X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FTreeDescriptor.java;h=8e675f34c1b5107dd485aacf652adda19bc118eb;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=5beffc172079692e09181ddb58ef76fe50b041b8;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index 5beffc1..8e675f3 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Tree;
@@ -18,798 +18,978 @@ import jalview.schemabinding.version2.Tree;
  * 
  * @version $Revision$ $Date$
  */
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public TreeDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "tree";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getFontName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setFontName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontSize()) { return null; }
-                return new java.lang.Integer(target.getFontSize());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontSize();
-                        return;
-                    }
-                    target.setFontSize( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class TreeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public TreeDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "tree";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _fontName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_fontName", "fontName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getFontName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setFontName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontStyle()) { return null; }
-                return new java.lang.Integer(target.getFontStyle());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontStyle();
-                        return;
-                    }
-                    target.setFontStyle( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontSize
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontSize", "fontSize",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontSize())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasThreshold()) { return null; }
-                return new java.lang.Float(target.getThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getFontSize());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontSize();
+            return;
+          }
+          target.setFontSize(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showBootstrap
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowBootstrap()) { return null; }
-                return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowBootstrap();
-                        return;
-                    }
-                    target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBootstrap
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontStyle
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontStyle())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showDistances
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowDistances()) { return null; }
-                return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowDistances();
-                        return;
-                    }
-                    target.setShowDistances( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showDistances
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getFontStyle());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontStyle();
+            return;
+          }
+          target.setFontStyle(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _markUnlinked
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasMarkUnlinked()) { return null; }
-                return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMarkUnlinked();
-                        return;
-                    }
-                    target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _markUnlinked
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _fitToWindow
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFitToWindow()) { return null; }
-                return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFitToWindow();
-                        return;
-                    }
-                    target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fitToWindow
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Float(target.getThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _currentTree
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasCurrentTree()) { return null; }
-                return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteCurrentTree();
-                        return;
-                    }
-                    target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _currentTree
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showBootstrap
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasShowBootstrap())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        super.setIdentity(desc);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new java.lang.String();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IdValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IdValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getShowBootstrap() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowBootstrap();
+            return;
+          }
+          target.setShowBootstrap(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showBootstrap
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showDistances
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showDistances", "showDistances",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasShowDistances())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getShowDistances() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowDistances();
+            return;
+          }
+          target.setShowDistances(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showDistances
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _markUnlinked
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasMarkUnlinked())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMarkUnlinked();
+            return;
+          }
+          target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _title
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _markUnlinked
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fitToWindow
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFitToWindow())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _newick
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getNewick();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setNewick( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _newick
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getFitToWindow() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFitToWindow();
+            return;
+          }
+          target.setFitToWindow(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fitToWindow
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _currentTree
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_currentTree", "currentTree",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasCurrentTree())
+        {
+          return null;
+        }
+        return (target.getCurrentTree() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteCurrentTree();
+            return;
+          }
+          target.setCurrentTree(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _currentTree
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    super.setIdentity(desc);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getId();
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new java.lang.String();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IdValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasWidth())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getWidth());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Tree.class;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasXpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getYpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _title
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_title", "title",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getTitle();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _newick
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_newick", "newick",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getNewick();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setNewick((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _newick
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Tree.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }