.js
+            com/stevesoft/pat/Any.js
+            com/stevesoft/pat/BackG.js
+            com/stevesoft/pat/BackMatch.js
+            com/stevesoft/pat/Backup.js
+            com/stevesoft/pat/Boundary.js
+            com/stevesoft/pat/Bracket.js
+            com/stevesoft/pat/Or.js
+            com/stevesoft/pat/CaseMgr.js
+            com/stevesoft/pat/Ctrl.js
+            com/stevesoft/pat/Custom.js
+            com/stevesoft/pat/PatternSub.js
+            com/stevesoft/pat/CustomEndpoint.js
+            com/stevesoft/pat/DotMulti.js
+            com/stevesoft/pat/End.js
+            com/stevesoft/pat/FastMulti.js
+            com/stevesoft/pat/RegSyntaxError.js
+            com/stevesoft/pat/RegSyntax.js
+            com/stevesoft/pat/Group.js
+            com/stevesoft/pat/Multi.js
+            com/stevesoft/pat/Multi_stage2.js
+            com/stevesoft/pat/NullPattern.js
+            com/stevesoft/pat/OrMark.js
+            com/stevesoft/pat/SubMark.js
+            com/stevesoft/pat/Prop.js
+            com/stevesoft/pat/Bits.js
+            com/stevesoft/pat/Range.js
+            com/stevesoft/pat/oneChar.js
+            com/stevesoft/pat/RegOpt.js
+            com/stevesoft/pat/FastBracket.js
+            java/util/BitSet.js
+            com/stevesoft/pat/ReplaceRule.js
+            com/stevesoft/pat/Transformer.js
+            com/stevesoft/pat/Replacer.js
+            com/stevesoft/pat/AmpersandRule.js
+            com/stevesoft/pat/ChangeRule.js
+            com/stevesoft/pat/SpecialRule.js
+            com/stevesoft/pat/PopRule.js
+            com/stevesoft/pat/PushRule.js
+            com/stevesoft/pat/RuleHolder.js
+            com/stevesoft/pat/StringBufferLike.js
+            com/stevesoft/pat/BasicStringBufferLike.js
+            com/stevesoft/pat/WantMoreTextReplaceRule.js
+            com/stevesoft/pat/wrap/StringWrap.js
+            com/stevesoft/pat/StringLike.js
+            com/stevesoft/pat/wrap/StringBufferWrap.js
+            com/stevesoft/pat/TransPat.js
+            com/stevesoft/pat/Rthings.js
+            com/stevesoft/pat/Skip.js
+            com/stevesoft/pat/Skipped.js
+            com/stevesoft/pat/Start.js
+            com/stevesoft/pat/StrPos.js
+            com/stevesoft/pat/lookAhead.js
+            com/stevesoft/pat/parsePerl.js
+            com/stevesoft/pat/StringRule.js
+            jalview/datamodel/AlignmentAnnotation.js
+            jalview/analysis/Rna.js
+            jalview/analysis/SecStrConsensus.js
+            jalview/analysis/WUSSParseException.js
+            java/util/Stack.js
+            jalview/datamodel/Annotation.js
+            jalview/datamodel/GraphLine.js
+            jalview/datamodel/DBRefEntry.js
+            jalview/datamodel/DBRefSource.js
+            jalview/datamodel/PDBEntry.js
+            jalview/util/StringUtils.js
+            java/util/regex/Pattern.js
+            java/util/regex/Matcher.js
+            java/util/regex/MatchResult.js
+            jalview/util/Format.js
+            jalview/util/ReverseListIterator.js
+            jalview/commands/OrderCommand.js
+            jalview/datamodel/AlignmentOrder.js
+            jalview/datamodel/ColumnSelection.js
+            jalview/util/ShiftList.js
+            jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js
+            jalview/datamodel/SearchResults.js
+            jalview/datamodel/SequenceGroup.js
+            jalview/datamodel/AnnotatedCollectionI.js
+            jalview/datamodel/SequenceCollectionI.js
+            jalview/analysis/AAFrequency.js
+            jalview/analysis/CodingUtils.js
+            jalview/analysis/Conservation.js
+            jalview/datamodel/Alignment.js
+            jalview/datamodel/AlignmentI.js
+            jalview/datamodel/HiddenSequences.js
+            java/util/LinkedHashSet.js
+            java/util/LinkedHashMap.js
+            jalview/datamodel/CigarArray.js
+            jalview/datamodel/CigarBase.js
+            jalview/datamodel/CigarCigar.js
+            jalview/datamodel/CigarSimple.js
+            jalview/datamodel/SeqCigar.js
+            jalview/analysis/SeqsetUtils.js
+            jalview/datamodel/FeatureProperties.js
+            jalview/util/DBRefUtils.js
+            java/util/TreeMap.js
+            jalview/appletgui/AlignViewport.js
+            jalview/structure/CommandListener.js
+            jalview/structure/SelectionSource.js
+            jalview/structure/VamsasSource.js
+            jalview/viewmodel/AlignmentViewport.js
+            jalview/api/AlignViewportI.js
+            jalview/api/ViewStyleI.js
+            jalview/viewmodel/styles/ViewStyle.js
+            jalview/workers/AlignCalcManager.js
+            jalview/api/AlignCalcManagerI.js
+            java/util/ArrayDeque.js
+            java/util/Deque.js
+            jalview/datamodel/AlignmentView.js
+            jalview/schemes/Blosum62ColourScheme.js
+            jalview/schemes/ResidueColourScheme.js
+            jalview/schemes/ColourSchemeI.js
+            jalview/schemes/PIDColourScheme.js
+            jalview/workers/ComplementConsensusThread.js
+            jalview/workers/ConsensusThread.js
+            jalview/api/AlignCalcWorkerI.js
+            jalview/workers/AlignCalcWorker.js
+            jalview/workers/ConservationThread.js
+            jalview/workers/StrucConsensusThread.js
+            jalview/analysis/StructureFrequency.js
+            jalview/schemes/ColourSchemeProperty.js
+            jalview/schemes/BuriedColourScheme.js
+            jalview/schemes/ScoreColourScheme.js
+            jalview/schemes/ClustalxColourScheme.js
+            jalview/schemes/Consensus.js
+            jalview/schemes/HelixColourScheme.js
+            jalview/schemes/HydrophobicColourScheme.js
+            jalview/schemes/NucleotideColourScheme.js
+            jalview/schemes/PurinePyrimidineColourScheme.js
+            jalview/schemes/RNAHelicesColour.js
+            jalview/util/ColorUtils.js
+            jalview/schemes/StrandColourScheme.js
+            jalview/schemes/TCoffeeColourScheme.js
+            jalview/schemes/TaylorColourScheme.js
+            jalview/schemes/TurnColourScheme.js
+            jalview/schemes/UserColourScheme.js
+            jalview/schemes/ZappoColourScheme.js
+            jalview/structure/StructureSelectionManager.js
+            MCview/PDBfile.js
+            jalview/io/AlignFile.js
+            jalview/io/FileParse.js
+            jalview/io/AppletFormatAdapter.js
+            jalview/io/IdentifyFile.js
+            jalview/jsdev/GenericFileAdapter.js
+            java/util/zip/GZIPInputStream.js
+            java/util/zip/InflaterInputStream.js
+            JU/InflaterInputStream.js
+            java/util/zip/CRC32.js
+            JU/CRC32.js
+            JU/Checksum.js
+            java/util/zip/CheckedInputStream.js
+            java/util/zip/Inflater.js
+            JU/Inflater.js
+            JU/ZStream.js
+            JU/Adler32.js
+            JU/Inflate.js
+            JU/GZIPHeader.js
+            JU/InfBlocks.js
+            JU/InfTree.js
+            JU/InfCodes.js
+            java/io/ByteArrayOutputStream.js
+            java/io/OutputStream.js
+            java/util/zip/ZipException.js
+            MCview/Atom.js
+            MCview/PDBChain.js
+            MCview/Bond.js
+            MCview/Residue.js
+            jalview/structure/AtomSpec.js
+            jalview/structure/SecondaryStructureListener.js
+            jalview/structure/SequenceListener.js
+            jalview/structure/StructureListener.js
+            jalview/structure/StructureMapping.js
+            jalview/structure/VamsasListener.js
+            jalview/appletgui/AlignmentPanel.js
+            jalview/api/AlignmentViewPanel.js
+            jalview/api/OOMHandlerI.js
+            awt2swing/Scrollbar.js
+            javax/swing/JScrollBar.js
+            java/awt/Adjustable.js
+            java/awt/event/AdjustmentEvent.js
+            jalview/appletgui/AnnotationLabels.js
+            awt2swing/Checkbox.js
+            jalview/appletgui/CutAndPasteTransfer.js
+            awt2swing/Button.js
+            awt2swing/TextArea.js
+            javax/swing/JTextArea.js
+            jalview/api/ComplexAlignFile.js
+            jalview/appletgui/AppletJmol.js
+            jalview/appletgui/JVDialog.js
+            jalview/appletgui/SplitFrame.js
+            java/awt/GridLayout.js
+            jalview/io/AnnotationFile.js
+            jalview/io/NewickFile.js
+            jalview/datamodel/SequenceNode.js
+            jalview/datamodel/BinaryNode.js
+            jalview/appletgui/EditNameDialog.js
+            awt2swing/TextField.js
+            java/awt/event/TextEvent.js
+            jalview/appletgui/PaintRefresher.js
+            jalview/appletgui/Tooltip.js
+            jalview/util/ParseHtmlBodyAndLinks.js
+            jalview/appletgui/AnnotationPanel.js
+            jalview/renderer/AwtRenderPanelI.js
+            jalview/appletgui/UserDefinedColours.js
+            jalview/appletgui/AnnotationColourChooser.js
+            awt2swing/Choice.js
+            javax/swing/JComboBox.js
+            javax/swing/event/ListDataListener.js
+            javax/swing/DefaultComboBoxModel.js
+            javax/swing/AbstractListModel.js
+            javax/swing/ListModel.js
+            javax/swing/event/ListDataEvent.js
+            javax/swing/MutableComboBoxModel.js
+            javax/swing/ComboBoxModel.js
+            jalview/schemes/AnnotationColourGradient.js
+            jalview/schemes/FollowerColourScheme.js
+            jalview/renderer/AnnotationRenderer.js
+            jalview/appletgui/FeatureColourChooser.js
+            jalview/schemes/GraduatedColor.js
+            jalview/appletgui/FeatureRenderer.js
+            jalview/renderer/seqfeatures/FeatureRenderer.js
+            jalview/viewmodel/seqfeatures/FeatureRendererModel.js
+            jalview/api/FeatureRenderer.js
+            java/util/concurrent/ConcurrentHashMap.js
+            jalview/viewmodel/seqfeatures/FeatureRendererSettings.js
+            jalview/viewmodel/seqfeatures/FeaturesDisplayed.js
+            jalview/api/FeaturesDisplayedI.js
+            java/awt/AlphaComposite.js
+            java/awt/Composite.js
+            jssun/java2d/SunCompositeContext.js
+            java/awt/CompositeContext.js
+            java/awt/image/BufferedImage.js
+            java/awt/Image.js
+            java/awt/image/DirectColorModel.js
+            java/awt/image/PackedColorModel.js
+            java/awt/image/Raster.js
+            java/awt/image/MultiPixelPackedSampleModel.js
+            java/awt/image/SampleModel.js
+            java/awt/image/DataBuffer.js
+            jssun/java2d/StateTrackable.js
+            jssun/java2d/StateTrackableDelegate.js
+            jssun/java2d/StateTracker.js
+            java/awt/image/DataBufferByte.js
+            java/awt/image/DataBufferInt.js
+            java/awt/image/RasterFormatException.js
+            java/awt/image/SinglePixelPackedSampleModel.js
+            jssun/awt/image/OffScreenImageSource.js
+            java/awt/image/WritableRaster.js
+            jssun/java2d/loops/CompositeType.js
+            awt2swing/ScrollPane.js
+            javax/swing/JScrollPane.js
+            javax/swing/ScrollPaneConstants.js
+            javax/swing/ScrollPaneLayout.js
+            jalview/io/FeaturesFile.js
+            jalview/datamodel/SequenceDummy.js
+            java/awt/event/MouseAdapter.js
+            jalview/appletgui/FeatureSettings.js
+            jalview/api/FeatureSettingsControllerI.js
+            jalview/appletgui/IdPanel.js
+            jalview/appletgui/APopupMenu.js
+            jalview/analysis/AlignmentAnnotationUtils.js
+            jalview/appletgui/SliderPanel.js
+            jalview/commands/ChangeCaseCommand.js
+            jalview/io/SequenceAnnotationReport.js
+            jalview/util/UrlLink.js
+            jalview/appletgui/IdCanvas.js
+            jalview/appletgui/IdwidthAdjuster.js
+            jalview/appletgui/ScalePanel.js
+            jalview/appletgui/SeqPanel.js
+            jalview/structure/SelectionListener.js
+            jalview/appletgui/SeqCanvas.js
+            jalview/appletgui/SequenceRenderer.js
+            jalview/api/SequenceRenderer.js
+            jalview/appletgui/AnnotationColumnChooser.js
+            jalview/appletgui/AnnotationRowFilter.js
+            jalview/appletgui/TitledPanel.js
+            java/awt/CardLayout.js
+            java/io/ObjectStreamField.js
+            jalview/appletgui/Finder.js
+            jalview/analysis/Finder.js
+            java/awt/event/KeyAdapter.js
+            jalview/appletgui/FontChooser.js
+            jalview/appletgui/OverviewPanel.js
+            jalview/appletgui/PCAPanel.js
+            jalview/appletgui/RotatableCanvas.js
+            jalview/api/RotatableCanvasI.js
+            jalview/math/RotatableMatrix.js
+            jalview/viewmodel/PCAModel.js
+            jalview/analysis/PCA.js
+            jalview/datamodel/BinarySequence.js
+            jalview/math/Matrix.js
+            jalview/datamodel/SequencePoint.js
+            jalview/appletgui/PairwiseAlignPanel.js
+            jalview/appletgui/RedundancyPanel.js
+            jalview/appletgui/TreePanel.js
+            jalview/analysis/NJTree.js
+            jalview/datamodel/NodeTransformI.js
+            jalview/appletgui/TreeCanvas.js
+            jalview/commands/RemoveGapColCommand.js
+            jalview/commands/RemoveGapsCommand.js
+            jalview/commands/SlideSequencesCommand.js
+            jalview/commands/TrimRegionCommand.js
+            jalview/controller/AlignViewController.js
+            jalview/api/AlignViewControllerI.js
+            jalview/analysis/Grouping.js
+            jalview/io/AlignmentProperties.js
+            jalview/schemes/RNAHelicesColourChooser.js
+            jalview/schemes/RNAInteractionColourScheme.js
+            java/net/URLEncoder.js
+            jalview/io/JnetAnnotationMaker.js
+            jalview/javascript/JSFunctionExec.js
+            netscape/javascript/JSException.js
+            netscape/javascript/JSObject.js
+            jalview/javascript/JsSelectionSender.js
+            jalview/javascript/JsCallBack.js
+            jalview/javascript/MouseOverListener.js
+            jalview/javascript/MouseOverStructureListener.js
+            jalview/ext/jmol/JmolCommands.js
+            jalview/structure/StructureMappingcommandSet.js
+            java/util/Properties.js
+            jssun/util/ResourceBundleEnumeration.js
+            jalview/io/FastaFile.js
+            swingjs/plaf/JSMenuBarUI.js
+            swingjs/plaf/JSMenuUI.js
+            swingjs/plaf/JSMenuItemUI.js
+            swingjs/plaf/JSCheckBoxMenuItemUI.js
+            swingjs/plaf/JSCheckBoxUI.js
+            swingjs/plaf/JSLabelUI.js
+            swingjs/plaf/JSPopupMenuUI.js
+            swingjs/plaf/JSPopupMenuSeparatorUI.js
+            swingjs/plaf/JSScrollBarUI.js
+            swingjs/JSImagekit.js
+            swingjs/JSImage.js
+            jssun/awt/image/IntegerInterleavedRaster.js
+            jssun/awt/image/IntegerComponentRaster.js
+            jssun/awt/image/SunWritableRaster.js
+            jssun/awt/image/DataStealer.js
+        	"/>
+    </antcall>
 
-  	<replace dir="site/swingjs/js" includes="core2.js" token="Clazz." value="Clazz_"/>
-  	<replace dir="site/swingjs/js" includes="core2.js" token="Clazz__" value="Clazz._"/>
-  	<replace dir="site/swingjs/js" includes="core2.js" token="($fz = " value=""/>
-  	<replace dir="site/swingjs/js" includes="core2.js" token=", $fz.isPrivate = true, $fz)" value=""/> 	
-  	<replace dir="site/swingjs/js" includes="core2.js" token="Clazz_CheckPrivate" value="Clazz.CheckPrivate"/> 	
-   	<concat destfile="site/swingjs/js/core${call-core.name}.js"><filelist dir="site/swingjs/js" files="
-   		core/coretop2.js
-   		core2.js
-   		core/corebottom2.js
-   		" />
-   	</concat>
-   	<echo>......Generating core${call-core.name}.z.js</echo> 	
-   	<java jar="jars/closure_compiler.jar" fork="true" dir="site/swingjs/js" failonerror="false">
-   		<arg line="--js core${call-core.name}.js --js_output_file ../j2s/core/core${call-core.name}.z.js" />
-    </java>
-  </target>
+  	<!--    
+
+   	put classes in here temporarily to exclude them from the 
+   	core load and make them easier to debug
+   	
+        	
+   	minimize additional JSmol JavaScript -->
 
-  <target name="call-min" id="call-min">
-   	<echo>......Creating JSmol.${call-min.minname}.js</echo> 	
-   	<concat destfile="site/swingjs/js/SwingJS.${call-min.fullname}.js">
-   		<filelist dir="jsmoljs" files="${call-min.list}" />
-   	</concat>   
-   	<java jar="jars/closure_compiler.jar" fork="true" dir="" failonerror="false">
-   		<arg line="--js site/swingjs/js/SwingJS.${call-min.fullname}.js --js_output_file site/swingjs/SwingJS.${call-min.minname}.js" />
-    </java>
   </target>
-	
+
+
+	  <target name="call-core" id="call-core">
+	   	<echo>......Creating core${call-core.name}.js</echo> 	
+	   	<concat destfile="site/js/core/tmp.js">
+	   		<filelist dir="site/j2s" files="${call-core.list}" />
+	   	</concat> 
+	  	<!--
+		   	<echo>...removing unnecessary Clazz.defineStatics blocks</echo>
+	  	  This next replacement does not work, because the j2s compiler does not 
+	  	  distinguish between final and non-final static variable.
+	  	  We will have to do this on a case-by-case basis. 
+	  	   
+	  	<replaceregexp file="site/js/core2.js" match="(Clazz.defineStatics ?\(((?![\[\(]).)*?\);)" flags="gs" replace="/*\1*/" /> 
+	  	<copy file="site/js/core2.js" tofile="site/js/core${call-core.name}3.js" />
+	  	
+	  	
+	  	        java/io/InputStreamReader.js
+	            javax/swing/text/JTextComponent.js
+	            javax/swing/text/DefaultCaret.js
+	            javax/swing/text/Caret.js
+	            javax/swing/text/NavigationFilter.js
+	            javax/swing/text/AbstractDocument.js
+	            javax/swing/event/DocumentEvent.js
+	            javax/swing/text/Document.js
+	            javax/swing/text/DocumentFilter.js
+	            javax/swing/text/Element.js
+	            javax/swing/text/MutableAttributeSet.js
+	            javax/swing/text/AttributeSet.js
+	            javax/swing/tree/TreeNode.js
+	            javax/swing/undo/AbstractUndoableEdit.js
+	            javax/swing/undo/UndoableEdit.js
+	            javax/swing/undo/CannotRedoException.js
+	            javax/swing/undo/CannotUndoException.js
+	            javax/swing/undo/CompoundEdit.js
+	            javax/swing/event/UndoableEditEvent.js
+	            javax/swing/event/UndoableEditListener.js
+	            javax/swing/text/BadLocationException.js
+	            javax/swing/text/SegmentCache.js
+	            javax/swing/text/Segment.js
+	            javax/swing/text/SimpleAttributeSet.js
+	            javax/swing/text/StyleConstants.js
+	            javax/swing/text/StateInvariantError.js
+	            javax/swing/text/StyleContext.js
+	            javax/swing/text/Style.js
+	            javax/swing/text/Utilities.js
+	            javax/swing/text/CompositeView.js
+	            javax/swing/text/View.js
+	            javax/swing/text/Position.js
+	            javax/swing/text/StyledDocument.js
+	        	javax/swing/text/DefaultEditorKit.js
+	        	javax/swing/text/EditorKit.js
+	            javax/swing/text/TextAction.js
+	            javax/swing/text/PlainDocument.js
+	            javax/swing/text/DefaultHighlighter.js
+	            javax/swing/text/Highlighter.js
+	            javax/swing/text/LayeredHighlighter.js
+	            javax/swing/text/Keymap.js
+	  	
+	  	 -->
+
+	  	<replace dir="site/js/core" includes="tmp.js" token="Clazz." value="Clazz_"/>
+	  	<replace dir="site/js/core" includes="tmp.js" token="Clazz__" value="Clazz._"/>
+	  	<replace dir="site/js/core" includes="tmp.js" token="($fz = " value=""/>
+	  	<replace dir="site/js/core" includes="tmp.js" token=", $fz.isPrivate = true, $fz)" value=""/> 	
+	   	<concat destfile="site/j2s/core/core${call-core.name}.js"><filelist dir="site/js" files="
+	   		core/coretop2.js
+	   		core/tmp.js
+	   		core/corebottom2.js
+	   		" />
+	   	</concat>
+	   	<echo>......Generating core${call-core.name}.z.js</echo> 	
+	   	<java jar="jars/closure_compiler.jar" fork="true" dir="site/j2s/core" failonerror="false">
+	   		<arg line="--js core${call-core.name}.js --js_output_file core${call-core.name}.z.js" />
+	    </java>
+	 	<delete quiet="true" file="site/js/core/tmp.js" />
+	  </target>
+
 </project>