Saves Jmol status

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index c9f79cb..61f9413 100755 (executable)
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,626 +7,610 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Annotation.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Annotation\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _graph\r
-   */\r
-  private boolean _graph;\r
-\r
-  /**\r
-   * keeps track of state for field: _graph\r
-   */\r
-  private boolean _has_graph;\r
-\r
-  /**\r
-   * Field _graphType\r
-   */\r
-  private int _graphType;\r
-\r
-  /**\r
-   * keeps track of state for field: _graphType\r
-   */\r
-  private boolean _has_graphType;\r
-\r
-  /**\r
-   * Field _sequenceRef\r
-   */\r
-  private java.lang.String _sequenceRef;\r
-\r
-  /**\r
-   * Field _graphColour\r
-   */\r
-  private int _graphColour;\r
-\r
-  /**\r
-   * keeps track of state for field: _graphColour\r
-   */\r
-  private boolean _has_graphColour;\r
-\r
-  /**\r
-   * Field _graphGroup\r
-   */\r
-  private int _graphGroup;\r
-\r
-  /**\r
-   * keeps track of state for field: _graphGroup\r
-   */\r
-  private boolean _has_graphGroup;\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private java.lang.String _id;\r
-\r
-  /**\r
-   * Field _annotationElementList\r
-   */\r
-  private java.util.Vector _annotationElementList;\r
-\r
-  /**\r
-   * Field _label\r
-   */\r
-  private java.lang.String _label;\r
-\r
-  /**\r
-   * Field _description\r
-   */\r
-  private java.lang.String _description;\r
-\r
-  /**\r
-   * Field _thresholdLine\r
-   */\r
-  private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Annotation()\r
-  {\r
-    super();\r
-    _annotationElementList = new Vector();\r
-  } //-- jalview.schemabinding.version2.Annotation()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param vAnnotationElement\r
-   */\r
-  public void addAnnotationElement(jalview.schemabinding.version2.\r
-                                   AnnotationElement vAnnotationElement)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _annotationElementList.addElement(vAnnotationElement);\r
-  } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement)\r
-\r
-  /**\r
-   * Method addAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vAnnotationElement\r
-   */\r
-  public void addAnnotationElement(int index,\r
-                                   jalview.schemabinding.version2.AnnotationElement\r
-                                   vAnnotationElement)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _annotationElementList.insertElementAt(vAnnotationElement, index);\r
-  } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)\r
-\r
-  /**\r
-   * Method deleteGraph\r
-   *\r
-   */\r
-  public void deleteGraph()\r
-  {\r
-    this._has_graph = false;\r
-  } //-- void deleteGraph()\r
-\r
-  /**\r
-   * Method deleteGraphColour\r
-   *\r
-   */\r
-  public void deleteGraphColour()\r
-  {\r
-    this._has_graphColour = false;\r
-  } //-- void deleteGraphColour()\r
-\r
-  /**\r
-   * Method deleteGraphGroup\r
-   *\r
-   */\r
-  public void deleteGraphGroup()\r
-  {\r
-    this._has_graphGroup = false;\r
-  } //-- void deleteGraphGroup()\r
-\r
-  /**\r
-   * Method deleteGraphType\r
-   *\r
-   */\r
-  public void deleteGraphType()\r
-  {\r
-    this._has_graphType = false;\r
-  } //-- void deleteGraphType()\r
-\r
-  /**\r
-   * Method enumerateAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateAnnotationElement()\r
-  {\r
-    return _annotationElementList.elements();\r
-  } //-- java.util.Enumeration enumerateAnnotationElement()\r
-\r
-  /**\r
-   * Method getAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return AnnotationElement\r
-   */\r
-  public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int\r
-      index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _annotationElementList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.AnnotationElement)\r
-        _annotationElementList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int)\r
-\r
-  /**\r
-   * Method getAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @return AnnotationElement\r
-   */\r
-  public jalview.schemabinding.version2.AnnotationElement[]\r
-      getAnnotationElement()\r
-  {\r
-    int size = _annotationElementList.size();\r
-    jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.\r
-        schemabinding.version2.AnnotationElement[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.AnnotationElement)\r
-          _annotationElementList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
-\r
-  /**\r
-   * Method getAnnotationElementCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getAnnotationElementCount()\r
-  {\r
-    return _annotationElementList.size();\r
-  } //-- int getAnnotationElementCount()\r
-\r
-  /**\r
-   * Returns the value of field 'description'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'description'.\r
-   */\r
-  public java.lang.String getDescription()\r
-  {\r
-    return this._description;\r
-  } //-- java.lang.String getDescription()\r
-\r
-  /**\r
-   * Returns the value of field 'graph'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'graph'.\r
-   */\r
-  public boolean getGraph()\r
-  {\r
-    return this._graph;\r
-  } //-- boolean getGraph()\r
-\r
-  /**\r
-   * Returns the value of field 'graphColour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'graphColour'.\r
-   */\r
-  public int getGraphColour()\r
-  {\r
-    return this._graphColour;\r
-  } //-- int getGraphColour()\r
-\r
-  /**\r
-   * Returns the value of field 'graphGroup'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'graphGroup'.\r
-   */\r
-  public int getGraphGroup()\r
-  {\r
-    return this._graphGroup;\r
-  } //-- int getGraphGroup()\r
-\r
-  /**\r
-   * Returns the value of field 'graphType'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'graphType'.\r
-   */\r
-  public int getGraphType()\r
-  {\r
-    return this._graphType;\r
-  } //-- int getGraphType()\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'id'.\r
-   */\r
-  public java.lang.String getId()\r
-  {\r
-    return this._id;\r
-  } //-- java.lang.String getId()\r
-\r
-  /**\r
-   * Returns the value of field 'label'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'label'.\r
-   */\r
-  public java.lang.String getLabel()\r
-  {\r
-    return this._label;\r
-  } //-- java.lang.String getLabel()\r
-\r
-  /**\r
-   * Returns the value of field 'sequenceRef'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'sequenceRef'.\r
-   */\r
-  public java.lang.String getSequenceRef()\r
-  {\r
-    return this._sequenceRef;\r
-  } //-- java.lang.String getSequenceRef()\r
-\r
-  /**\r
-   * Returns the value of field 'thresholdLine'.\r
-   *\r
-   * @return ThresholdLine\r
-   * @return the value of field 'thresholdLine'.\r
-   */\r
-  public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
-  {\r
-    return this._thresholdLine;\r
-  } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
-\r
-  /**\r
-   * Method hasGraph\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasGraph()\r
-  {\r
-    return this._has_graph;\r
-  } //-- boolean hasGraph()\r
-\r
-  /**\r
-   * Method hasGraphColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasGraphColour()\r
-  {\r
-    return this._has_graphColour;\r
-  } //-- boolean hasGraphColour()\r
-\r
-  /**\r
-   * Method hasGraphGroup\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasGraphGroup()\r
-  {\r
-    return this._has_graphGroup;\r
-  } //-- boolean hasGraphGroup()\r
-\r
-  /**\r
-   * Method hasGraphType\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasGraphType()\r
-  {\r
-    return this._has_graphType;\r
-  } //-- boolean hasGraphType()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllAnnotationElement\r
-   *\r
-   */\r
-  public void removeAllAnnotationElement()\r
-  {\r
-    _annotationElementList.removeAllElements();\r
-  } //-- void removeAllAnnotationElement()\r
-\r
-  /**\r
-   * Method removeAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return AnnotationElement\r
-   */\r
-  public jalview.schemabinding.version2.AnnotationElement\r
-      removeAnnotationElement(int index)\r
-  {\r
-    java.lang.Object obj = _annotationElementList.elementAt(index);\r
-    _annotationElementList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.AnnotationElement) obj;\r
-  } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int)\r
-\r
-  /**\r
-   * Method setAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vAnnotationElement\r
-   */\r
-  public void setAnnotationElement(int index,\r
-                                   jalview.schemabinding.version2.AnnotationElement\r
-                                   vAnnotationElement)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _annotationElementList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _annotationElementList.setElementAt(vAnnotationElement, index);\r
-  } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)\r
-\r
-  /**\r
-   * Method setAnnotationElement\r
-   *\r
-   *\r
-   *\r
-   * @param annotationElementArray\r
-   */\r
-  public void setAnnotationElement(jalview.schemabinding.version2.\r
-                                   AnnotationElement[] annotationElementArray)\r
-  {\r
-    //-- copy array\r
-    _annotationElementList.removeAllElements();\r
-    for (int i = 0; i < annotationElementArray.length; i++)\r
-    {\r
-      _annotationElementList.addElement(annotationElementArray[i]);\r
-    }\r
-  } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement)\r
-\r
-  /**\r
-   * Sets the value of field 'description'.\r
-   *\r
-   * @param description the value of field 'description'.\r
-   */\r
-  public void setDescription(java.lang.String description)\r
-  {\r
-    this._description = description;\r
-  } //-- void setDescription(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'graph'.\r
-   *\r
-   * @param graph the value of field 'graph'.\r
-   */\r
-  public void setGraph(boolean graph)\r
-  {\r
-    this._graph = graph;\r
-    this._has_graph = true;\r
-  } //-- void setGraph(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'graphColour'.\r
-   *\r
-   * @param graphColour the value of field 'graphColour'.\r
-   */\r
-  public void setGraphColour(int graphColour)\r
-  {\r
-    this._graphColour = graphColour;\r
-    this._has_graphColour = true;\r
-  } //-- void setGraphColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'graphGroup'.\r
-   *\r
-   * @param graphGroup the value of field 'graphGroup'.\r
-   */\r
-  public void setGraphGroup(int graphGroup)\r
-  {\r
-    this._graphGroup = graphGroup;\r
-    this._has_graphGroup = true;\r
-  } //-- void setGraphGroup(int)\r
-\r
-  /**\r
-   * Sets the value of field 'graphType'.\r
-   *\r
-   * @param graphType the value of field 'graphType'.\r
-   */\r
-  public void setGraphType(int graphType)\r
-  {\r
-    this._graphType = graphType;\r
-    this._has_graphType = true;\r
-  } //-- void setGraphType(int)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(java.lang.String id)\r
-  {\r
-    this._id = id;\r
-  } //-- void setId(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'label'.\r
-   *\r
-   * @param label the value of field 'label'.\r
-   */\r
-  public void setLabel(java.lang.String label)\r
-  {\r
-    this._label = label;\r
-  } //-- void setLabel(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'sequenceRef'.\r
-   *\r
-   * @param sequenceRef the value of field 'sequenceRef'.\r
-   */\r
-  public void setSequenceRef(java.lang.String sequenceRef)\r
-  {\r
-    this._sequenceRef = sequenceRef;\r
-  } //-- void setSequenceRef(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'thresholdLine'.\r
-   *\r
-   * @param thresholdLine the value of field 'thresholdLine'.\r
-   */\r
-  public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine\r
-                               thresholdLine)\r
-  {\r
-    this._thresholdLine = thresholdLine;\r
-  } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Annotation.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class Annotation implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _graph\r
+     */\r
+    private boolean _graph;\r
+\r
+    /**\r
+     * keeps track of state for field: _graph\r
+     */\r
+    private boolean _has_graph;\r
+\r
+    /**\r
+     * Field _graphType\r
+     */\r
+    private int _graphType;\r
+\r
+    /**\r
+     * keeps track of state for field: _graphType\r
+     */\r
+    private boolean _has_graphType;\r
+\r
+    /**\r
+     * Field _sequenceRef\r
+     */\r
+    private java.lang.String _sequenceRef;\r
+\r
+    /**\r
+     * Field _graphColour\r
+     */\r
+    private int _graphColour;\r
+\r
+    /**\r
+     * keeps track of state for field: _graphColour\r
+     */\r
+    private boolean _has_graphColour;\r
+\r
+    /**\r
+     * Field _graphGroup\r
+     */\r
+    private int _graphGroup;\r
+\r
+    /**\r
+     * keeps track of state for field: _graphGroup\r
+     */\r
+    private boolean _has_graphGroup;\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _annotationElementList\r
+     */\r
+    private java.util.Vector _annotationElementList;\r
+\r
+    /**\r
+     * Field _label\r
+     */\r
+    private java.lang.String _label;\r
+\r
+    /**\r
+     * Field _description\r
+     */\r
+    private java.lang.String _description;\r
+\r
+    /**\r
+     * Field _thresholdLine\r
+     */\r
+    private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Annotation() {\r
+        super();\r
+        _annotationElementList = new Vector();\r
+    } //-- jalview.schemabinding.version2.Annotation()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param vAnnotationElement\r
+     */\r
+    public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _annotationElementList.addElement(vAnnotationElement);\r
+    } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \r
+\r
+    /**\r
+     * Method addAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vAnnotationElement\r
+     */\r
+    public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _annotationElementList.insertElementAt(vAnnotationElement, index);\r
+    } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
+\r
+    /**\r
+     * Method deleteGraph\r
+     * \r
+     */\r
+    public void deleteGraph()\r
+    {\r
+        this._has_graph= false;\r
+    } //-- void deleteGraph() \r
+\r
+    /**\r
+     * Method deleteGraphColour\r
+     * \r
+     */\r
+    public void deleteGraphColour()\r
+    {\r
+        this._has_graphColour= false;\r
+    } //-- void deleteGraphColour() \r
+\r
+    /**\r
+     * Method deleteGraphGroup\r
+     * \r
+     */\r
+    public void deleteGraphGroup()\r
+    {\r
+        this._has_graphGroup= false;\r
+    } //-- void deleteGraphGroup() \r
+\r
+    /**\r
+     * Method deleteGraphType\r
+     * \r
+     */\r
+    public void deleteGraphType()\r
+    {\r
+        this._has_graphType= false;\r
+    } //-- void deleteGraphType() \r
+\r
+    /**\r
+     * Method enumerateAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateAnnotationElement()\r
+    {\r
+        return _annotationElementList.elements();\r
+    } //-- java.util.Enumeration enumerateAnnotationElement() \r
+\r
+    /**\r
+     * Method getAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return AnnotationElement\r
+     */\r
+    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _annotationElementList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) \r
+\r
+    /**\r
+     * Method getAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @return AnnotationElement\r
+     */\r
+    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
+    {\r
+        int size = _annotationElementList.size();\r
+        jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() \r
+\r
+    /**\r
+     * Method getAnnotationElementCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getAnnotationElementCount()\r
+    {\r
+        return _annotationElementList.size();\r
+    } //-- int getAnnotationElementCount() \r
+\r
+    /**\r
+     * Returns the value of field 'description'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'description'.\r
+     */\r
+    public java.lang.String getDescription()\r
+    {\r
+        return this._description;\r
+    } //-- java.lang.String getDescription() \r
+\r
+    /**\r
+     * Returns the value of field 'graph'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'graph'.\r
+     */\r
+    public boolean getGraph()\r
+    {\r
+        return this._graph;\r
+    } //-- boolean getGraph() \r
+\r
+    /**\r
+     * Returns the value of field 'graphColour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'graphColour'.\r
+     */\r
+    public int getGraphColour()\r
+    {\r
+        return this._graphColour;\r
+    } //-- int getGraphColour() \r
+\r
+    /**\r
+     * Returns the value of field 'graphGroup'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'graphGroup'.\r
+     */\r
+    public int getGraphGroup()\r
+    {\r
+        return this._graphGroup;\r
+    } //-- int getGraphGroup() \r
+\r
+    /**\r
+     * Returns the value of field 'graphType'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'graphType'.\r
+     */\r
+    public int getGraphType()\r
+    {\r
+        return this._graphType;\r
+    } //-- int getGraphType() \r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'id'.\r
+     */\r
+    public java.lang.String getId()\r
+    {\r
+        return this._id;\r
+    } //-- java.lang.String getId() \r
+\r
+    /**\r
+     * Returns the value of field 'label'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'label'.\r
+     */\r
+    public java.lang.String getLabel()\r
+    {\r
+        return this._label;\r
+    } //-- java.lang.String getLabel() \r
+\r
+    /**\r
+     * Returns the value of field 'sequenceRef'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'sequenceRef'.\r
+     */\r
+    public java.lang.String getSequenceRef()\r
+    {\r
+        return this._sequenceRef;\r
+    } //-- java.lang.String getSequenceRef() \r
+\r
+    /**\r
+     * Returns the value of field 'thresholdLine'.\r
+     * \r
+     * @return ThresholdLine\r
+     * @return the value of field 'thresholdLine'.\r
+     */\r
+    public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
+    {\r
+        return this._thresholdLine;\r
+    } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() \r
+\r
+    /**\r
+     * Method hasGraph\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGraph()\r
+    {\r
+        return this._has_graph;\r
+    } //-- boolean hasGraph() \r
+\r
+    /**\r
+     * Method hasGraphColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGraphColour()\r
+    {\r
+        return this._has_graphColour;\r
+    } //-- boolean hasGraphColour() \r
+\r
+    /**\r
+     * Method hasGraphGroup\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGraphGroup()\r
+    {\r
+        return this._has_graphGroup;\r
+    } //-- boolean hasGraphGroup() \r
+\r
+    /**\r
+     * Method hasGraphType\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGraphType()\r
+    {\r
+        return this._has_graphType;\r
+    } //-- boolean hasGraphType() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllAnnotationElement\r
+     * \r
+     */\r
+    public void removeAllAnnotationElement()\r
+    {\r
+        _annotationElementList.removeAllElements();\r
+    } //-- void removeAllAnnotationElement() \r
+\r
+    /**\r
+     * Method removeAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return AnnotationElement\r
+     */\r
+    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)\r
+    {\r
+        java.lang.Object obj = _annotationElementList.elementAt(index);\r
+        _annotationElementList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.AnnotationElement) obj;\r
+    } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) \r
+\r
+    /**\r
+     * Method setAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vAnnotationElement\r
+     */\r
+    public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _annotationElementList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _annotationElementList.setElementAt(vAnnotationElement, index);\r
+    } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) \r
+\r
+    /**\r
+     * Method setAnnotationElement\r
+     * \r
+     * \r
+     * \r
+     * @param annotationElementArray\r
+     */\r
+    public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)\r
+    {\r
+        //-- copy array\r
+        _annotationElementList.removeAllElements();\r
+        for (int i = 0; i < annotationElementArray.length; i++) {\r
+            _annotationElementList.addElement(annotationElementArray[i]);\r
+        }\r
+    } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) \r
+\r
+    /**\r
+     * Sets the value of field 'description'.\r
+     * \r
+     * @param description the value of field 'description'.\r
+     */\r
+    public void setDescription(java.lang.String description)\r
+    {\r
+        this._description = description;\r
+    } //-- void setDescription(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'graph'.\r
+     * \r
+     * @param graph the value of field 'graph'.\r
+     */\r
+    public void setGraph(boolean graph)\r
+    {\r
+        this._graph = graph;\r
+        this._has_graph = true;\r
+    } //-- void setGraph(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'graphColour'.\r
+     * \r
+     * @param graphColour the value of field 'graphColour'.\r
+     */\r
+    public void setGraphColour(int graphColour)\r
+    {\r
+        this._graphColour = graphColour;\r
+        this._has_graphColour = true;\r
+    } //-- void setGraphColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'graphGroup'.\r
+     * \r
+     * @param graphGroup the value of field 'graphGroup'.\r
+     */\r
+    public void setGraphGroup(int graphGroup)\r
+    {\r
+        this._graphGroup = graphGroup;\r
+        this._has_graphGroup = true;\r
+    } //-- void setGraphGroup(int) \r
+\r
+    /**\r
+     * Sets the value of field 'graphType'.\r
+     * \r
+     * @param graphType the value of field 'graphType'.\r
+     */\r
+    public void setGraphType(int graphType)\r
+    {\r
+        this._graphType = graphType;\r
+        this._has_graphType = true;\r
+    } //-- void setGraphType(int) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(java.lang.String id)\r
+    {\r
+        this._id = id;\r
+    } //-- void setId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'label'.\r
+     * \r
+     * @param label the value of field 'label'.\r
+     */\r
+    public void setLabel(java.lang.String label)\r
+    {\r
+        this._label = label;\r
+    } //-- void setLabel(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'sequenceRef'.\r
+     * \r
+     * @param sequenceRef the value of field 'sequenceRef'.\r
+     */\r
+    public void setSequenceRef(java.lang.String sequenceRef)\r
+    {\r
+        this._sequenceRef = sequenceRef;\r
+    } //-- void setSequenceRef(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'thresholdLine'.\r
+     * \r
+     * @param thresholdLine the value of field 'thresholdLine'.\r
+     */\r
+    public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)\r
+    {\r
+        this._thresholdLine = thresholdLine;\r
+    } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index 67d6ad8..b2af2c4 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,379 +7,379 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class AnnotationColours.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AnnotationColours\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _aboveThreshold\r
-   */\r
-  private int _aboveThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _aboveThreshold\r
-   */\r
-  private boolean _has_aboveThreshold;\r
-\r
-  /**\r
-   * Field _annotation\r
-   */\r
-  private java.lang.String _annotation;\r
-\r
-  /**\r
-   * Field _minColour\r
-   */\r
-  private int _minColour;\r
-\r
-  /**\r
-   * keeps track of state for field: _minColour\r
-   */\r
-  private boolean _has_minColour;\r
-\r
-  /**\r
-   * Field _maxColour\r
-   */\r
-  private int _maxColour;\r
-\r
-  /**\r
-   * keeps track of state for field: _maxColour\r
-   */\r
-  private boolean _has_maxColour;\r
-\r
-  /**\r
-   * Field _colourScheme\r
-   */\r
-  private java.lang.String _colourScheme;\r
-\r
-  /**\r
-   * Field _threshold\r
-   */\r
-  private float _threshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _threshold\r
-   */\r
-  private boolean _has_threshold;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public AnnotationColours()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.AnnotationColours()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteAboveThreshold\r
-   *\r
-   */\r
-  public void deleteAboveThreshold()\r
-  {\r
-    this._has_aboveThreshold = false;\r
-  } //-- void deleteAboveThreshold()\r
-\r
-  /**\r
-   * Method deleteMaxColour\r
-   *\r
-   */\r
-  public void deleteMaxColour()\r
-  {\r
-    this._has_maxColour = false;\r
-  } //-- void deleteMaxColour()\r
-\r
-  /**\r
-   * Method deleteMinColour\r
-   *\r
-   */\r
-  public void deleteMinColour()\r
-  {\r
-    this._has_minColour = false;\r
-  } //-- void deleteMinColour()\r
-\r
-  /**\r
-   * Method deleteThreshold\r
-   *\r
-   */\r
-  public void deleteThreshold()\r
-  {\r
-    this._has_threshold = false;\r
-  } //-- void deleteThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'aboveThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'aboveThreshold'.\r
-   */\r
-  public int getAboveThreshold()\r
-  {\r
-    return this._aboveThreshold;\r
-  } //-- int getAboveThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'annotation'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'annotation'.\r
-   */\r
-  public java.lang.String getAnnotation()\r
-  {\r
-    return this._annotation;\r
-  } //-- java.lang.String getAnnotation()\r
-\r
-  /**\r
-   * Returns the value of field 'colourScheme'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'colourScheme'.\r
-   */\r
-  public java.lang.String getColourScheme()\r
-  {\r
-    return this._colourScheme;\r
-  } //-- java.lang.String getColourScheme()\r
-\r
-  /**\r
-   * Returns the value of field 'maxColour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'maxColour'.\r
-   */\r
-  public int getMaxColour()\r
-  {\r
-    return this._maxColour;\r
-  } //-- int getMaxColour()\r
-\r
-  /**\r
-   * Returns the value of field 'minColour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'minColour'.\r
-   */\r
-  public int getMinColour()\r
-  {\r
-    return this._minColour;\r
-  } //-- int getMinColour()\r
-\r
-  /**\r
-   * Returns the value of field 'threshold'.\r
-   *\r
-   * @return float\r
-   * @return the value of field 'threshold'.\r
-   */\r
-  public float getThreshold()\r
-  {\r
-    return this._threshold;\r
-  } //-- float getThreshold()\r
-\r
-  /**\r
-   * Method hasAboveThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasAboveThreshold()\r
-  {\r
-    return this._has_aboveThreshold;\r
-  } //-- boolean hasAboveThreshold()\r
-\r
-  /**\r
-   * Method hasMaxColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasMaxColour()\r
-  {\r
-    return this._has_maxColour;\r
-  } //-- boolean hasMaxColour()\r
-\r
-  /**\r
-   * Method hasMinColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasMinColour()\r
-  {\r
-    return this._has_minColour;\r
-  } //-- boolean hasMinColour()\r
-\r
-  /**\r
-   * Method hasThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasThreshold()\r
-  {\r
-    return this._has_threshold;\r
-  } //-- boolean hasThreshold()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class AnnotationColours implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _aboveThreshold\r
+     */\r
+    private int _aboveThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _aboveThreshold\r
+     */\r
+    private boolean _has_aboveThreshold;\r
+\r
+    /**\r
+     * Field _annotation\r
+     */\r
+    private java.lang.String _annotation;\r
+\r
+    /**\r
+     * Field _minColour\r
+     */\r
+    private int _minColour;\r
+\r
+    /**\r
+     * keeps track of state for field: _minColour\r
+     */\r
+    private boolean _has_minColour;\r
+\r
+    /**\r
+     * Field _maxColour\r
+     */\r
+    private int _maxColour;\r
+\r
+    /**\r
+     * keeps track of state for field: _maxColour\r
+     */\r
+    private boolean _has_maxColour;\r
+\r
+    /**\r
+     * Field _colourScheme\r
+     */\r
+    private java.lang.String _colourScheme;\r
+\r
+    /**\r
+     * Field _threshold\r
+     */\r
+    private float _threshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _threshold\r
+     */\r
+    private boolean _has_threshold;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public AnnotationColours() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.AnnotationColours()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteAboveThreshold\r
+     * \r
+     */\r
+    public void deleteAboveThreshold()\r
+    {\r
+        this._has_aboveThreshold= false;\r
+    } //-- void deleteAboveThreshold() \r
+\r
+    /**\r
+     * Method deleteMaxColour\r
+     * \r
+     */\r
+    public void deleteMaxColour()\r
+    {\r
+        this._has_maxColour= false;\r
+    } //-- void deleteMaxColour() \r
+\r
+    /**\r
+     * Method deleteMinColour\r
+     * \r
+     */\r
+    public void deleteMinColour()\r
+    {\r
+        this._has_minColour= false;\r
+    } //-- void deleteMinColour() \r
+\r
+    /**\r
+     * Method deleteThreshold\r
+     * \r
+     */\r
+    public void deleteThreshold()\r
+    {\r
+        this._has_threshold= false;\r
+    } //-- void deleteThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'aboveThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'aboveThreshold'.\r
+     */\r
+    public int getAboveThreshold()\r
+    {\r
+        return this._aboveThreshold;\r
+    } //-- int getAboveThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'annotation'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'annotation'.\r
+     */\r
+    public java.lang.String getAnnotation()\r
+    {\r
+        return this._annotation;\r
+    } //-- java.lang.String getAnnotation() \r
+\r
+    /**\r
+     * Returns the value of field 'colourScheme'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'colourScheme'.\r
+     */\r
+    public java.lang.String getColourScheme()\r
+    {\r
+        return this._colourScheme;\r
+    } //-- java.lang.String getColourScheme() \r
+\r
+    /**\r
+     * Returns the value of field 'maxColour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'maxColour'.\r
+     */\r
+    public int getMaxColour()\r
+    {\r
+        return this._maxColour;\r
+    } //-- int getMaxColour() \r
+\r
+    /**\r
+     * Returns the value of field 'minColour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'minColour'.\r
+     */\r
+    public int getMinColour()\r
+    {\r
+        return this._minColour;\r
+    } //-- int getMinColour() \r
+\r
+    /**\r
+     * Returns the value of field 'threshold'.\r
+     * \r
+     * @return float\r
+     * @return the value of field 'threshold'.\r
+     */\r
+    public float getThreshold()\r
+    {\r
+        return this._threshold;\r
+    } //-- float getThreshold() \r
+\r
+    /**\r
+     * Method hasAboveThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasAboveThreshold()\r
+    {\r
+        return this._has_aboveThreshold;\r
+    } //-- boolean hasAboveThreshold() \r
+\r
+    /**\r
+     * Method hasMaxColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasMaxColour()\r
+    {\r
+        return this._has_maxColour;\r
+    } //-- boolean hasMaxColour() \r
+\r
+    /**\r
+     * Method hasMinColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasMinColour()\r
+    {\r
+        return this._has_minColour;\r
+    } //-- boolean hasMinColour() \r
+\r
+    /**\r
+     * Method hasThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasThreshold()\r
+    {\r
+        return this._has_threshold;\r
+    } //-- boolean hasThreshold() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'aboveThreshold'.\r
+     * \r
+     * @param aboveThreshold the value of field 'aboveThreshold'.\r
+     */\r
+    public void setAboveThreshold(int aboveThreshold)\r
+    {\r
+        this._aboveThreshold = aboveThreshold;\r
+        this._has_aboveThreshold = true;\r
+    } //-- void setAboveThreshold(int) \r
+\r
+    /**\r
+     * Sets the value of field 'annotation'.\r
+     * \r
+     * @param annotation the value of field 'annotation'.\r
+     */\r
+    public void setAnnotation(java.lang.String annotation)\r
+    {\r
+        this._annotation = annotation;\r
+    } //-- void setAnnotation(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'colourScheme'.\r
+     * \r
+     * @param colourScheme the value of field 'colourScheme'.\r
+     */\r
+    public void setColourScheme(java.lang.String colourScheme)\r
+    {\r
+        this._colourScheme = colourScheme;\r
+    } //-- void setColourScheme(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'maxColour'.\r
+     * \r
+     * @param maxColour the value of field 'maxColour'.\r
+     */\r
+    public void setMaxColour(int maxColour)\r
+    {\r
+        this._maxColour = maxColour;\r
+        this._has_maxColour = true;\r
+    } //-- void setMaxColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'minColour'.\r
+     * \r
+     * @param minColour the value of field 'minColour'.\r
+     */\r
+    public void setMinColour(int minColour)\r
+    {\r
+        this._minColour = minColour;\r
+        this._has_minColour = true;\r
+    } //-- void setMinColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'threshold'.\r
+     * \r
+     * @param threshold the value of field 'threshold'.\r
+     */\r
+    public void setThreshold(float threshold)\r
+    {\r
+        this._threshold = threshold;\r
+        this._has_threshold = true;\r
+    } //-- void setThreshold(float) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'aboveThreshold'.\r
-   *\r
-   * @param aboveThreshold the value of field 'aboveThreshold'.\r
-   */\r
-  public void setAboveThreshold(int aboveThreshold)\r
-  {\r
-    this._aboveThreshold = aboveThreshold;\r
-    this._has_aboveThreshold = true;\r
-  } //-- void setAboveThreshold(int)\r
-\r
-  /**\r
-   * Sets the value of field 'annotation'.\r
-   *\r
-   * @param annotation the value of field 'annotation'.\r
-   */\r
-  public void setAnnotation(java.lang.String annotation)\r
-  {\r
-    this._annotation = annotation;\r
-  } //-- void setAnnotation(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'colourScheme'.\r
-   *\r
-   * @param colourScheme the value of field 'colourScheme'.\r
-   */\r
-  public void setColourScheme(java.lang.String colourScheme)\r
-  {\r
-    this._colourScheme = colourScheme;\r
-  } //-- void setColourScheme(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'maxColour'.\r
-   *\r
-   * @param maxColour the value of field 'maxColour'.\r
-   */\r
-  public void setMaxColour(int maxColour)\r
-  {\r
-    this._maxColour = maxColour;\r
-    this._has_maxColour = true;\r
-  } //-- void setMaxColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'minColour'.\r
-   *\r
-   * @param minColour the value of field 'minColour'.\r
-   */\r
-  public void setMinColour(int minColour)\r
-  {\r
-    this._minColour = minColour;\r
-    this._has_minColour = true;\r
-  } //-- void setMinColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'threshold'.\r
-   *\r
-   * @param threshold the value of field 'threshold'.\r
-   */\r
-  public void setThreshold(float threshold)\r
-  {\r
-    this._threshold = threshold;\r
-    this._has_threshold = true;\r
-  } //-- void setThreshold(float)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.AnnotationColours.class,\r
-                  reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
index f8cc3a1..c3c06e6 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,456 +7,400 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class AnnotationColoursDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AnnotationColoursDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public AnnotationColoursDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "AnnotationColours";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _aboveThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_aboveThreshold", "aboveThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        if (!target.hasAboveThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getAboveThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteAboveThreshold();\r
-            return;\r
-          }\r
-          target.setAboveThreshold( ( (java.lang.Integer) value).intValue());\r
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public AnnotationColoursDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "AnnotationColours";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _aboveThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                if(!target.hasAboveThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getAboveThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteAboveThreshold();\r
+                        return;\r
+                    }\r
+                    target.setAboveThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _aboveThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _aboveThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _annotation\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_annotation", "annotation",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        return target.getAnnotation();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          target.setAnnotation( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _annotation\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                return target.getAnnotation();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    target.setAnnotation( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _annotation\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _minColour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                if(!target.hasMinColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getMinColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteMinColour();\r
+                        return;\r
+                    }\r
+                    target.setMinColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _minColour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _annotation\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _minColour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_minColour", "minColour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        if (!target.hasMinColour())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- _maxColour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                if(!target.hasMaxColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getMaxColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteMaxColour();\r
+                        return;\r
+                    }\r
+                    target.setMaxColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _maxColour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getMinColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteMinColour();\r
-            return;\r
-          }\r
-          target.setMinColour( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colourScheme\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                return target.getColourScheme();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    target.setColourScheme( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colourScheme\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _threshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationColours target = (AnnotationColours) object;\r
+                if(!target.hasThreshold())\r
+                    return null;\r
+                return new java.lang.Float(target.getThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationColours target = (AnnotationColours) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteThreshold();\r
+                        return;\r
+                    }\r
+                    target.setThreshold( ((java.lang.Float)value).floatValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _threshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            FloatValidator typeValidator = new FloatValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _minColour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _maxColour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_maxColour", "maxColour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.AnnotationColoursDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        if (!target.hasMaxColour())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getMaxColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteMaxColour();\r
-            return;\r
-          }\r
-          target.setMaxColour( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _maxColour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colourScheme\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_colourScheme", "colourScheme",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        return target.getColourScheme();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          target.setColourScheme( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colourScheme\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _threshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,\r
-        "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationColours target = (AnnotationColours) object;\r
-        if (!target.hasThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Float(target.getThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationColours target = (AnnotationColours) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteThreshold();\r
-            return;\r
-          }\r
-          target.setThreshold( ( (java.lang.Float) value).floatValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _threshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      FloatValidator typeValidator = new FloatValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.AnnotationColoursDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.AnnotationColours.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.AnnotationColours.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
index 7ba7e67..34047b3 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,643 +7,550 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class AnnotationDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AnnotationDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public AnnotationDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "Annotation";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _graph\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_graph", "graph",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        if (!target.hasGraph())\r
-        {\r
-          return null;\r
+public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public AnnotationDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "Annotation";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _graph\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if(!target.hasGraph())\r
+                    return null;\r
+                return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setGraph( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _graph\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return (target.getGraph() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setGraph( ( (java.lang.Boolean) value).booleanValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _graphType\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if(!target.hasGraphType())\r
+                    return null;\r
+                return new java.lang.Integer(target.getGraphType());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteGraphType();\r
+                        return;\r
+                    }\r
+                    target.setGraphType( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _graphType\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _sequenceRef\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getSequenceRef();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setSequenceRef( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequenceRef\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _graph\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _graphType\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_graphType", "graphType",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        if (!target.hasGraphType())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- _graphColour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if(!target.hasGraphColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getGraphColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteGraphColour();\r
+                        return;\r
+                    }\r
+                    target.setGraphColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _graphColour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getGraphType());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteGraphType();\r
-            return;\r
-          }\r
-          target.setGraphType( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _graphGroup\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if(!target.hasGraphGroup())\r
+                    return null;\r
+                return new java.lang.Integer(target.getGraphGroup());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteGraphGroup();\r
+                        return;\r
+                    }\r
+                    target.setGraphGroup( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _graphGroup\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _id\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _id\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _graphType\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _sequenceRef\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_sequenceRef", "sequenceRef",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getSequenceRef();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.setSequenceRef( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _annotationElementList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getAnnotationElement();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.AnnotationElement();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _annotationElementList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _sequenceRef\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _graphColour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_graphColour", "graphColour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        if (!target.hasGraphColour())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- _label\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getLabel();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setLabel( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _label\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getGraphColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteGraphColour();\r
-            return;\r
-          }\r
-          target.setGraphColour( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _description\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getDescription();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setDescription( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _description\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _thresholdLine\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getThresholdLine();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.ThresholdLine();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _thresholdLine\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _graphColour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _graphGroup\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_graphGroup", "graphGroup",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.AnnotationDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        if (!target.hasGraphGroup())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getGraphGroup());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteGraphGroup();\r
-            return;\r
-          }\r
-          target.setGraphGroup( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _graphGroup\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _id\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.setId( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _id\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _annotationElementList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.AnnotationElement.class,\r
-        "_annotationElementList", "annotationElement",\r
-                 org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getAnnotationElement();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.addAnnotationElement( (jalview.schemabinding.version2.\r
-                                        AnnotationElement) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.AnnotationElement();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _annotationElementList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _label\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getLabel();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.setLabel( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _label\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _description\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_description", "description",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.Annotation.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getDescription();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.setDescription( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _description\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _thresholdLine\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.ThresholdLine.class, "_thresholdLine",\r
-        "thresholdLine", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Annotation target = (Annotation) object;\r
-        return target.getThresholdLine();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Annotation target = (Annotation) object;\r
-          target.setThresholdLine( (jalview.schemabinding.version2.\r
-                                    ThresholdLine) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.ThresholdLine();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _thresholdLine\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.AnnotationDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Annotation.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index 57c0b2c..2507197 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,353 +7,353 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class AnnotationElement.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AnnotationElement\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _position\r
-   */\r
-  private int _position;\r
-\r
-  /**\r
-   * keeps track of state for field: _position\r
-   */\r
-  private boolean _has_position;\r
-\r
-  /**\r
-   * Field _colour\r
-   */\r
-  private int _colour;\r
-\r
-  /**\r
-   * keeps track of state for field: _colour\r
-   */\r
-  private boolean _has_colour;\r
-\r
-  /**\r
-   * Field _displayCharacter\r
-   */\r
-  private java.lang.String _displayCharacter;\r
-\r
-  /**\r
-   * Field _description\r
-   */\r
-  private java.lang.String _description;\r
-\r
-  /**\r
-   * Field _secondaryStructure\r
-   */\r
-  private java.lang.String _secondaryStructure;\r
-\r
-  /**\r
-   * Field _value\r
-   */\r
-  private float _value;\r
-\r
-  /**\r
-   * keeps track of state for field: _value\r
-   */\r
-  private boolean _has_value;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public AnnotationElement()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.AnnotationElement()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteColour\r
-   *\r
-   */\r
-  public void deleteColour()\r
-  {\r
-    this._has_colour = false;\r
-  } //-- void deleteColour()\r
-\r
-  /**\r
-   * Method deletePosition\r
-   *\r
-   */\r
-  public void deletePosition()\r
-  {\r
-    this._has_position = false;\r
-  } //-- void deletePosition()\r
-\r
-  /**\r
-   * Method deleteValue\r
-   *\r
-   */\r
-  public void deleteValue()\r
-  {\r
-    this._has_value = false;\r
-  } //-- void deleteValue()\r
-\r
-  /**\r
-   * Returns the value of field 'colour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'colour'.\r
-   */\r
-  public int getColour()\r
-  {\r
-    return this._colour;\r
-  } //-- int getColour()\r
-\r
-  /**\r
-   * Returns the value of field 'description'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'description'.\r
-   */\r
-  public java.lang.String getDescription()\r
-  {\r
-    return this._description;\r
-  } //-- java.lang.String getDescription()\r
-\r
-  /**\r
-   * Returns the value of field 'displayCharacter'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'displayCharacter'.\r
-   */\r
-  public java.lang.String getDisplayCharacter()\r
-  {\r
-    return this._displayCharacter;\r
-  } //-- java.lang.String getDisplayCharacter()\r
-\r
-  /**\r
-   * Returns the value of field 'position'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'position'.\r
-   */\r
-  public int getPosition()\r
-  {\r
-    return this._position;\r
-  } //-- int getPosition()\r
-\r
-  /**\r
-   * Returns the value of field 'secondaryStructure'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'secondaryStructure'.\r
-   */\r
-  public java.lang.String getSecondaryStructure()\r
-  {\r
-    return this._secondaryStructure;\r
-  } //-- java.lang.String getSecondaryStructure()\r
-\r
-  /**\r
-   * Returns the value of field 'value'.\r
-   *\r
-   * @return float\r
-   * @return the value of field 'value'.\r
-   */\r
-  public float getValue()\r
-  {\r
-    return this._value;\r
-  } //-- float getValue()\r
-\r
-  /**\r
-   * Method hasColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasColour()\r
-  {\r
-    return this._has_colour;\r
-  } //-- boolean hasColour()\r
-\r
-  /**\r
-   * Method hasPosition\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasPosition()\r
-  {\r
-    return this._has_position;\r
-  } //-- boolean hasPosition()\r
-\r
-  /**\r
-   * Method hasValue\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasValue()\r
-  {\r
-    return this._has_value;\r
-  } //-- boolean hasValue()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class AnnotationElement implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _position\r
+     */\r
+    private int _position;\r
+\r
+    /**\r
+     * keeps track of state for field: _position\r
+     */\r
+    private boolean _has_position;\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private int _colour;\r
+\r
+    /**\r
+     * keeps track of state for field: _colour\r
+     */\r
+    private boolean _has_colour;\r
+\r
+    /**\r
+     * Field _displayCharacter\r
+     */\r
+    private java.lang.String _displayCharacter;\r
+\r
+    /**\r
+     * Field _description\r
+     */\r
+    private java.lang.String _description;\r
+\r
+    /**\r
+     * Field _secondaryStructure\r
+     */\r
+    private java.lang.String _secondaryStructure;\r
+\r
+    /**\r
+     * Field _value\r
+     */\r
+    private float _value;\r
+\r
+    /**\r
+     * keeps track of state for field: _value\r
+     */\r
+    private boolean _has_value;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public AnnotationElement() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.AnnotationElement()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteColour\r
+     * \r
+     */\r
+    public void deleteColour()\r
+    {\r
+        this._has_colour= false;\r
+    } //-- void deleteColour() \r
+\r
+    /**\r
+     * Method deletePosition\r
+     * \r
+     */\r
+    public void deletePosition()\r
+    {\r
+        this._has_position= false;\r
+    } //-- void deletePosition() \r
+\r
+    /**\r
+     * Method deleteValue\r
+     * \r
+     */\r
+    public void deleteValue()\r
+    {\r
+        this._has_value= false;\r
+    } //-- void deleteValue() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public int getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- int getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'description'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'description'.\r
+     */\r
+    public java.lang.String getDescription()\r
+    {\r
+        return this._description;\r
+    } //-- java.lang.String getDescription() \r
+\r
+    /**\r
+     * Returns the value of field 'displayCharacter'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'displayCharacter'.\r
+     */\r
+    public java.lang.String getDisplayCharacter()\r
+    {\r
+        return this._displayCharacter;\r
+    } //-- java.lang.String getDisplayCharacter() \r
+\r
+    /**\r
+     * Returns the value of field 'position'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'position'.\r
+     */\r
+    public int getPosition()\r
+    {\r
+        return this._position;\r
+    } //-- int getPosition() \r
+\r
+    /**\r
+     * Returns the value of field 'secondaryStructure'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'secondaryStructure'.\r
+     */\r
+    public java.lang.String getSecondaryStructure()\r
+    {\r
+        return this._secondaryStructure;\r
+    } //-- java.lang.String getSecondaryStructure() \r
+\r
+    /**\r
+     * Returns the value of field 'value'.\r
+     * \r
+     * @return float\r
+     * @return the value of field 'value'.\r
+     */\r
+    public float getValue()\r
+    {\r
+        return this._value;\r
+    } //-- float getValue() \r
+\r
+    /**\r
+     * Method hasColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColour()\r
+    {\r
+        return this._has_colour;\r
+    } //-- boolean hasColour() \r
+\r
+    /**\r
+     * Method hasPosition\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasPosition()\r
+    {\r
+        return this._has_position;\r
+    } //-- boolean hasPosition() \r
+\r
+    /**\r
+     * Method hasValue\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasValue()\r
+    {\r
+        return this._has_value;\r
+    } //-- boolean hasValue() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(int colour)\r
+    {\r
+        this._colour = colour;\r
+        this._has_colour = true;\r
+    } //-- void setColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'description'.\r
+     * \r
+     * @param description the value of field 'description'.\r
+     */\r
+    public void setDescription(java.lang.String description)\r
+    {\r
+        this._description = description;\r
+    } //-- void setDescription(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'displayCharacter'.\r
+     * \r
+     * @param displayCharacter the value of field 'displayCharacter'\r
+     */\r
+    public void setDisplayCharacter(java.lang.String displayCharacter)\r
+    {\r
+        this._displayCharacter = displayCharacter;\r
+    } //-- void setDisplayCharacter(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'position'.\r
+     * \r
+     * @param position the value of field 'position'.\r
+     */\r
+    public void setPosition(int position)\r
+    {\r
+        this._position = position;\r
+        this._has_position = true;\r
+    } //-- void setPosition(int) \r
+\r
+    /**\r
+     * Sets the value of field 'secondaryStructure'.\r
+     * \r
+     * @param secondaryStructure the value of field\r
+     * 'secondaryStructure'.\r
+     */\r
+    public void setSecondaryStructure(java.lang.String secondaryStructure)\r
+    {\r
+        this._secondaryStructure = secondaryStructure;\r
+    } //-- void setSecondaryStructure(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'value'.\r
+     * \r
+     * @param value the value of field 'value'.\r
+     */\r
+    public void setValue(float value)\r
+    {\r
+        this._value = value;\r
+        this._has_value = true;\r
+    } //-- void setValue(float) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'colour'.\r
-   *\r
-   * @param colour the value of field 'colour'.\r
-   */\r
-  public void setColour(int colour)\r
-  {\r
-    this._colour = colour;\r
-    this._has_colour = true;\r
-  } //-- void setColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'description'.\r
-   *\r
-   * @param description the value of field 'description'.\r
-   */\r
-  public void setDescription(java.lang.String description)\r
-  {\r
-    this._description = description;\r
-  } //-- void setDescription(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'displayCharacter'.\r
-   *\r
-   * @param displayCharacter the value of field 'displayCharacter'\r
-   */\r
-  public void setDisplayCharacter(java.lang.String displayCharacter)\r
-  {\r
-    this._displayCharacter = displayCharacter;\r
-  } //-- void setDisplayCharacter(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'position'.\r
-   *\r
-   * @param position the value of field 'position'.\r
-   */\r
-  public void setPosition(int position)\r
-  {\r
-    this._position = position;\r
-    this._has_position = true;\r
-  } //-- void setPosition(int)\r
-\r
-  /**\r
-   * Sets the value of field 'secondaryStructure'.\r
-   *\r
-   * @param secondaryStructure the value of field\r
-   * 'secondaryStructure'.\r
-   */\r
-  public void setSecondaryStructure(java.lang.String secondaryStructure)\r
-  {\r
-    this._secondaryStructure = secondaryStructure;\r
-  } //-- void setSecondaryStructure(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'value'.\r
-   *\r
-   * @param value the value of field 'value'.\r
-   */\r
-  public void setValue(float value)\r
-  {\r
-    this._value = value;\r
-    this._has_value = true;\r
-  } //-- void setValue(float)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.AnnotationElement.class,\r
-                  reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
index 058788d..0eab95b 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,462 +7,407 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class AnnotationElementDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AnnotationElementDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public AnnotationElementDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "annotationElement";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _position\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_position", "position",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        if (!target.hasPosition())\r
-        {\r
-          return null;\r
+public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public AnnotationElementDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "annotationElement";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _position\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                if(!target.hasPosition())\r
+                    return null;\r
+                return new java.lang.Integer(target.getPosition());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setPosition( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _position\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getPosition());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setPosition( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                if(!target.hasColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteColour();\r
+                        return;\r
+                    }\r
+                    target.setColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _displayCharacter\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                return target.getDisplayCharacter();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    target.setDisplayCharacter( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _displayCharacter\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _position\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_colour", "colour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        if (!target.hasColour())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- _description\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                return target.getDescription();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    target.setDescription( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _description\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteColour();\r
-            return;\r
-          }\r
-          target.setColour( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _secondaryStructure\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                return target.getSecondaryStructure();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    target.setSecondaryStructure( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _secondaryStructure\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setLength(1);\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _value\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                AnnotationElement target = (AnnotationElement) object;\r
+                if(!target.hasValue())\r
+                    return null;\r
+                return new java.lang.Float(target.getValue());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    AnnotationElement target = (AnnotationElement) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteValue();\r
+                        return;\r
+                    }\r
+                    target.setValue( ((java.lang.Float)value).floatValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _value\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            FloatValidator typeValidator = new FloatValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _displayCharacter\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_displayCharacter", "displayCharacter",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.AnnotationElementDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        return target.getDisplayCharacter();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          target.setDisplayCharacter( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _displayCharacter\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _description\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_description", "description",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        return target.getDescription();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          target.setDescription( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _description\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _secondaryStructure\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_secondaryStructure", "secondaryStructure",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        return target.getSecondaryStructure();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          target.setSecondaryStructure( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _secondaryStructure\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setLength(1);\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _value\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,\r
-        "_value", "value", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        AnnotationElement target = (AnnotationElement) object;\r
-        if (!target.hasValue())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Float(target.getValue());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          AnnotationElement target = (AnnotationElement) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteValue();\r
-            return;\r
-          }\r
-          target.setValue( ( (java.lang.Float) value).floatValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _value\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      FloatValidator typeValidator = new FloatValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.AnnotationElementDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.AnnotationElement.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return jalview.schemabinding.version2.AnnotationElement.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 2b2dba7..bcc4642 100755 (executable)
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,166 +7,167 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Colour.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Colour\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _name\r
-   */\r
-  private java.lang.String _name;\r
-\r
-  /**\r
-   * Field _RGB\r
-   */\r
-  private java.lang.String _RGB;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Colour()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Colour()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'name'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'name'.\r
-   */\r
-  public java.lang.String getName()\r
-  {\r
-    return this._name;\r
-  } //-- java.lang.String getName()\r
-\r
-  /**\r
-   * Returns the value of field 'RGB'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'RGB'.\r
-   */\r
-  public java.lang.String getRGB()\r
-  {\r
-    return this._RGB;\r
-  } //-- java.lang.String getRGB()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class Colour implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+    /**\r
+     * Field _RGB\r
+     */\r
+    private java.lang.String _RGB;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Colour() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.Colour()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'RGB'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'RGB'.\r
+     */\r
+    public java.lang.String getRGB()\r
+    {\r
+        return this._RGB;\r
+    } //-- java.lang.String getRGB() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'RGB'.\r
+     * \r
+     * @param RGB the value of field 'RGB'.\r
+     */\r
+    public void setRGB(java.lang.String RGB)\r
+    {\r
+        this._RGB = RGB;\r
+    } //-- void setRGB(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'name'.\r
-   *\r
-   * @param name the value of field 'name'.\r
-   */\r
-  public void setName(java.lang.String name)\r
-  {\r
-    this._name = name;\r
-  } //-- void setName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'RGB'.\r
-   *\r
-   * @param RGB the value of field 'RGB'.\r
-   */\r
-  public void setRGB(java.lang.String RGB)\r
-  {\r
-    this._RGB = RGB;\r
-  } //-- void setRGB(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Colour.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/ColourDescriptor.java b/src/jalview/schemabinding/version2/ColourDescriptor.java
index 7865ccf..7aa3a82 100755 (executable)
--- a/src/jalview/schemabinding/version2/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/ColourDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,248 +7,237 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class ColourDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class ColourDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public ColourDescriptor()\r
-  {\r
-    super();\r
-    xmlName = "colour";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _name\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Colour target = (Colour) object;\r
-        return target.getName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Colour target = (Colour) object;\r
-          target.setName( (java.lang.String) value);\r
+public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public ColourDescriptor() {\r
+        super();\r
+        xmlName = "colour";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _name\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Colour target = (Colour) object;\r
+                return target.getName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Colour target = (Colour) object;\r
+                    target.setName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _name\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _RGB\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Colour target = (Colour) object;\r
+                return target.getRGB();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Colour target = (Colour) object;\r
+                    target.setRGB( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _RGB\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.ColourDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _name\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _RGB\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Colour target = (Colour) object;\r
-        return target.getRGB();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Colour target = (Colour) object;\r
-          target.setRGB( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _RGB\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.ColourDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Colour.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Colour.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index 7c98b4e..576a4ad 100644 (file)
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,192 +7,193 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class DBRef.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class DBRef\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _source\r
-   */\r
-  private java.lang.String _source;\r
-\r
-  /**\r
-   * Field _version\r
-   */\r
-  private java.lang.String _version;\r
-\r
-  /**\r
-   * Field _accessionId\r
-   */\r
-  private java.lang.String _accessionId;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public DBRef()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.DBRef()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'accessionId'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'accessionId'.\r
-   */\r
-  public java.lang.String getAccessionId()\r
-  {\r
-    return this._accessionId;\r
-  } //-- java.lang.String getAccessionId()\r
-\r
-  /**\r
-   * Returns the value of field 'source'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'source'.\r
-   */\r
-  public java.lang.String getSource()\r
-  {\r
-    return this._source;\r
-  } //-- java.lang.String getSource()\r
-\r
-  /**\r
-   * Returns the value of field 'version'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'version'.\r
-   */\r
-  public java.lang.String getVersion()\r
-  {\r
-    return this._version;\r
-  } //-- java.lang.String getVersion()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class DBRef implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _source\r
+     */\r
+    private java.lang.String _source;\r
+\r
+    /**\r
+     * Field _version\r
+     */\r
+    private java.lang.String _version;\r
+\r
+    /**\r
+     * Field _accessionId\r
+     */\r
+    private java.lang.String _accessionId;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public DBRef() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.DBRef()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'accessionId'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'accessionId'.\r
+     */\r
+    public java.lang.String getAccessionId()\r
+    {\r
+        return this._accessionId;\r
+    } //-- java.lang.String getAccessionId() \r
+\r
+    /**\r
+     * Returns the value of field 'source'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'source'.\r
+     */\r
+    public java.lang.String getSource()\r
+    {\r
+        return this._source;\r
+    } //-- java.lang.String getSource() \r
+\r
+    /**\r
+     * Returns the value of field 'version'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'version'.\r
+     */\r
+    public java.lang.String getVersion()\r
+    {\r
+        return this._version;\r
+    } //-- java.lang.String getVersion() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'accessionId'.\r
+     * \r
+     * @param accessionId the value of field 'accessionId'.\r
+     */\r
+    public void setAccessionId(java.lang.String accessionId)\r
+    {\r
+        this._accessionId = accessionId;\r
+    } //-- void setAccessionId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'source'.\r
+     * \r
+     * @param source the value of field 'source'.\r
+     */\r
+    public void setSource(java.lang.String source)\r
+    {\r
+        this._source = source;\r
+    } //-- void setSource(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'version'.\r
+     * \r
+     * @param version the value of field 'version'.\r
+     */\r
+    public void setVersion(java.lang.String version)\r
+    {\r
+        this._version = version;\r
+    } //-- void setVersion(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'accessionId'.\r
-   *\r
-   * @param accessionId the value of field 'accessionId'.\r
-   */\r
-  public void setAccessionId(java.lang.String accessionId)\r
-  {\r
-    this._accessionId = accessionId;\r
-  } //-- void setAccessionId(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'source'.\r
-   *\r
-   * @param source the value of field 'source'.\r
-   */\r
-  public void setSource(java.lang.String source)\r
-  {\r
-    this._source = source;\r
-  } //-- void setSource(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'version'.\r
-   *\r
-   * @param version the value of field 'version'.\r
-   */\r
-  public void setVersion(java.lang.String version)\r
-  {\r
-    this._version = version;\r
-  } //-- void setVersion(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.DBRef.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/DBRefDescriptor.java b/src/jalview/schemabinding/version2/DBRefDescriptor.java
index 9ab9112..939d5b1 100644 (file)
--- a/src/jalview/schemabinding/version2/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/DBRefDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,293 +7,272 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class DBRefDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class DBRefDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public DBRefDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "DBRef";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _source\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_source", "source",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        DBRef target = (DBRef) object;\r
-        return target.getSource();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          DBRef target = (DBRef) object;\r
-          target.setSource( (java.lang.String) value);\r
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public DBRefDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "DBRef";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _source\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getSource();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setSource( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _source\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _version\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getVersion();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setVersion( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _version\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _source\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _version\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_version", "version",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        DBRef target = (DBRef) object;\r
-        return target.getVersion();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          DBRef target = (DBRef) object;\r
-          target.setVersion( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _accessionId\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getAccessionId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setAccessionId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _accessionId\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.DBRefDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _version\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _accessionId\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_accessionId", "accessionId",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        DBRef target = (DBRef) object;\r
-        return target.getAccessionId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          DBRef target = (DBRef) object;\r
-          target.setAccessionId( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _accessionId\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.DBRefDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.DBRef.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.DBRef.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 2f7f2fa..305e287 100755 (executable)
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,540 +7,531 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Feature.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Feature\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _begin\r
-   */\r
-  private int _begin;\r
-\r
-  /**\r
-   * keeps track of state for field: _begin\r
-   */\r
-  private boolean _has_begin;\r
-\r
-  /**\r
-   * Field _end\r
-   */\r
-  private int _end;\r
-\r
-  /**\r
-   * keeps track of state for field: _end\r
-   */\r
-  private boolean _has_end;\r
-\r
-  /**\r
-   * Field _type\r
-   */\r
-  private java.lang.String _type;\r
-\r
-  /**\r
-   * Field _description\r
-   */\r
-  private java.lang.String _description;\r
-\r
-  /**\r
-   * Field _status\r
-   */\r
-  private java.lang.String _status;\r
-\r
-  /**\r
-   * Field _featureGroup\r
-   */\r
-  private java.lang.String _featureGroup;\r
-\r
-  /**\r
-   * Field _score\r
-   */\r
-  private float _score;\r
-\r
-  /**\r
-   * keeps track of state for field: _score\r
-   */\r
-  private boolean _has_score;\r
-\r
-  /**\r
-   * Field _otherDataList\r
-   */\r
-  private java.util.Vector _otherDataList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Feature()\r
-  {\r
-    super();\r
-    _otherDataList = new Vector();\r
-  } //-- jalview.schemabinding.version2.Feature()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param vOtherData\r
-   */\r
-  public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _otherDataList.addElement(vOtherData);\r
-  } //-- void addOtherData(jalview.schemabinding.version2.OtherData)\r
-\r
-  /**\r
-   * Method addOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vOtherData\r
-   */\r
-  public void addOtherData(int index,\r
-                           jalview.schemabinding.version2.OtherData vOtherData)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _otherDataList.insertElementAt(vOtherData, index);\r
-  } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData)\r
-\r
-  /**\r
-   * Method deleteBegin\r
-   *\r
-   */\r
-  public void deleteBegin()\r
-  {\r
-    this._has_begin = false;\r
-  } //-- void deleteBegin()\r
-\r
-  /**\r
-   * Method deleteEnd\r
-   *\r
-   */\r
-  public void deleteEnd()\r
-  {\r
-    this._has_end = false;\r
-  } //-- void deleteEnd()\r
-\r
-  /**\r
-   * Method deleteScore\r
-   *\r
-   */\r
-  public void deleteScore()\r
-  {\r
-    this._has_score = false;\r
-  } //-- void deleteScore()\r
-\r
-  /**\r
-   * Method enumerateOtherData\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateOtherData()\r
-  {\r
-    return _otherDataList.elements();\r
-  } //-- java.util.Enumeration enumerateOtherData()\r
-\r
-  /**\r
-   * Returns the value of field 'begin'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'begin'.\r
-   */\r
-  public int getBegin()\r
-  {\r
-    return this._begin;\r
-  } //-- int getBegin()\r
-\r
-  /**\r
-   * Returns the value of field 'description'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'description'.\r
-   */\r
-  public java.lang.String getDescription()\r
-  {\r
-    return this._description;\r
-  } //-- java.lang.String getDescription()\r
-\r
-  /**\r
-   * Returns the value of field 'end'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'end'.\r
-   */\r
-  public int getEnd()\r
-  {\r
-    return this._end;\r
-  } //-- int getEnd()\r
-\r
-  /**\r
-   * Returns the value of field 'featureGroup'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'featureGroup'.\r
-   */\r
-  public java.lang.String getFeatureGroup()\r
-  {\r
-    return this._featureGroup;\r
-  } //-- java.lang.String getFeatureGroup()\r
-\r
-  /**\r
-   * Method getOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return OtherData\r
-   */\r
-  public jalview.schemabinding.version2.OtherData getOtherData(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _otherDataList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.OtherData getOtherData(int)\r
-\r
-  /**\r
-   * Method getOtherData\r
-   *\r
-   *\r
-   *\r
-   * @return OtherData\r
-   */\r
-  public jalview.schemabinding.version2.OtherData[] getOtherData()\r
-  {\r
-    int size = _otherDataList.size();\r
-    jalview.schemabinding.version2.OtherData[] mArray = new jalview.\r
-        schemabinding.version2.OtherData[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.OtherData[] getOtherData()\r
-\r
-  /**\r
-   * Method getOtherDataCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getOtherDataCount()\r
-  {\r
-    return _otherDataList.size();\r
-  } //-- int getOtherDataCount()\r
-\r
-  /**\r
-   * Returns the value of field 'score'.\r
-   *\r
-   * @return float\r
-   * @return the value of field 'score'.\r
-   */\r
-  public float getScore()\r
-  {\r
-    return this._score;\r
-  } //-- float getScore()\r
-\r
-  /**\r
-   * Returns the value of field 'status'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'status'.\r
-   */\r
-  public java.lang.String getStatus()\r
-  {\r
-    return this._status;\r
-  } //-- java.lang.String getStatus()\r
-\r
-  /**\r
-   * Returns the value of field 'type'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'type'.\r
-   */\r
-  public java.lang.String getType()\r
-  {\r
-    return this._type;\r
-  } //-- java.lang.String getType()\r
-\r
-  /**\r
-   * Method hasBegin\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasBegin()\r
-  {\r
-    return this._has_begin;\r
-  } //-- boolean hasBegin()\r
-\r
-  /**\r
-   * Method hasEnd\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasEnd()\r
-  {\r
-    return this._has_end;\r
-  } //-- boolean hasEnd()\r
-\r
-  /**\r
-   * Method hasScore\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasScore()\r
-  {\r
-    return this._has_score;\r
-  } //-- boolean hasScore()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllOtherData\r
-   *\r
-   */\r
-  public void removeAllOtherData()\r
-  {\r
-    _otherDataList.removeAllElements();\r
-  } //-- void removeAllOtherData()\r
-\r
-  /**\r
-   * Method removeOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return OtherData\r
-   */\r
-  public jalview.schemabinding.version2.OtherData removeOtherData(int index)\r
-  {\r
-    java.lang.Object obj = _otherDataList.elementAt(index);\r
-    _otherDataList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.OtherData) obj;\r
-  } //-- jalview.schemabinding.version2.OtherData removeOtherData(int)\r
-\r
-  /**\r
-   * Sets the value of field 'begin'.\r
-   *\r
-   * @param begin the value of field 'begin'.\r
-   */\r
-  public void setBegin(int begin)\r
-  {\r
-    this._begin = begin;\r
-    this._has_begin = true;\r
-  } //-- void setBegin(int)\r
-\r
-  /**\r
-   * Sets the value of field 'description'.\r
-   *\r
-   * @param description the value of field 'description'.\r
-   */\r
-  public void setDescription(java.lang.String description)\r
-  {\r
-    this._description = description;\r
-  } //-- void setDescription(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'end'.\r
-   *\r
-   * @param end the value of field 'end'.\r
-   */\r
-  public void setEnd(int end)\r
-  {\r
-    this._end = end;\r
-    this._has_end = true;\r
-  } //-- void setEnd(int)\r
-\r
-  /**\r
-   * Sets the value of field 'featureGroup'.\r
-   *\r
-   * @param featureGroup the value of field 'featureGroup'.\r
-   */\r
-  public void setFeatureGroup(java.lang.String featureGroup)\r
-  {\r
-    this._featureGroup = featureGroup;\r
-  } //-- void setFeatureGroup(java.lang.String)\r
-\r
-  /**\r
-   * Method setOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vOtherData\r
-   */\r
-  public void setOtherData(int index,\r
-                           jalview.schemabinding.version2.OtherData vOtherData)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _otherDataList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _otherDataList.setElementAt(vOtherData, index);\r
-  } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData)\r
-\r
-  /**\r
-   * Method setOtherData\r
-   *\r
-   *\r
-   *\r
-   * @param otherDataArray\r
-   */\r
-  public void setOtherData(jalview.schemabinding.version2.OtherData[]\r
-                           otherDataArray)\r
-  {\r
-    //-- copy array\r
-    _otherDataList.removeAllElements();\r
-    for (int i = 0; i < otherDataArray.length; i++)\r
-    {\r
-      _otherDataList.addElement(otherDataArray[i]);\r
-    }\r
-  } //-- void setOtherData(jalview.schemabinding.version2.OtherData)\r
-\r
-  /**\r
-   * Sets the value of field 'score'.\r
-   *\r
-   * @param score the value of field 'score'.\r
-   */\r
-  public void setScore(float score)\r
-  {\r
-    this._score = score;\r
-    this._has_score = true;\r
-  } //-- void setScore(float)\r
-\r
-  /**\r
-   * Sets the value of field 'status'.\r
-   *\r
-   * @param status the value of field 'status'.\r
-   */\r
-  public void setStatus(java.lang.String status)\r
-  {\r
-    this._status = status;\r
-  } //-- void setStatus(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'type'.\r
-   *\r
-   * @param type the value of field 'type'.\r
-   */\r
-  public void setType(java.lang.String type)\r
-  {\r
-    this._type = type;\r
-  } //-- void setType(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Feature.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class Feature implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _begin\r
+     */\r
+    private int _begin;\r
+\r
+    /**\r
+     * keeps track of state for field: _begin\r
+     */\r
+    private boolean _has_begin;\r
+\r
+    /**\r
+     * Field _end\r
+     */\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
+\r
+    /**\r
+     * Field _type\r
+     */\r
+    private java.lang.String _type;\r
+\r
+    /**\r
+     * Field _description\r
+     */\r
+    private java.lang.String _description;\r
+\r
+    /**\r
+     * Field _status\r
+     */\r
+    private java.lang.String _status;\r
+\r
+    /**\r
+     * Field _featureGroup\r
+     */\r
+    private java.lang.String _featureGroup;\r
+\r
+    /**\r
+     * Field _score\r
+     */\r
+    private float _score;\r
+\r
+    /**\r
+     * keeps track of state for field: _score\r
+     */\r
+    private boolean _has_score;\r
+\r
+    /**\r
+     * Field _otherDataList\r
+     */\r
+    private java.util.Vector _otherDataList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Feature() {\r
+        super();\r
+        _otherDataList = new Vector();\r
+    } //-- jalview.schemabinding.version2.Feature()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param vOtherData\r
+     */\r
+    public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _otherDataList.addElement(vOtherData);\r
+    } //-- void addOtherData(jalview.schemabinding.version2.OtherData) \r
+\r
+    /**\r
+     * Method addOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vOtherData\r
+     */\r
+    public void addOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _otherDataList.insertElementAt(vOtherData, index);\r
+    } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) \r
+\r
+    /**\r
+     * Method deleteBegin\r
+     * \r
+     */\r
+    public void deleteBegin()\r
+    {\r
+        this._has_begin= false;\r
+    } //-- void deleteBegin() \r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
+     * Method deleteScore\r
+     * \r
+     */\r
+    public void deleteScore()\r
+    {\r
+        this._has_score= false;\r
+    } //-- void deleteScore() \r
+\r
+    /**\r
+     * Method enumerateOtherData\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateOtherData()\r
+    {\r
+        return _otherDataList.elements();\r
+    } //-- java.util.Enumeration enumerateOtherData() \r
+\r
+    /**\r
+     * Returns the value of field 'begin'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'begin'.\r
+     */\r
+    public int getBegin()\r
+    {\r
+        return this._begin;\r
+    } //-- int getBegin() \r
+\r
+    /**\r
+     * Returns the value of field 'description'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'description'.\r
+     */\r
+    public java.lang.String getDescription()\r
+    {\r
+        return this._description;\r
+    } //-- java.lang.String getDescription() \r
+\r
+    /**\r
+     * Returns the value of field 'end'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'end'.\r
+     */\r
+    public int getEnd()\r
+    {\r
+        return this._end;\r
+    } //-- int getEnd() \r
+\r
+    /**\r
+     * Returns the value of field 'featureGroup'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'featureGroup'.\r
+     */\r
+    public java.lang.String getFeatureGroup()\r
+    {\r
+        return this._featureGroup;\r
+    } //-- java.lang.String getFeatureGroup() \r
+\r
+    /**\r
+     * Method getOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return OtherData\r
+     */\r
+    public jalview.schemabinding.version2.OtherData getOtherData(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _otherDataList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.OtherData getOtherData(int) \r
+\r
+    /**\r
+     * Method getOtherData\r
+     * \r
+     * \r
+     * \r
+     * @return OtherData\r
+     */\r
+    public jalview.schemabinding.version2.OtherData[] getOtherData()\r
+    {\r
+        int size = _otherDataList.size();\r
+        jalview.schemabinding.version2.OtherData[] mArray = new jalview.schemabinding.version2.OtherData[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.OtherData[] getOtherData() \r
+\r
+    /**\r
+     * Method getOtherDataCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getOtherDataCount()\r
+    {\r
+        return _otherDataList.size();\r
+    } //-- int getOtherDataCount() \r
+\r
+    /**\r
+     * Returns the value of field 'score'.\r
+     * \r
+     * @return float\r
+     * @return the value of field 'score'.\r
+     */\r
+    public float getScore()\r
+    {\r
+        return this._score;\r
+    } //-- float getScore() \r
+\r
+    /**\r
+     * Returns the value of field 'status'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'status'.\r
+     */\r
+    public java.lang.String getStatus()\r
+    {\r
+        return this._status;\r
+    } //-- java.lang.String getStatus() \r
+\r
+    /**\r
+     * Returns the value of field 'type'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'type'.\r
+     */\r
+    public java.lang.String getType()\r
+    {\r
+        return this._type;\r
+    } //-- java.lang.String getType() \r
+\r
+    /**\r
+     * Method hasBegin\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasBegin()\r
+    {\r
+        return this._has_begin;\r
+    } //-- boolean hasBegin() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
+     * Method hasScore\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasScore()\r
+    {\r
+        return this._has_score;\r
+    } //-- boolean hasScore() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllOtherData\r
+     * \r
+     */\r
+    public void removeAllOtherData()\r
+    {\r
+        _otherDataList.removeAllElements();\r
+    } //-- void removeAllOtherData() \r
+\r
+    /**\r
+     * Method removeOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return OtherData\r
+     */\r
+    public jalview.schemabinding.version2.OtherData removeOtherData(int index)\r
+    {\r
+        java.lang.Object obj = _otherDataList.elementAt(index);\r
+        _otherDataList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.OtherData) obj;\r
+    } //-- jalview.schemabinding.version2.OtherData removeOtherData(int) \r
+\r
+    /**\r
+     * Sets the value of field 'begin'.\r
+     * \r
+     * @param begin the value of field 'begin'.\r
+     */\r
+    public void setBegin(int begin)\r
+    {\r
+        this._begin = begin;\r
+        this._has_begin = true;\r
+    } //-- void setBegin(int) \r
+\r
+    /**\r
+     * Sets the value of field 'description'.\r
+     * \r
+     * @param description the value of field 'description'.\r
+     */\r
+    public void setDescription(java.lang.String description)\r
+    {\r
+        this._description = description;\r
+    } //-- void setDescription(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'end'.\r
+     * \r
+     * @param end the value of field 'end'.\r
+     */\r
+    public void setEnd(int end)\r
+    {\r
+        this._end = end;\r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
+\r
+    /**\r
+     * Sets the value of field 'featureGroup'.\r
+     * \r
+     * @param featureGroup the value of field 'featureGroup'.\r
+     */\r
+    public void setFeatureGroup(java.lang.String featureGroup)\r
+    {\r
+        this._featureGroup = featureGroup;\r
+    } //-- void setFeatureGroup(java.lang.String) \r
+\r
+    /**\r
+     * Method setOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vOtherData\r
+     */\r
+    public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _otherDataList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _otherDataList.setElementAt(vOtherData, index);\r
+    } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData) \r
+\r
+    /**\r
+     * Method setOtherData\r
+     * \r
+     * \r
+     * \r
+     * @param otherDataArray\r
+     */\r
+    public void setOtherData(jalview.schemabinding.version2.OtherData[] otherDataArray)\r
+    {\r
+        //-- copy array\r
+        _otherDataList.removeAllElements();\r
+        for (int i = 0; i < otherDataArray.length; i++) {\r
+            _otherDataList.addElement(otherDataArray[i]);\r
+        }\r
+    } //-- void setOtherData(jalview.schemabinding.version2.OtherData) \r
+\r
+    /**\r
+     * Sets the value of field 'score'.\r
+     * \r
+     * @param score the value of field 'score'.\r
+     */\r
+    public void setScore(float score)\r
+    {\r
+        this._score = score;\r
+        this._has_score = true;\r
+    } //-- void setScore(float) \r
+\r
+    /**\r
+     * Sets the value of field 'status'.\r
+     * \r
+     * @param status the value of field 'status'.\r
+     */\r
+    public void setStatus(java.lang.String status)\r
+    {\r
+        this._status = status;\r
+    } //-- void setStatus(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'type'.\r
+     * \r
+     * @param type the value of field 'type'.\r
+     */\r
+    public void setType(java.lang.String type)\r
+    {\r
+        this._type = type;\r
+    } //-- void setType(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/FeatureDescriptor.java b/src/jalview/schemabinding/version2/FeatureDescriptor.java
index 0641afa..d0b9372 100755 (executable)
--- a/src/jalview/schemabinding/version2/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeatureDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,542 +7,471 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class FeatureDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class FeatureDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public FeatureDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "feature";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _begin\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_begin", "begin",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        if (!target.hasBegin())\r
-        {\r
-          return null;\r
+public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public FeatureDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "feature";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _begin\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                if(!target.hasBegin())\r
+                    return null;\r
+                return new java.lang.Integer(target.getBegin());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setBegin( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _begin\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getBegin());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setBegin( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _end\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _end\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _type\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                return target.getType();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    target.setType( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _type\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _begin\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _end\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        if (!target.hasEnd())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- _description\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                return target.getDescription();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    target.setDescription( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _description\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getEnd());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setEnd( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _status\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                return target.getStatus();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    target.setStatus( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _status\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _featureGroup\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                return target.getFeatureGroup();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    target.setFeatureGroup( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _featureGroup\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _end\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _type\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        return target.getType();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          target.setType( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _score\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                if(!target.hasScore())\r
+                    return null;\r
+                return new java.lang.Float(target.getScore());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteScore();\r
+                        return;\r
+                    }\r
+                    target.setScore( ((java.lang.Float)value).floatValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _score\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            FloatValidator typeValidator = new FloatValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _otherDataList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Feature target = (Feature) object;\r
+                return target.getOtherData();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Feature target = (Feature) object;\r
+                    target.addOtherData( (jalview.schemabinding.version2.OtherData) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.OtherData();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _otherDataList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _type\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _description\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_description", "description",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.FeatureDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        return target.getDescription();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          target.setDescription( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _description\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _status\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_status", "status",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        return target.getStatus();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          target.setStatus( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _status\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _featureGroup\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_featureGroup", "featureGroup",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        return target.getFeatureGroup();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          target.setFeatureGroup( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _featureGroup\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _score\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,\r
-        "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        if (!target.hasScore())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Float(target.getScore());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteScore();\r
-            return;\r
-          }\r
-          target.setScore( ( (java.lang.Float) value).floatValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _score\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      FloatValidator typeValidator = new FloatValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _otherDataList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.OtherData.class, "_otherDataList", "otherData",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.Feature.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Feature target = (Feature) object;\r
-        return target.getOtherData();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Feature target = (Feature) object;\r
-          target.addOtherData( (jalview.schemabinding.version2.OtherData) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.OtherData();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _otherDataList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.FeatureDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Feature.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index 2dad54a..c20a83c 100755 (executable)
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,276 +7,268 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class FeatureSettings.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class FeatureSettings\r
-    implements java.io.Serializable\r
-{\r
+public class FeatureSettings implements java.io.Serializable {\r
 \r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
 \r
-  /**\r
-   * Field _settingList\r
-   */\r
-  private java.util.Vector _settingList;\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
+    /**\r
+     * Field _settingList\r
+     */\r
+    private java.util.Vector _settingList;\r
 \r
-  public FeatureSettings()\r
-  {\r
-    super();\r
-    _settingList = new Vector();\r
-  } //-- jalview.schemabinding.version2.FeatureSettings()\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  /**\r
-   * Method addSetting\r
-   *\r
-   *\r
-   *\r
-   * @param vSetting\r
-   */\r
-  public void addSetting(jalview.schemabinding.version2.Setting vSetting)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _settingList.addElement(vSetting);\r
-  } //-- void addSetting(jalview.schemabinding.version2.Setting)\r
+    public FeatureSettings() {\r
+        super();\r
+        _settingList = new Vector();\r
+    } //-- jalview.schemabinding.version2.FeatureSettings()\r
 \r
-  /**\r
-   * Method addSetting\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSetting\r
-   */\r
-  public void addSetting(int index,\r
-                         jalview.schemabinding.version2.Setting vSetting)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _settingList.insertElementAt(vSetting, index);\r
-  } //-- void addSetting(int, jalview.schemabinding.version2.Setting)\r
 \r
-  /**\r
-   * Method enumerateSetting\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateSetting()\r
-  {\r
-    return _settingList.elements();\r
-  } //-- java.util.Enumeration enumerateSetting()\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-  /**\r
-   * Method getSetting\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Setting\r
-   */\r
-  public jalview.schemabinding.version2.Setting getSetting(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _settingList.size()))\r
+    /**\r
+     * Method addSetting\r
+     * \r
+     * \r
+     * \r
+     * @param vSetting\r
+     */\r
+    public void addSetting(jalview.schemabinding.version2.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
+        _settingList.addElement(vSetting);\r
+    } //-- void addSetting(jalview.schemabinding.version2.Setting) \r
 \r
-    return (jalview.schemabinding.version2.Setting) _settingList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.Setting getSetting(int)\r
-\r
-  /**\r
-   * Method getSetting\r
-   *\r
-   *\r
-   *\r
-   * @return Setting\r
-   */\r
-  public jalview.schemabinding.version2.Setting[] getSetting()\r
-  {\r
-    int size = _settingList.size();\r
-    jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.\r
-        version2.Setting[size];\r
-    for (int index = 0; index < size; index++)\r
+    /**\r
+     * Method addSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSetting\r
+     */\r
+    public void addSetting(int index, jalview.schemabinding.version2.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Setting[] getSetting()\r
+        _settingList.insertElementAt(vSetting, index);\r
+    } //-- void addSetting(int, jalview.schemabinding.version2.Setting) \r
 \r
-  /**\r
-   * Method getSettingCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getSettingCount()\r
-  {\r
-    return _settingList.size();\r
-  } //-- int getSettingCount()\r
+    /**\r
+     * Method enumerateSetting\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateSetting()\r
+    {\r
+        return _settingList.elements();\r
+    } //-- java.util.Enumeration enumerateSetting() \r
 \r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+    /**\r
+     * Method getSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Setting\r
+     */\r
+    public jalview.schemabinding.version2.Setting getSetting(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _settingList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Setting getSetting(int) \r
+\r
+    /**\r
+     * Method getSetting\r
+     * \r
+     * \r
+     * \r
+     * @return Setting\r
+     */\r
+    public jalview.schemabinding.version2.Setting[] getSetting()\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
+        int size = _settingList.size();\r
+        jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.version2.Setting[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Setting[] getSetting() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method getSettingCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSettingCount()\r
+    {\r
+        return _settingList.size();\r
+    } //-- int getSettingCount() \r
 \r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
 \r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
-  /**\r
-   * Method removeAllSetting\r
-   *\r
-   */\r
-  public void removeAllSetting()\r
-  {\r
-    _settingList.removeAllElements();\r
-  } //-- void removeAllSetting()\r
+    /**\r
+     * Method removeAllSetting\r
+     * \r
+     */\r
+    public void removeAllSetting()\r
+    {\r
+        _settingList.removeAllElements();\r
+    } //-- void removeAllSetting() \r
 \r
-  /**\r
-   * Method removeSetting\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Setting\r
-   */\r
-  public jalview.schemabinding.version2.Setting removeSetting(int index)\r
-  {\r
-    java.lang.Object obj = _settingList.elementAt(index);\r
-    _settingList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Setting) obj;\r
-  } //-- jalview.schemabinding.version2.Setting removeSetting(int)\r
+    /**\r
+     * Method removeSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Setting\r
+     */\r
+    public jalview.schemabinding.version2.Setting removeSetting(int index)\r
+    {\r
+        java.lang.Object obj = _settingList.elementAt(index);\r
+        _settingList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Setting) obj;\r
+    } //-- jalview.schemabinding.version2.Setting removeSetting(int) \r
 \r
-  /**\r
-   * Method setSetting\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSetting\r
-   */\r
-  public void setSetting(int index,\r
-                         jalview.schemabinding.version2.Setting vSetting)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _settingList.size()))\r
+    /**\r
+     * Method setSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSetting\r
+     */\r
+    public void setSetting(int index, jalview.schemabinding.version2.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _settingList.setElementAt(vSetting, index);\r
-  } //-- void setSetting(int, jalview.schemabinding.version2.Setting)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _settingList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _settingList.setElementAt(vSetting, index);\r
+    } //-- void setSetting(int, jalview.schemabinding.version2.Setting) \r
 \r
-  /**\r
-   * Method setSetting\r
-   *\r
-   *\r
-   *\r
-   * @param settingArray\r
-   */\r
-  public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)\r
-  {\r
-    //-- copy array\r
-    _settingList.removeAllElements();\r
-    for (int i = 0; i < settingArray.length; i++)\r
+    /**\r
+     * Method setSetting\r
+     * \r
+     * \r
+     * \r
+     * @param settingArray\r
+     */\r
+    public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)\r
     {\r
-      _settingList.addElement(settingArray[i]);\r
-    }\r
-  } //-- void setSetting(jalview.schemabinding.version2.Setting)\r
+        //-- copy array\r
+        _settingList.removeAllElements();\r
+        for (int i = 0; i < settingArray.length; i++) {\r
+            _settingList.addElement(settingArray[i]);\r
+        }\r
+    } //-- void setSetting(jalview.schemabinding.version2.Setting) \r
 \r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
index d355c81..219037e 100755 (executable)
--- a/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,207 +7,202 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class FeatureSettingsDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class FeatureSettingsDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public FeatureSettingsDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "FeatureSettings";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _settingList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Setting.class, "_settingList", "setting",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        FeatureSettings target = (FeatureSettings) object;\r
-        return target.getSetting();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          FeatureSettings target = (FeatureSettings) object;\r
-          target.addSetting( (jalview.schemabinding.version2.Setting) value);\r
+public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public FeatureSettingsDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "FeatureSettings";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _settingList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                FeatureSettings target = (FeatureSettings) object;\r
+                return target.getSetting();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    FeatureSettings target = (FeatureSettings) object;\r
+                    target.addSetting( (jalview.schemabinding.version2.Setting) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Setting();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _settingList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Setting();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _settingList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.FeatureSettingsDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.FeatureSettings.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.FeatureSettingsDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.FeatureSettings.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index f0ca998..72321c6 100755 (executable)
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,110 +7,112 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Features.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Features\r
-    extends Feature implements java.io.Serializable\r
+public class Features extends Feature \r
+implements java.io.Serializable\r
 {\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
 \r
-  public Features()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Features()\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+    public Features() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.Features()\r
 \r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
 \r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Features.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
index a0a98b9..5eea818 100755 (executable)
--- a/src/jalview/schemabinding/version2/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,159 +7,160 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class FeaturesDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class FeaturesDescriptor\r
-    extends FeatureDescriptor\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public FeaturesDescriptor()\r
-  {\r
-    super();\r
-    setExtendsWithoutFlatten(new FeatureDescriptor());\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "features";\r
-  } //-- jalview.schemabinding.version2.FeaturesDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return super.getExtends();\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    if (identity == null)\r
+public class FeaturesDescriptor extends FeatureDescriptor {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public FeaturesDescriptor() {\r
+        super();\r
+        setExtendsWithoutFlatten(new FeatureDescriptor());\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "features";\r
+    } //-- jalview.schemabinding.version2.FeaturesDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return super.getExtends();\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        if (identity == null)\r
+            return super.getIdentity();\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Features.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      return super.getIdentity();\r
-    }\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Features.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index 305fa16..5b83e64 100644 (file)
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,220 +7,221 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class HiddenColumns.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class HiddenColumns\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _start\r
-   */\r
-  private int _start;\r
-\r
-  /**\r
-   * keeps track of state for field: _start\r
-   */\r
-  private boolean _has_start;\r
-\r
-  /**\r
-   * Field _end\r
-   */\r
-  private int _end;\r
-\r
-  /**\r
-   * keeps track of state for field: _end\r
-   */\r
-  private boolean _has_end;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public HiddenColumns()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.HiddenColumns()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteEnd\r
-   *\r
-   */\r
-  public void deleteEnd()\r
-  {\r
-    this._has_end = false;\r
-  } //-- void deleteEnd()\r
-\r
-  /**\r
-   * Method deleteStart\r
-   *\r
-   */\r
-  public void deleteStart()\r
-  {\r
-    this._has_start = false;\r
-  } //-- void deleteStart()\r
-\r
-  /**\r
-   * Returns the value of field 'end'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'end'.\r
-   */\r
-  public int getEnd()\r
-  {\r
-    return this._end;\r
-  } //-- int getEnd()\r
-\r
-  /**\r
-   * Returns the value of field 'start'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'start'.\r
-   */\r
-  public int getStart()\r
-  {\r
-    return this._start;\r
-  } //-- int getStart()\r
-\r
-  /**\r
-   * Method hasEnd\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasEnd()\r
-  {\r
-    return this._has_end;\r
-  } //-- boolean hasEnd()\r
-\r
-  /**\r
-   * Method hasStart\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasStart()\r
-  {\r
-    return this._has_start;\r
-  } //-- boolean hasStart()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class HiddenColumns implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _start\r
+     */\r
+    private int _start;\r
+\r
+    /**\r
+     * keeps track of state for field: _start\r
+     */\r
+    private boolean _has_start;\r
+\r
+    /**\r
+     * Field _end\r
+     */\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public HiddenColumns() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.HiddenColumns()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
+     * Method deleteStart\r
+     * \r
+     */\r
+    public void deleteStart()\r
+    {\r
+        this._has_start= false;\r
+    } //-- void deleteStart() \r
+\r
+    /**\r
+     * Returns the value of field 'end'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'end'.\r
+     */\r
+    public int getEnd()\r
+    {\r
+        return this._end;\r
+    } //-- int getEnd() \r
+\r
+    /**\r
+     * Returns the value of field 'start'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'start'.\r
+     */\r
+    public int getStart()\r
+    {\r
+        return this._start;\r
+    } //-- int getStart() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
+     * Method hasStart\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStart()\r
+    {\r
+        return this._has_start;\r
+    } //-- boolean hasStart() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'end'.\r
+     * \r
+     * @param end the value of field 'end'.\r
+     */\r
+    public void setEnd(int end)\r
+    {\r
+        this._end = end;\r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
+\r
+    /**\r
+     * Sets the value of field 'start'.\r
+     * \r
+     * @param start the value of field 'start'.\r
+     */\r
+    public void setStart(int start)\r
+    {\r
+        this._start = start;\r
+        this._has_start = true;\r
+    } //-- void setStart(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'end'.\r
-   *\r
-   * @param end the value of field 'end'.\r
-   */\r
-  public void setEnd(int end)\r
-  {\r
-    this._end = end;\r
-    this._has_end = true;\r
-  } //-- void setEnd(int)\r
-\r
-  /**\r
-   * Sets the value of field 'start'.\r
-   *\r
-   * @param start the value of field 'start'.\r
-   */\r
-  public void setStart(int start)\r
-  {\r
-    this._start = start;\r
-    this._has_start = true;\r
-  } //-- void setStart(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
index 2d92682..df99628 100644 (file)
--- a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,264 +7,246 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class HiddenColumnsDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class HiddenColumnsDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public HiddenColumnsDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "hiddenColumns";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _start\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_start", "start",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        HiddenColumns target = (HiddenColumns) object;\r
-        if (!target.hasStart())\r
-        {\r
-          return null;\r
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public HiddenColumnsDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "hiddenColumns";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _start\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                HiddenColumns target = (HiddenColumns) object;\r
+                if(!target.hasStart())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStart());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    HiddenColumns target = (HiddenColumns) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteStart();\r
+                        return;\r
+                    }\r
+                    target.setStart( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _start\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getStart());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          HiddenColumns target = (HiddenColumns) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteStart();\r
-            return;\r
-          }\r
-          target.setStart( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _end\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                HiddenColumns target = (HiddenColumns) object;\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    HiddenColumns target = (HiddenColumns) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteEnd();\r
+                        return;\r
+                    }\r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _end\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _start\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _end\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        HiddenColumns target = (HiddenColumns) object;\r
-        if (!target.hasEnd())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getEnd());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          HiddenColumns target = (HiddenColumns) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteEnd();\r
-            return;\r
-          }\r
-          target.setEnd( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _end\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.HiddenColumns.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.HiddenColumns.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 49edb8d..06eb940 100755 (executable)
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,906 +7,903 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class JGroup.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JGroup\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _start\r
-   */\r
-  private int _start;\r
-\r
-  /**\r
-   * keeps track of state for field: _start\r
-   */\r
-  private boolean _has_start;\r
-\r
-  /**\r
-   * Field _end\r
-   */\r
-  private int _end;\r
-\r
-  /**\r
-   * keeps track of state for field: _end\r
-   */\r
-  private boolean _has_end;\r
-\r
-  /**\r
-   * Field _name\r
-   */\r
-  private java.lang.String _name;\r
-\r
-  /**\r
-   * Field _colour\r
-   */\r
-  private java.lang.String _colour;\r
-\r
-  /**\r
-   * Field _consThreshold\r
-   */\r
-  private int _consThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _consThreshold\r
-   */\r
-  private boolean _has_consThreshold;\r
-\r
-  /**\r
-   * Field _pidThreshold\r
-   */\r
-  private int _pidThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _pidThreshold\r
-   */\r
-  private boolean _has_pidThreshold;\r
-\r
-  /**\r
-   * Field _outlineColour\r
-   */\r
-  private int _outlineColour;\r
-\r
-  /**\r
-   * keeps track of state for field: _outlineColour\r
-   */\r
-  private boolean _has_outlineColour;\r
-\r
-  /**\r
-   * Field _displayBoxes\r
-   */\r
-  private boolean _displayBoxes;\r
-\r
-  /**\r
-   * keeps track of state for field: _displayBoxes\r
-   */\r
-  private boolean _has_displayBoxes;\r
-\r
-  /**\r
-   * Field _displayText\r
-   */\r
-  private boolean _displayText;\r
-\r
-  /**\r
-   * keeps track of state for field: _displayText\r
-   */\r
-  private boolean _has_displayText;\r
-\r
-  /**\r
-   * Field _colourText\r
-   */\r
-  private boolean _colourText;\r
-\r
-  /**\r
-   * keeps track of state for field: _colourText\r
-   */\r
-  private boolean _has_colourText;\r
-\r
-  /**\r
-   * Field _textCol1\r
-   */\r
-  private int _textCol1;\r
-\r
-  /**\r
-   * keeps track of state for field: _textCol1\r
-   */\r
-  private boolean _has_textCol1;\r
-\r
-  /**\r
-   * Field _textCol2\r
-   */\r
-  private int _textCol2;\r
-\r
-  /**\r
-   * keeps track of state for field: _textCol2\r
-   */\r
-  private boolean _has_textCol2;\r
-\r
-  /**\r
-   * Field _textColThreshold\r
-   */\r
-  private int _textColThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _textColThreshold\r
-   */\r
-  private boolean _has_textColThreshold;\r
-\r
-  /**\r
-   * Field _seqList\r
-   */\r
-  private java.util.Vector _seqList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JGroup()\r
-  {\r
-    super();\r
-    _seqList = new Vector();\r
-  } //-- jalview.schemabinding.version2.JGroup()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addSeq\r
-   *\r
-   *\r
-   *\r
-   * @param vSeq\r
-   */\r
-  public void addSeq(int vSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _seqList.addElement(new java.lang.Integer(vSeq));\r
-  } //-- void addSeq(int)\r
-\r
-  /**\r
-   * Method addSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSeq\r
-   */\r
-  public void addSeq(int index, int vSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
-  } //-- void addSeq(int, int)\r
-\r
-  /**\r
-   * Method deleteColourText\r
-   *\r
-   */\r
-  public void deleteColourText()\r
-  {\r
-    this._has_colourText = false;\r
-  } //-- void deleteColourText()\r
-\r
-  /**\r
-   * Method deleteConsThreshold\r
-   *\r
-   */\r
-  public void deleteConsThreshold()\r
-  {\r
-    this._has_consThreshold = false;\r
-  } //-- void deleteConsThreshold()\r
-\r
-  /**\r
-   * Method deleteDisplayBoxes\r
-   *\r
-   */\r
-  public void deleteDisplayBoxes()\r
-  {\r
-    this._has_displayBoxes = false;\r
-  } //-- void deleteDisplayBoxes()\r
-\r
-  /**\r
-   * Method deleteDisplayText\r
-   *\r
-   */\r
-  public void deleteDisplayText()\r
-  {\r
-    this._has_displayText = false;\r
-  } //-- void deleteDisplayText()\r
-\r
-  /**\r
-   * Method deleteEnd\r
-   *\r
-   */\r
-  public void deleteEnd()\r
-  {\r
-    this._has_end = false;\r
-  } //-- void deleteEnd()\r
-\r
-  /**\r
-   * Method deleteOutlineColour\r
-   *\r
-   */\r
-  public void deleteOutlineColour()\r
-  {\r
-    this._has_outlineColour = false;\r
-  } //-- void deleteOutlineColour()\r
-\r
-  /**\r
-   * Method deletePidThreshold\r
-   *\r
-   */\r
-  public void deletePidThreshold()\r
-  {\r
-    this._has_pidThreshold = false;\r
-  } //-- void deletePidThreshold()\r
-\r
-  /**\r
-   * Method deleteStart\r
-   *\r
-   */\r
-  public void deleteStart()\r
-  {\r
-    this._has_start = false;\r
-  } //-- void deleteStart()\r
-\r
-  /**\r
-   * Method deleteTextCol1\r
-   *\r
-   */\r
-  public void deleteTextCol1()\r
-  {\r
-    this._has_textCol1 = false;\r
-  } //-- void deleteTextCol1()\r
-\r
-  /**\r
-   * Method deleteTextCol2\r
-   *\r
-   */\r
-  public void deleteTextCol2()\r
-  {\r
-    this._has_textCol2 = false;\r
-  } //-- void deleteTextCol2()\r
-\r
-  /**\r
-   * Method deleteTextColThreshold\r
-   *\r
-   */\r
-  public void deleteTextColThreshold()\r
-  {\r
-    this._has_textColThreshold = false;\r
-  } //-- void deleteTextColThreshold()\r
-\r
-  /**\r
-   * Method enumerateSeq\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateSeq()\r
-  {\r
-    return _seqList.elements();\r
-  } //-- java.util.Enumeration enumerateSeq()\r
-\r
-  /**\r
-   * Returns the value of field 'colour'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'colour'.\r
-   */\r
-  public java.lang.String getColour()\r
-  {\r
-    return this._colour;\r
-  } //-- java.lang.String getColour()\r
-\r
-  /**\r
-   * Returns the value of field 'colourText'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'colourText'.\r
-   */\r
-  public boolean getColourText()\r
-  {\r
-    return this._colourText;\r
-  } //-- boolean getColourText()\r
-\r
-  /**\r
-   * Returns the value of field 'consThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'consThreshold'.\r
-   */\r
-  public int getConsThreshold()\r
-  {\r
-    return this._consThreshold;\r
-  } //-- int getConsThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'displayBoxes'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'displayBoxes'.\r
-   */\r
-  public boolean getDisplayBoxes()\r
-  {\r
-    return this._displayBoxes;\r
-  } //-- boolean getDisplayBoxes()\r
-\r
-  /**\r
-   * Returns the value of field 'displayText'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'displayText'.\r
-   */\r
-  public boolean getDisplayText()\r
-  {\r
-    return this._displayText;\r
-  } //-- boolean getDisplayText()\r
-\r
-  /**\r
-   * Returns the value of field 'end'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'end'.\r
-   */\r
-  public int getEnd()\r
-  {\r
-    return this._end;\r
-  } //-- int getEnd()\r
-\r
-  /**\r
-   * Returns the value of field 'name'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'name'.\r
-   */\r
-  public java.lang.String getName()\r
-  {\r
-    return this._name;\r
-  } //-- java.lang.String getName()\r
-\r
-  /**\r
-   * Returns the value of field 'outlineColour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'outlineColour'.\r
-   */\r
-  public int getOutlineColour()\r
-  {\r
-    return this._outlineColour;\r
-  } //-- int getOutlineColour()\r
-\r
-  /**\r
-   * Returns the value of field 'pidThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'pidThreshold'.\r
-   */\r
-  public int getPidThreshold()\r
-  {\r
-    return this._pidThreshold;\r
-  } //-- int getPidThreshold()\r
-\r
-  /**\r
-   * Method getSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return int\r
-   */\r
-  public int getSeq(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _seqList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return ( (java.lang.Integer) _seqList.elementAt(index)).intValue();\r
-  } //-- int getSeq(int)\r
-\r
-  /**\r
-   * Method getSeq\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int[] getSeq()\r
-  {\r
-    int size = _seqList.size();\r
-    int[] mArray = new int[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = ( (java.lang.Integer) _seqList.elementAt(index)).intValue();\r
-    }\r
-    return mArray;\r
-  } //-- int[] getSeq()\r
-\r
-  /**\r
-   * Method getSeqCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getSeqCount()\r
-  {\r
-    return _seqList.size();\r
-  } //-- int getSeqCount()\r
-\r
-  /**\r
-   * Returns the value of field 'start'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'start'.\r
-   */\r
-  public int getStart()\r
-  {\r
-    return this._start;\r
-  } //-- int getStart()\r
-\r
-  /**\r
-   * Returns the value of field 'textCol1'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textCol1'.\r
-   */\r
-  public int getTextCol1()\r
-  {\r
-    return this._textCol1;\r
-  } //-- int getTextCol1()\r
-\r
-  /**\r
-   * Returns the value of field 'textCol2'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textCol2'.\r
-   */\r
-  public int getTextCol2()\r
-  {\r
-    return this._textCol2;\r
-  } //-- int getTextCol2()\r
-\r
-  /**\r
-   * Returns the value of field 'textColThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textColThreshold'.\r
-   */\r
-  public int getTextColThreshold()\r
-  {\r
-    return this._textColThreshold;\r
-  } //-- int getTextColThreshold()\r
-\r
-  /**\r
-   * Method hasColourText\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasColourText()\r
-  {\r
-    return this._has_colourText;\r
-  } //-- boolean hasColourText()\r
-\r
-  /**\r
-   * Method hasConsThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasConsThreshold()\r
-  {\r
-    return this._has_consThreshold;\r
-  } //-- boolean hasConsThreshold()\r
-\r
-  /**\r
-   * Method hasDisplayBoxes\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasDisplayBoxes()\r
-  {\r
-    return this._has_displayBoxes;\r
-  } //-- boolean hasDisplayBoxes()\r
-\r
-  /**\r
-   * Method hasDisplayText\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasDisplayText()\r
-  {\r
-    return this._has_displayText;\r
-  } //-- boolean hasDisplayText()\r
-\r
-  /**\r
-   * Method hasEnd\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasEnd()\r
-  {\r
-    return this._has_end;\r
-  } //-- boolean hasEnd()\r
-\r
-  /**\r
-   * Method hasOutlineColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasOutlineColour()\r
-  {\r
-    return this._has_outlineColour;\r
-  } //-- boolean hasOutlineColour()\r
-\r
-  /**\r
-   * Method hasPidThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasPidThreshold()\r
-  {\r
-    return this._has_pidThreshold;\r
-  } //-- boolean hasPidThreshold()\r
-\r
-  /**\r
-   * Method hasStart\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasStart()\r
-  {\r
-    return this._has_start;\r
-  } //-- boolean hasStart()\r
-\r
-  /**\r
-   * Method hasTextCol1\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextCol1()\r
-  {\r
-    return this._has_textCol1;\r
-  } //-- boolean hasTextCol1()\r
-\r
-  /**\r
-   * Method hasTextCol2\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextCol2()\r
-  {\r
-    return this._has_textCol2;\r
-  } //-- boolean hasTextCol2()\r
-\r
-  /**\r
-   * Method hasTextColThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextColThreshold()\r
-  {\r
-    return this._has_textColThreshold;\r
-  } //-- boolean hasTextColThreshold()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllSeq\r
-   *\r
-   */\r
-  public void removeAllSeq()\r
-  {\r
-    _seqList.removeAllElements();\r
-  } //-- void removeAllSeq()\r
-\r
-  /**\r
-   * Method removeSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return int\r
-   */\r
-  public int removeSeq(int index)\r
-  {\r
-    java.lang.Object obj = _seqList.elementAt(index);\r
-    _seqList.removeElementAt(index);\r
-    return ( (java.lang.Integer) obj).intValue();\r
-  } //-- int removeSeq(int)\r
-\r
-  /**\r
-   * Sets the value of field 'colour'.\r
-   *\r
-   * @param colour the value of field 'colour'.\r
-   */\r
-  public void setColour(java.lang.String colour)\r
-  {\r
-    this._colour = colour;\r
-  } //-- void setColour(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'colourText'.\r
-   *\r
-   * @param colourText the value of field 'colourText'.\r
-   */\r
-  public void setColourText(boolean colourText)\r
-  {\r
-    this._colourText = colourText;\r
-    this._has_colourText = true;\r
-  } //-- void setColourText(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'consThreshold'.\r
-   *\r
-   * @param consThreshold the value of field 'consThreshold'.\r
-   */\r
-  public void setConsThreshold(int consThreshold)\r
-  {\r
-    this._consThreshold = consThreshold;\r
-    this._has_consThreshold = true;\r
-  } //-- void setConsThreshold(int)\r
-\r
-  /**\r
-   * Sets the value of field 'displayBoxes'.\r
-   *\r
-   * @param displayBoxes the value of field 'displayBoxes'.\r
-   */\r
-  public void setDisplayBoxes(boolean displayBoxes)\r
-  {\r
-    this._displayBoxes = displayBoxes;\r
-    this._has_displayBoxes = true;\r
-  } //-- void setDisplayBoxes(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'displayText'.\r
-   *\r
-   * @param displayText the value of field 'displayText'.\r
-   */\r
-  public void setDisplayText(boolean displayText)\r
-  {\r
-    this._displayText = displayText;\r
-    this._has_displayText = true;\r
-  } //-- void setDisplayText(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'end'.\r
-   *\r
-   * @param end the value of field 'end'.\r
-   */\r
-  public void setEnd(int end)\r
-  {\r
-    this._end = end;\r
-    this._has_end = true;\r
-  } //-- void setEnd(int)\r
-\r
-  /**\r
-   * Sets the value of field 'name'.\r
-   *\r
-   * @param name the value of field 'name'.\r
-   */\r
-  public void setName(java.lang.String name)\r
-  {\r
-    this._name = name;\r
-  } //-- void setName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'outlineColour'.\r
-   *\r
-   * @param outlineColour the value of field 'outlineColour'.\r
-   */\r
-  public void setOutlineColour(int outlineColour)\r
-  {\r
-    this._outlineColour = outlineColour;\r
-    this._has_outlineColour = true;\r
-  } //-- void setOutlineColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'pidThreshold'.\r
-   *\r
-   * @param pidThreshold the value of field 'pidThreshold'.\r
-   */\r
-  public void setPidThreshold(int pidThreshold)\r
-  {\r
-    this._pidThreshold = pidThreshold;\r
-    this._has_pidThreshold = true;\r
-  } //-- void setPidThreshold(int)\r
-\r
-  /**\r
-   * Method setSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSeq\r
-   */\r
-  public void setSeq(int index, int vSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _seqList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
-  } //-- void setSeq(int, int)\r
-\r
-  /**\r
-   * Method setSeq\r
-   *\r
-   *\r
-   *\r
-   * @param seqArray\r
-   */\r
-  public void setSeq(int[] seqArray)\r
-  {\r
-    //-- copy array\r
-    _seqList.removeAllElements();\r
-    for (int i = 0; i < seqArray.length; i++)\r
-    {\r
-      _seqList.addElement(new java.lang.Integer(seqArray[i]));\r
-    }\r
-  } //-- void setSeq(int)\r
-\r
-  /**\r
-   * Sets the value of field 'start'.\r
-   *\r
-   * @param start the value of field 'start'.\r
-   */\r
-  public void setStart(int start)\r
-  {\r
-    this._start = start;\r
-    this._has_start = true;\r
-  } //-- void setStart(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textCol1'.\r
-   *\r
-   * @param textCol1 the value of field 'textCol1'.\r
-   */\r
-  public void setTextCol1(int textCol1)\r
-  {\r
-    this._textCol1 = textCol1;\r
-    this._has_textCol1 = true;\r
-  } //-- void setTextCol1(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textCol2'.\r
-   *\r
-   * @param textCol2 the value of field 'textCol2'.\r
-   */\r
-  public void setTextCol2(int textCol2)\r
-  {\r
-    this._textCol2 = textCol2;\r
-    this._has_textCol2 = true;\r
-  } //-- void setTextCol2(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textColThreshold'.\r
-   *\r
-   * @param textColThreshold the value of field 'textColThreshold'\r
-   */\r
-  public void setTextColThreshold(int textColThreshold)\r
-  {\r
-    this._textColThreshold = textColThreshold;\r
-    this._has_textColThreshold = true;\r
-  } //-- void setTextColThreshold(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.JGroup.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class JGroup implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _start\r
+     */\r
+    private int _start;\r
+\r
+    /**\r
+     * keeps track of state for field: _start\r
+     */\r
+    private boolean _has_start;\r
+\r
+    /**\r
+     * Field _end\r
+     */\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private java.lang.String _colour;\r
+\r
+    /**\r
+     * Field _consThreshold\r
+     */\r
+    private int _consThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _consThreshold\r
+     */\r
+    private boolean _has_consThreshold;\r
+\r
+    /**\r
+     * Field _pidThreshold\r
+     */\r
+    private int _pidThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _pidThreshold\r
+     */\r
+    private boolean _has_pidThreshold;\r
+\r
+    /**\r
+     * Field _outlineColour\r
+     */\r
+    private int _outlineColour;\r
+\r
+    /**\r
+     * keeps track of state for field: _outlineColour\r
+     */\r
+    private boolean _has_outlineColour;\r
+\r
+    /**\r
+     * Field _displayBoxes\r
+     */\r
+    private boolean _displayBoxes;\r
+\r
+    /**\r
+     * keeps track of state for field: _displayBoxes\r
+     */\r
+    private boolean _has_displayBoxes;\r
+\r
+    /**\r
+     * Field _displayText\r
+     */\r
+    private boolean _displayText;\r
+\r
+    /**\r
+     * keeps track of state for field: _displayText\r
+     */\r
+    private boolean _has_displayText;\r
+\r
+    /**\r
+     * Field _colourText\r
+     */\r
+    private boolean _colourText;\r
+\r
+    /**\r
+     * keeps track of state for field: _colourText\r
+     */\r
+    private boolean _has_colourText;\r
+\r
+    /**\r
+     * Field _textCol1\r
+     */\r
+    private int _textCol1;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol1\r
+     */\r
+    private boolean _has_textCol1;\r
+\r
+    /**\r
+     * Field _textCol2\r
+     */\r
+    private int _textCol2;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol2\r
+     */\r
+    private boolean _has_textCol2;\r
+\r
+    /**\r
+     * Field _textColThreshold\r
+     */\r
+    private int _textColThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _textColThreshold\r
+     */\r
+    private boolean _has_textColThreshold;\r
+\r
+    /**\r
+     * Field _seqList\r
+     */\r
+    private java.util.Vector _seqList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JGroup() {\r
+        super();\r
+        _seqList = new Vector();\r
+    } //-- jalview.schemabinding.version2.JGroup()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addSeq\r
+     * \r
+     * \r
+     * \r
+     * @param vSeq\r
+     */\r
+    public void addSeq(int vSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _seqList.addElement(new java.lang.Integer(vSeq));\r
+    } //-- void addSeq(int) \r
+\r
+    /**\r
+     * Method addSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSeq\r
+     */\r
+    public void addSeq(int index, int vSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
+    } //-- void addSeq(int, int) \r
+\r
+    /**\r
+     * Method deleteColourText\r
+     * \r
+     */\r
+    public void deleteColourText()\r
+    {\r
+        this._has_colourText= false;\r
+    } //-- void deleteColourText() \r
+\r
+    /**\r
+     * Method deleteConsThreshold\r
+     * \r
+     */\r
+    public void deleteConsThreshold()\r
+    {\r
+        this._has_consThreshold= false;\r
+    } //-- void deleteConsThreshold() \r
+\r
+    /**\r
+     * Method deleteDisplayBoxes\r
+     * \r
+     */\r
+    public void deleteDisplayBoxes()\r
+    {\r
+        this._has_displayBoxes= false;\r
+    } //-- void deleteDisplayBoxes() \r
+\r
+    /**\r
+     * Method deleteDisplayText\r
+     * \r
+     */\r
+    public void deleteDisplayText()\r
+    {\r
+        this._has_displayText= false;\r
+    } //-- void deleteDisplayText() \r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
+     * Method deleteOutlineColour\r
+     * \r
+     */\r
+    public void deleteOutlineColour()\r
+    {\r
+        this._has_outlineColour= false;\r
+    } //-- void deleteOutlineColour() \r
+\r
+    /**\r
+     * Method deletePidThreshold\r
+     * \r
+     */\r
+    public void deletePidThreshold()\r
+    {\r
+        this._has_pidThreshold= false;\r
+    } //-- void deletePidThreshold() \r
+\r
+    /**\r
+     * Method deleteStart\r
+     * \r
+     */\r
+    public void deleteStart()\r
+    {\r
+        this._has_start= false;\r
+    } //-- void deleteStart() \r
+\r
+    /**\r
+     * Method deleteTextCol1\r
+     * \r
+     */\r
+    public void deleteTextCol1()\r
+    {\r
+        this._has_textCol1= false;\r
+    } //-- void deleteTextCol1() \r
+\r
+    /**\r
+     * Method deleteTextCol2\r
+     * \r
+     */\r
+    public void deleteTextCol2()\r
+    {\r
+        this._has_textCol2= false;\r
+    } //-- void deleteTextCol2() \r
+\r
+    /**\r
+     * Method deleteTextColThreshold\r
+     * \r
+     */\r
+    public void deleteTextColThreshold()\r
+    {\r
+        this._has_textColThreshold= false;\r
+    } //-- void deleteTextColThreshold() \r
+\r
+    /**\r
+     * Method enumerateSeq\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateSeq()\r
+    {\r
+        return _seqList.elements();\r
+    } //-- java.util.Enumeration enumerateSeq() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public java.lang.String getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- java.lang.String getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'colourText'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'colourText'.\r
+     */\r
+    public boolean getColourText()\r
+    {\r
+        return this._colourText;\r
+    } //-- boolean getColourText() \r
+\r
+    /**\r
+     * Returns the value of field 'consThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'consThreshold'.\r
+     */\r
+    public int getConsThreshold()\r
+    {\r
+        return this._consThreshold;\r
+    } //-- int getConsThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'displayBoxes'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'displayBoxes'.\r
+     */\r
+    public boolean getDisplayBoxes()\r
+    {\r
+        return this._displayBoxes;\r
+    } //-- boolean getDisplayBoxes() \r
+\r
+    /**\r
+     * Returns the value of field 'displayText'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'displayText'.\r
+     */\r
+    public boolean getDisplayText()\r
+    {\r
+        return this._displayText;\r
+    } //-- boolean getDisplayText() \r
+\r
+    /**\r
+     * Returns the value of field 'end'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'end'.\r
+     */\r
+    public int getEnd()\r
+    {\r
+        return this._end;\r
+    } //-- int getEnd() \r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'outlineColour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'outlineColour'.\r
+     */\r
+    public int getOutlineColour()\r
+    {\r
+        return this._outlineColour;\r
+    } //-- int getOutlineColour() \r
+\r
+    /**\r
+     * Returns the value of field 'pidThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'pidThreshold'.\r
+     */\r
+    public int getPidThreshold()\r
+    {\r
+        return this._pidThreshold;\r
+    } //-- int getPidThreshold() \r
+\r
+    /**\r
+     * Method getSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int getSeq(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _seqList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+    } //-- int getSeq(int) \r
+\r
+    /**\r
+     * Method getSeq\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int[] getSeq()\r
+    {\r
+        int size = _seqList.size();\r
+        int[] mArray = new int[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+        }\r
+        return mArray;\r
+    } //-- int[] getSeq() \r
+\r
+    /**\r
+     * Method getSeqCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSeqCount()\r
+    {\r
+        return _seqList.size();\r
+    } //-- int getSeqCount() \r
+\r
+    /**\r
+     * Returns the value of field 'start'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'start'.\r
+     */\r
+    public int getStart()\r
+    {\r
+        return this._start;\r
+    } //-- int getStart() \r
+\r
+    /**\r
+     * Returns the value of field 'textCol1'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textCol1'.\r
+     */\r
+    public int getTextCol1()\r
+    {\r
+        return this._textCol1;\r
+    } //-- int getTextCol1() \r
+\r
+    /**\r
+     * Returns the value of field 'textCol2'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textCol2'.\r
+     */\r
+    public int getTextCol2()\r
+    {\r
+        return this._textCol2;\r
+    } //-- int getTextCol2() \r
+\r
+    /**\r
+     * Returns the value of field 'textColThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textColThreshold'.\r
+     */\r
+    public int getTextColThreshold()\r
+    {\r
+        return this._textColThreshold;\r
+    } //-- int getTextColThreshold() \r
+\r
+    /**\r
+     * Method hasColourText\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColourText()\r
+    {\r
+        return this._has_colourText;\r
+    } //-- boolean hasColourText() \r
+\r
+    /**\r
+     * Method hasConsThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasConsThreshold()\r
+    {\r
+        return this._has_consThreshold;\r
+    } //-- boolean hasConsThreshold() \r
+\r
+    /**\r
+     * Method hasDisplayBoxes\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasDisplayBoxes()\r
+    {\r
+        return this._has_displayBoxes;\r
+    } //-- boolean hasDisplayBoxes() \r
+\r
+    /**\r
+     * Method hasDisplayText\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasDisplayText()\r
+    {\r
+        return this._has_displayText;\r
+    } //-- boolean hasDisplayText() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
+     * Method hasOutlineColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasOutlineColour()\r
+    {\r
+        return this._has_outlineColour;\r
+    } //-- boolean hasOutlineColour() \r
+\r
+    /**\r
+     * Method hasPidThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasPidThreshold()\r
+    {\r
+        return this._has_pidThreshold;\r
+    } //-- boolean hasPidThreshold() \r
+\r
+    /**\r
+     * Method hasStart\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStart()\r
+    {\r
+        return this._has_start;\r
+    } //-- boolean hasStart() \r
+\r
+    /**\r
+     * Method hasTextCol1\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextCol1()\r
+    {\r
+        return this._has_textCol1;\r
+    } //-- boolean hasTextCol1() \r
+\r
+    /**\r
+     * Method hasTextCol2\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextCol2()\r
+    {\r
+        return this._has_textCol2;\r
+    } //-- boolean hasTextCol2() \r
+\r
+    /**\r
+     * Method hasTextColThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextColThreshold()\r
+    {\r
+        return this._has_textColThreshold;\r
+    } //-- boolean hasTextColThreshold() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllSeq\r
+     * \r
+     */\r
+    public void removeAllSeq()\r
+    {\r
+        _seqList.removeAllElements();\r
+    } //-- void removeAllSeq() \r
+\r
+    /**\r
+     * Method removeSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int removeSeq(int index)\r
+    {\r
+        java.lang.Object obj = _seqList.elementAt(index);\r
+        _seqList.removeElementAt(index);\r
+        return ((java.lang.Integer)obj).intValue();\r
+    } //-- int removeSeq(int) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(java.lang.String colour)\r
+    {\r
+        this._colour = colour;\r
+    } //-- void setColour(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'colourText'.\r
+     * \r
+     * @param colourText the value of field 'colourText'.\r
+     */\r
+    public void setColourText(boolean colourText)\r
+    {\r
+        this._colourText = colourText;\r
+        this._has_colourText = true;\r
+    } //-- void setColourText(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'consThreshold'.\r
+     * \r
+     * @param consThreshold the value of field 'consThreshold'.\r
+     */\r
+    public void setConsThreshold(int consThreshold)\r
+    {\r
+        this._consThreshold = consThreshold;\r
+        this._has_consThreshold = true;\r
+    } //-- void setConsThreshold(int) \r
+\r
+    /**\r
+     * Sets the value of field 'displayBoxes'.\r
+     * \r
+     * @param displayBoxes the value of field 'displayBoxes'.\r
+     */\r
+    public void setDisplayBoxes(boolean displayBoxes)\r
+    {\r
+        this._displayBoxes = displayBoxes;\r
+        this._has_displayBoxes = true;\r
+    } //-- void setDisplayBoxes(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'displayText'.\r
+     * \r
+     * @param displayText the value of field 'displayText'.\r
+     */\r
+    public void setDisplayText(boolean displayText)\r
+    {\r
+        this._displayText = displayText;\r
+        this._has_displayText = true;\r
+    } //-- void setDisplayText(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'end'.\r
+     * \r
+     * @param end the value of field 'end'.\r
+     */\r
+    public void setEnd(int end)\r
+    {\r
+        this._end = end;\r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'outlineColour'.\r
+     * \r
+     * @param outlineColour the value of field 'outlineColour'.\r
+     */\r
+    public void setOutlineColour(int outlineColour)\r
+    {\r
+        this._outlineColour = outlineColour;\r
+        this._has_outlineColour = true;\r
+    } //-- void setOutlineColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'pidThreshold'.\r
+     * \r
+     * @param pidThreshold the value of field 'pidThreshold'.\r
+     */\r
+    public void setPidThreshold(int pidThreshold)\r
+    {\r
+        this._pidThreshold = pidThreshold;\r
+        this._has_pidThreshold = true;\r
+    } //-- void setPidThreshold(int) \r
+\r
+    /**\r
+     * Method setSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSeq\r
+     */\r
+    public void setSeq(int index, int vSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _seqList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
+    } //-- void setSeq(int, int) \r
+\r
+    /**\r
+     * Method setSeq\r
+     * \r
+     * \r
+     * \r
+     * @param seqArray\r
+     */\r
+    public void setSeq(int[] seqArray)\r
+    {\r
+        //-- copy array\r
+        _seqList.removeAllElements();\r
+        for (int i = 0; i < seqArray.length; i++) {\r
+            _seqList.addElement(new java.lang.Integer(seqArray[i]));\r
+        }\r
+    } //-- void setSeq(int) \r
+\r
+    /**\r
+     * Sets the value of field 'start'.\r
+     * \r
+     * @param start the value of field 'start'.\r
+     */\r
+    public void setStart(int start)\r
+    {\r
+        this._start = start;\r
+        this._has_start = true;\r
+    } //-- void setStart(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textCol1'.\r
+     * \r
+     * @param textCol1 the value of field 'textCol1'.\r
+     */\r
+    public void setTextCol1(int textCol1)\r
+    {\r
+        this._textCol1 = textCol1;\r
+        this._has_textCol1 = true;\r
+    } //-- void setTextCol1(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textCol2'.\r
+     * \r
+     * @param textCol2 the value of field 'textCol2'.\r
+     */\r
+    public void setTextCol2(int textCol2)\r
+    {\r
+        this._textCol2 = textCol2;\r
+        this._has_textCol2 = true;\r
+    } //-- void setTextCol2(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textColThreshold'.\r
+     * \r
+     * @param textColThreshold the value of field 'textColThreshold'\r
+     */\r
+    public void setTextColThreshold(int textColThreshold)\r
+    {\r
+        this._textColThreshold = textColThreshold;\r
+        this._has_textColThreshold = true;\r
+    } //-- void setTextColThreshold(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JGroupDescriptor.java b/src/jalview/schemabinding/version2/JGroupDescriptor.java
index 15aeb79..1985c61 100755 (executable)
--- a/src/jalview/schemabinding/version2/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/JGroupDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,876 +7,731 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class JGroupDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JGroupDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JGroupDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "JGroup";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _start\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_start", "start",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasStart())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getStart());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteStart();\r
-            return;\r
-          }\r
-          target.setStart( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _start\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _end\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasEnd())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getEnd());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteEnd();\r
-            return;\r
-          }\r
-          target.setEnd( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _end\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _name\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        return target.getName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          target.setName( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _name\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_colour", "colour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        return target.getColour();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          target.setColour( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _consThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_consThreshold", "consThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasConsThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getConsThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteConsThreshold();\r
-            return;\r
-          }\r
-          target.setConsThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _consThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _pidThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_pidThreshold", "pidThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JGroupDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "JGroup";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _start\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasStart())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStart());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteStart();\r
+                        return;\r
+                    }\r
+                    target.setStart( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _start\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _end\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteEnd();\r
+                        return;\r
+                    }\r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _end\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _name\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                return target.getName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    target.setName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _name\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                return target.getColour();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    target.setColour( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _consThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasConsThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getConsThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteConsThreshold();\r
+                        return;\r
+                    }\r
+                    target.setConsThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _consThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _pidThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasPidThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getPidThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deletePidThreshold();\r
+                        return;\r
+                    }\r
+                    target.setPidThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _pidThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _outlineColour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasOutlineColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getOutlineColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteOutlineColour();\r
+                        return;\r
+                    }\r
+                    target.setOutlineColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _outlineColour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _displayBoxes\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasDisplayBoxes())\r
+                    return null;\r
+                return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteDisplayBoxes();\r
+                        return;\r
+                    }\r
+                    target.setDisplayBoxes( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _displayBoxes\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _displayText\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasDisplayText())\r
+                    return null;\r
+                return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteDisplayText();\r
+                        return;\r
+                    }\r
+                    target.setDisplayText( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _displayText\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colourText\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasColourText())\r
+                    return null;\r
+                return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteColourText();\r
+                        return;\r
+                    }\r
+                    target.setColourText( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colourText\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textCol1\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasTextCol1())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextCol1());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextCol1();\r
+                        return;\r
+                    }\r
+                    target.setTextCol1( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textCol1\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textCol2\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasTextCol2())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextCol2());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextCol2();\r
+                        return;\r
+                    }\r
+                    target.setTextCol2( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textCol2\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textColThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                if(!target.hasTextColThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextColThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextColThreshold();\r
+                        return;\r
+                    }\r
+                    target.setTextColThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textColThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _seqList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JGroup target = (JGroup) object;\r
+                return target.getSeq();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JGroup target = (JGroup) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.addSeq( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _seqList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.JGroupDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasPidThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getPidThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deletePidThreshold();\r
-            return;\r
-          }\r
-          target.setPidThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _pidThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _outlineColour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_outlineColour", "outlineColour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasOutlineColour())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getOutlineColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteOutlineColour();\r
-            return;\r
-          }\r
-          target.setOutlineColour( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _outlineColour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _displayBoxes\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_displayBoxes", "displayBoxes",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasDisplayBoxes())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteDisplayBoxes();\r
-            return;\r
-          }\r
-          target.setDisplayBoxes( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _displayBoxes\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _displayText\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_displayText", "displayText",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasDisplayText())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getDisplayText() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteDisplayText();\r
-            return;\r
-          }\r
-          target.setDisplayText( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _displayText\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colourText\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_colourText", "colourText",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasColourText())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getColourText() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteColourText();\r
-            return;\r
-          }\r
-          target.setColourText( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colourText\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textCol1\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textCol1", "textCol1",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.JGroup.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasTextCol1())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextCol1());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextCol1();\r
-            return;\r
-          }\r
-          target.setTextCol1( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textCol1\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textCol2\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textCol2", "textCol2",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasTextCol2())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextCol2());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextCol2();\r
-            return;\r
-          }\r
-          target.setTextCol2( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textCol2\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textColThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textColThreshold", "textColThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        if (!target.hasTextColThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextColThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextColThreshold();\r
-            return;\r
-          }\r
-          target.setTextColThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textColThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _seqList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JGroup target = (JGroup) object;\r
-        return target.getSeq();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JGroup target = (JGroup) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.addSeq( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _seqList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.JGroupDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.JGroup.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 29221ad..19e2e6d 100755 (executable)
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,861 +7,835 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class JSeq.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JSeq\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _colour\r
-   */\r
-  private int _colour;\r
-\r
-  /**\r
-   * keeps track of state for field: _colour\r
-   */\r
-  private boolean _has_colour;\r
-\r
-  /**\r
-   * Field _start\r
-   */\r
-  private int _start;\r
-\r
-  /**\r
-   * keeps track of state for field: _start\r
-   */\r
-  private boolean _has_start;\r
-\r
-  /**\r
-   * Field _end\r
-   */\r
-  private int _end;\r
-\r
-  /**\r
-   * keeps track of state for field: _end\r
-   */\r
-  private boolean _has_end;\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private int _id;\r
-\r
-  /**\r
-   * keeps track of state for field: _id\r
-   */\r
-  private boolean _has_id;\r
-\r
-  /**\r
-   * Field _hidden\r
-   */\r
-  private boolean _hidden;\r
-\r
-  /**\r
-   * keeps track of state for field: _hidden\r
-   */\r
-  private boolean _has_hidden;\r
-\r
-  /**\r
-   * Field _featuresList\r
-   */\r
-  private java.util.Vector _featuresList;\r
-\r
-  /**\r
-   * Field _pdbidsList\r
-   */\r
-  private java.util.Vector _pdbidsList;\r
-\r
-  /**\r
-   * Field _hiddenSequencesList\r
-   */\r
-  private java.util.Vector _hiddenSequencesList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JSeq()\r
-  {\r
-    super();\r
-    _featuresList = new Vector();\r
-    _pdbidsList = new Vector();\r
-    _hiddenSequencesList = new Vector();\r
-  } //-- jalview.schemabinding.version2.JSeq()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param vFeatures\r
-   */\r
-  public void addFeatures(jalview.schemabinding.version2.Features vFeatures)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _featuresList.addElement(vFeatures);\r
-  } //-- void addFeatures(jalview.schemabinding.version2.Features)\r
-\r
-  /**\r
-   * Method addFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vFeatures\r
-   */\r
-  public void addFeatures(int index,\r
-                          jalview.schemabinding.version2.Features vFeatures)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _featuresList.insertElementAt(vFeatures, index);\r
-  } //-- void addFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
-  /**\r
-   * Method addHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param vHiddenSequences\r
-   */\r
-  public void addHiddenSequences(int vHiddenSequences)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
-  } //-- void addHiddenSequences(int)\r
-\r
-  /**\r
-   * Method addHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vHiddenSequences\r
-   */\r
-  public void addHiddenSequences(int index, int vHiddenSequences)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences),\r
-                                         index);\r
-  } //-- void addHiddenSequences(int, int)\r
-\r
-  /**\r
-   * Method addPdbids\r
-   *\r
-   *\r
-   *\r
-   * @param vPdbids\r
-   */\r
-  public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _pdbidsList.addElement(vPdbids);\r
-  } //-- void addPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
-  /**\r
-   * Method addPdbids\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vPdbids\r
-   */\r
-  public void addPdbids(int index,\r
-                        jalview.schemabinding.version2.Pdbids vPdbids)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _pdbidsList.insertElementAt(vPdbids, index);\r
-  } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
-  /**\r
-   * Method deleteColour\r
-   *\r
-   */\r
-  public void deleteColour()\r
-  {\r
-    this._has_colour = false;\r
-  } //-- void deleteColour()\r
-\r
-  /**\r
-   * Method deleteEnd\r
-   *\r
-   */\r
-  public void deleteEnd()\r
-  {\r
-    this._has_end = false;\r
-  } //-- void deleteEnd()\r
-\r
-  /**\r
-   * Method deleteHidden\r
-   *\r
-   */\r
-  public void deleteHidden()\r
-  {\r
-    this._has_hidden = false;\r
-  } //-- void deleteHidden()\r
-\r
-  /**\r
-   * Method deleteId\r
-   *\r
-   */\r
-  public void deleteId()\r
-  {\r
-    this._has_id = false;\r
-  } //-- void deleteId()\r
-\r
-  /**\r
-   * Method deleteStart\r
-   *\r
-   */\r
-  public void deleteStart()\r
-  {\r
-    this._has_start = false;\r
-  } //-- void deleteStart()\r
-\r
-  /**\r
-   * Method enumerateFeatures\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateFeatures()\r
-  {\r
-    return _featuresList.elements();\r
-  } //-- java.util.Enumeration enumerateFeatures()\r
-\r
-  /**\r
-   * Method enumerateHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateHiddenSequences()\r
-  {\r
-    return _hiddenSequencesList.elements();\r
-  } //-- java.util.Enumeration enumerateHiddenSequences()\r
-\r
-  /**\r
-   * Method enumeratePdbids\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumeratePdbids()\r
-  {\r
-    return _pdbidsList.elements();\r
-  } //-- java.util.Enumeration enumeratePdbids()\r
-\r
-  /**\r
-   * Returns the value of field 'colour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'colour'.\r
-   */\r
-  public int getColour()\r
-  {\r
-    return this._colour;\r
-  } //-- int getColour()\r
-\r
-  /**\r
-   * Returns the value of field 'end'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'end'.\r
-   */\r
-  public int getEnd()\r
-  {\r
-    return this._end;\r
-  } //-- int getEnd()\r
-\r
-  /**\r
-   * Method getFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Features\r
-   */\r
-  public jalview.schemabinding.version2.Features getFeatures(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _featuresList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Features) _featuresList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.Features getFeatures(int)\r
-\r
-  /**\r
-   * Method getFeatures\r
-   *\r
-   *\r
-   *\r
-   * @return Features\r
-   */\r
-  public jalview.schemabinding.version2.Features[] getFeatures()\r
-  {\r
-    int size = _featuresList.size();\r
-    jalview.schemabinding.version2.Features[] mArray = new jalview.\r
-        schemabinding.version2.Features[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Features[] getFeatures()\r
-\r
-  /**\r
-   * Method getFeaturesCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getFeaturesCount()\r
-  {\r
-    return _featuresList.size();\r
-  } //-- int getFeaturesCount()\r
-\r
-  /**\r
-   * Returns the value of field 'hidden'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'hidden'.\r
-   */\r
-  public boolean getHidden()\r
-  {\r
-    return this._hidden;\r
-  } //-- boolean getHidden()\r
-\r
-  /**\r
-   * Method getHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return int\r
-   */\r
-  public int getHiddenSequences(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return ( (java.lang.Integer) _hiddenSequencesList.elementAt(index)).\r
-        intValue();\r
-  } //-- int getHiddenSequences(int)\r
-\r
-  /**\r
-   * Method getHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int[] getHiddenSequences()\r
-  {\r
-    int size = _hiddenSequencesList.size();\r
-    int[] mArray = new int[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = ( (java.lang.Integer) _hiddenSequencesList.elementAt(\r
-          index)).intValue();\r
-    }\r
-    return mArray;\r
-  } //-- int[] getHiddenSequences()\r
-\r
-  /**\r
-   * Method getHiddenSequencesCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getHiddenSequencesCount()\r
-  {\r
-    return _hiddenSequencesList.size();\r
-  } //-- int getHiddenSequencesCount()\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'id'.\r
-   */\r
-  public int getId()\r
-  {\r
-    return this._id;\r
-  } //-- int getId()\r
-\r
-  /**\r
-   * Method getPdbids\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Pdbids\r
-   */\r
-  public jalview.schemabinding.version2.Pdbids getPdbids(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _pdbidsList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.Pdbids getPdbids(int)\r
-\r
-  /**\r
-   * Method getPdbids\r
-   *\r
-   *\r
-   *\r
-   * @return Pdbids\r
-   */\r
-  public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
-  {\r
-    int size = _pdbidsList.size();\r
-    jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.\r
-        version2.Pdbids[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Pdbids[] getPdbids()\r
-\r
-  /**\r
-   * Method getPdbidsCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getPdbidsCount()\r
-  {\r
-    return _pdbidsList.size();\r
-  } //-- int getPdbidsCount()\r
-\r
-  /**\r
-   * Returns the value of field 'start'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'start'.\r
-   */\r
-  public int getStart()\r
-  {\r
-    return this._start;\r
-  } //-- int getStart()\r
-\r
-  /**\r
-   * Method hasColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasColour()\r
-  {\r
-    return this._has_colour;\r
-  } //-- boolean hasColour()\r
-\r
-  /**\r
-   * Method hasEnd\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasEnd()\r
-  {\r
-    return this._has_end;\r
-  } //-- boolean hasEnd()\r
-\r
-  /**\r
-   * Method hasHidden\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasHidden()\r
-  {\r
-    return this._has_hidden;\r
-  } //-- boolean hasHidden()\r
-\r
-  /**\r
-   * Method hasId\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasId()\r
-  {\r
-    return this._has_id;\r
-  } //-- boolean hasId()\r
-\r
-  /**\r
-   * Method hasStart\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasStart()\r
-  {\r
-    return this._has_start;\r
-  } //-- boolean hasStart()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllFeatures\r
-   *\r
-   */\r
-  public void removeAllFeatures()\r
-  {\r
-    _featuresList.removeAllElements();\r
-  } //-- void removeAllFeatures()\r
-\r
-  /**\r
-   * Method removeAllHiddenSequences\r
-   *\r
-   */\r
-  public void removeAllHiddenSequences()\r
-  {\r
-    _hiddenSequencesList.removeAllElements();\r
-  } //-- void removeAllHiddenSequences()\r
-\r
-  /**\r
-   * Method removeAllPdbids\r
-   *\r
-   */\r
-  public void removeAllPdbids()\r
-  {\r
-    _pdbidsList.removeAllElements();\r
-  } //-- void removeAllPdbids()\r
-\r
-  /**\r
-   * Method removeFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Features\r
-   */\r
-  public jalview.schemabinding.version2.Features removeFeatures(int index)\r
-  {\r
-    java.lang.Object obj = _featuresList.elementAt(index);\r
-    _featuresList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Features) obj;\r
-  } //-- jalview.schemabinding.version2.Features removeFeatures(int)\r
-\r
-  /**\r
-   * Method removeHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return int\r
-   */\r
-  public int removeHiddenSequences(int index)\r
-  {\r
-    java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
-    _hiddenSequencesList.removeElementAt(index);\r
-    return ( (java.lang.Integer) obj).intValue();\r
-  } //-- int removeHiddenSequences(int)\r
-\r
-  /**\r
-   * Method removePdbids\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Pdbids\r
-   */\r
-  public jalview.schemabinding.version2.Pdbids removePdbids(int index)\r
-  {\r
-    java.lang.Object obj = _pdbidsList.elementAt(index);\r
-    _pdbidsList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Pdbids) obj;\r
-  } //-- jalview.schemabinding.version2.Pdbids removePdbids(int)\r
-\r
-  /**\r
-   * Sets the value of field 'colour'.\r
-   *\r
-   * @param colour the value of field 'colour'.\r
-   */\r
-  public void setColour(int colour)\r
-  {\r
-    this._colour = colour;\r
-    this._has_colour = true;\r
-  } //-- void setColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'end'.\r
-   *\r
-   * @param end the value of field 'end'.\r
-   */\r
-  public void setEnd(int end)\r
-  {\r
-    this._end = end;\r
-    this._has_end = true;\r
-  } //-- void setEnd(int)\r
-\r
-  /**\r
-   * Method setFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vFeatures\r
-   */\r
-  public void setFeatures(int index,\r
-                          jalview.schemabinding.version2.Features vFeatures)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _featuresList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _featuresList.setElementAt(vFeatures, index);\r
-  } //-- void setFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
-  /**\r
-   * Method setFeatures\r
-   *\r
-   *\r
-   *\r
-   * @param featuresArray\r
-   */\r
-  public void setFeatures(jalview.schemabinding.version2.Features[]\r
-                          featuresArray)\r
-  {\r
-    //-- copy array\r
-    _featuresList.removeAllElements();\r
-    for (int i = 0; i < featuresArray.length; i++)\r
-    {\r
-      _featuresList.addElement(featuresArray[i]);\r
-    }\r
-  } //-- void setFeatures(jalview.schemabinding.version2.Features)\r
-\r
-  /**\r
-   * Sets the value of field 'hidden'.\r
-   *\r
-   * @param hidden the value of field 'hidden'.\r
-   */\r
-  public void setHidden(boolean hidden)\r
-  {\r
-    this._hidden = hidden;\r
-    this._has_hidden = true;\r
-  } //-- void setHidden(boolean)\r
-\r
-  /**\r
-   * Method setHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vHiddenSequences\r
-   */\r
-  public void setHiddenSequences(int index, int vHiddenSequences)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences),\r
-                                      index);\r
-  } //-- void setHiddenSequences(int, int)\r
-\r
-  /**\r
-   * Method setHiddenSequences\r
-   *\r
-   *\r
-   *\r
-   * @param hiddenSequencesArray\r
-   */\r
-  public void setHiddenSequences(int[] hiddenSequencesArray)\r
-  {\r
-    //-- copy array\r
-    _hiddenSequencesList.removeAllElements();\r
-    for (int i = 0; i < hiddenSequencesArray.length; i++)\r
-    {\r
-      _hiddenSequencesList.addElement(new java.lang.Integer(\r
-          hiddenSequencesArray[i]));\r
-    }\r
-  } //-- void setHiddenSequences(int)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(int id)\r
-  {\r
-    this._id = id;\r
-    this._has_id = true;\r
-  } //-- void setId(int)\r
-\r
-  /**\r
-   * Method setPdbids\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vPdbids\r
-   */\r
-  public void setPdbids(int index,\r
-                        jalview.schemabinding.version2.Pdbids vPdbids)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _pdbidsList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _pdbidsList.setElementAt(vPdbids, index);\r
-  } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
-  /**\r
-   * Method setPdbids\r
-   *\r
-   *\r
-   *\r
-   * @param pdbidsArray\r
-   */\r
-  public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)\r
-  {\r
-    //-- copy array\r
-    _pdbidsList.removeAllElements();\r
-    for (int i = 0; i < pdbidsArray.length; i++)\r
-    {\r
-      _pdbidsList.addElement(pdbidsArray[i]);\r
-    }\r
-  } //-- void setPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
-  /**\r
-   * Sets the value of field 'start'.\r
-   *\r
-   * @param start the value of field 'start'.\r
-   */\r
-  public void setStart(int start)\r
-  {\r
-    this._start = start;\r
-    this._has_start = true;\r
-  } //-- void setStart(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.\r
-        schemabinding.version2.JSeq.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class JSeq implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private int _colour;\r
+\r
+    /**\r
+     * keeps track of state for field: _colour\r
+     */\r
+    private boolean _has_colour;\r
+\r
+    /**\r
+     * Field _start\r
+     */\r
+    private int _start;\r
+\r
+    /**\r
+     * keeps track of state for field: _start\r
+     */\r
+    private boolean _has_start;\r
+\r
+    /**\r
+     * Field _end\r
+     */\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private int _id;\r
+\r
+    /**\r
+     * keeps track of state for field: _id\r
+     */\r
+    private boolean _has_id;\r
+\r
+    /**\r
+     * Field _hidden\r
+     */\r
+    private boolean _hidden;\r
+\r
+    /**\r
+     * keeps track of state for field: _hidden\r
+     */\r
+    private boolean _has_hidden;\r
+\r
+    /**\r
+     * Field _featuresList\r
+     */\r
+    private java.util.Vector _featuresList;\r
+\r
+    /**\r
+     * Field _pdbidsList\r
+     */\r
+    private java.util.Vector _pdbidsList;\r
+\r
+    /**\r
+     * Field _hiddenSequencesList\r
+     */\r
+    private java.util.Vector _hiddenSequencesList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JSeq() {\r
+        super();\r
+        _featuresList = new Vector();\r
+        _pdbidsList = new Vector();\r
+        _hiddenSequencesList = new Vector();\r
+    } //-- jalview.schemabinding.version2.JSeq()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param vFeatures\r
+     */\r
+    public void addFeatures(jalview.schemabinding.version2.Features vFeatures)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _featuresList.addElement(vFeatures);\r
+    } //-- void addFeatures(jalview.schemabinding.version2.Features) \r
+\r
+    /**\r
+     * Method addFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vFeatures\r
+     */\r
+    public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _featuresList.insertElementAt(vFeatures, index);\r
+    } //-- void addFeatures(int, jalview.schemabinding.version2.Features) \r
+\r
+    /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+    } //-- void addHiddenSequences(int) \r
+\r
+    /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void addHiddenSequences(int, int) \r
+\r
+    /**\r
+     * Method addPdbids\r
+     * \r
+     * \r
+     * \r
+     * @param vPdbids\r
+     */\r
+    public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _pdbidsList.addElement(vPdbids);\r
+    } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) \r
+\r
+    /**\r
+     * Method addPdbids\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vPdbids\r
+     */\r
+    public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _pdbidsList.insertElementAt(vPdbids, index);\r
+    } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) \r
+\r
+    /**\r
+     * Method deleteColour\r
+     * \r
+     */\r
+    public void deleteColour()\r
+    {\r
+        this._has_colour= false;\r
+    } //-- void deleteColour() \r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
+     * Method deleteHidden\r
+     * \r
+     */\r
+    public void deleteHidden()\r
+    {\r
+        this._has_hidden= false;\r
+    } //-- void deleteHidden() \r
+\r
+    /**\r
+     * Method deleteId\r
+     * \r
+     */\r
+    public void deleteId()\r
+    {\r
+        this._has_id= false;\r
+    } //-- void deleteId() \r
+\r
+    /**\r
+     * Method deleteStart\r
+     * \r
+     */\r
+    public void deleteStart()\r
+    {\r
+        this._has_start= false;\r
+    } //-- void deleteStart() \r
+\r
+    /**\r
+     * Method enumerateFeatures\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateFeatures()\r
+    {\r
+        return _featuresList.elements();\r
+    } //-- java.util.Enumeration enumerateFeatures() \r
+\r
+    /**\r
+     * Method enumerateHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateHiddenSequences()\r
+    {\r
+        return _hiddenSequencesList.elements();\r
+    } //-- java.util.Enumeration enumerateHiddenSequences() \r
+\r
+    /**\r
+     * Method enumeratePdbids\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumeratePdbids()\r
+    {\r
+        return _pdbidsList.elements();\r
+    } //-- java.util.Enumeration enumeratePdbids() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public int getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- int getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'end'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'end'.\r
+     */\r
+    public int getEnd()\r
+    {\r
+        return this._end;\r
+    } //-- int getEnd() \r
+\r
+    /**\r
+     * Method getFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Features\r
+     */\r
+    public jalview.schemabinding.version2.Features getFeatures(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _featuresList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Features getFeatures(int) \r
+\r
+    /**\r
+     * Method getFeatures\r
+     * \r
+     * \r
+     * \r
+     * @return Features\r
+     */\r
+    public jalview.schemabinding.version2.Features[] getFeatures()\r
+    {\r
+        int size = _featuresList.size();\r
+        jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Features[] getFeatures() \r
+\r
+    /**\r
+     * Method getFeaturesCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getFeaturesCount()\r
+    {\r
+        return _featuresList.size();\r
+    } //-- int getFeaturesCount() \r
+\r
+    /**\r
+     * Returns the value of field 'hidden'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'hidden'.\r
+     */\r
+    public boolean getHidden()\r
+    {\r
+        return this._hidden;\r
+    } //-- boolean getHidden() \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int getHiddenSequences(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+    } //-- int getHiddenSequences(int) \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int[] getHiddenSequences()\r
+    {\r
+        int size = _hiddenSequencesList.size();\r
+        int[] mArray = new int[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+        }\r
+        return mArray;\r
+    } //-- int[] getHiddenSequences() \r
+\r
+    /**\r
+     * Method getHiddenSequencesCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getHiddenSequencesCount()\r
+    {\r
+        return _hiddenSequencesList.size();\r
+    } //-- int getHiddenSequencesCount() \r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'id'.\r
+     */\r
+    public int getId()\r
+    {\r
+        return this._id;\r
+    } //-- int getId() \r
+\r
+    /**\r
+     * Method getPdbids\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Pdbids\r
+     */\r
+    public jalview.schemabinding.version2.Pdbids getPdbids(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _pdbidsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) \r
+\r
+    /**\r
+     * Method getPdbids\r
+     * \r
+     * \r
+     * \r
+     * @return Pdbids\r
+     */\r
+    public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
+    {\r
+        int size = _pdbidsList.size();\r
+        jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() \r
+\r
+    /**\r
+     * Method getPdbidsCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getPdbidsCount()\r
+    {\r
+        return _pdbidsList.size();\r
+    } //-- int getPdbidsCount() \r
+\r
+    /**\r
+     * Returns the value of field 'start'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'start'.\r
+     */\r
+    public int getStart()\r
+    {\r
+        return this._start;\r
+    } //-- int getStart() \r
+\r
+    /**\r
+     * Method hasColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColour()\r
+    {\r
+        return this._has_colour;\r
+    } //-- boolean hasColour() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
+     * Method hasHidden\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHidden()\r
+    {\r
+        return this._has_hidden;\r
+    } //-- boolean hasHidden() \r
+\r
+    /**\r
+     * Method hasId\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasId()\r
+    {\r
+        return this._has_id;\r
+    } //-- boolean hasId() \r
+\r
+    /**\r
+     * Method hasStart\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStart()\r
+    {\r
+        return this._has_start;\r
+    } //-- boolean hasStart() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllFeatures\r
+     * \r
+     */\r
+    public void removeAllFeatures()\r
+    {\r
+        _featuresList.removeAllElements();\r
+    } //-- void removeAllFeatures() \r
+\r
+    /**\r
+     * Method removeAllHiddenSequences\r
+     * \r
+     */\r
+    public void removeAllHiddenSequences()\r
+    {\r
+        _hiddenSequencesList.removeAllElements();\r
+    } //-- void removeAllHiddenSequences() \r
+\r
+    /**\r
+     * Method removeAllPdbids\r
+     * \r
+     */\r
+    public void removeAllPdbids()\r
+    {\r
+        _pdbidsList.removeAllElements();\r
+    } //-- void removeAllPdbids() \r
+\r
+    /**\r
+     * Method removeFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Features\r
+     */\r
+    public jalview.schemabinding.version2.Features removeFeatures(int index)\r
+    {\r
+        java.lang.Object obj = _featuresList.elementAt(index);\r
+        _featuresList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Features) obj;\r
+    } //-- jalview.schemabinding.version2.Features removeFeatures(int) \r
+\r
+    /**\r
+     * Method removeHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int removeHiddenSequences(int index)\r
+    {\r
+        java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
+        _hiddenSequencesList.removeElementAt(index);\r
+        return ((java.lang.Integer)obj).intValue();\r
+    } //-- int removeHiddenSequences(int) \r
+\r
+    /**\r
+     * Method removePdbids\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Pdbids\r
+     */\r
+    public jalview.schemabinding.version2.Pdbids removePdbids(int index)\r
+    {\r
+        java.lang.Object obj = _pdbidsList.elementAt(index);\r
+        _pdbidsList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Pdbids) obj;\r
+    } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(int colour)\r
+    {\r
+        this._colour = colour;\r
+        this._has_colour = true;\r
+    } //-- void setColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'end'.\r
+     * \r
+     * @param end the value of field 'end'.\r
+     */\r
+    public void setEnd(int end)\r
+    {\r
+        this._end = end;\r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
+\r
+    /**\r
+     * Method setFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vFeatures\r
+     */\r
+    public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _featuresList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _featuresList.setElementAt(vFeatures, index);\r
+    } //-- void setFeatures(int, jalview.schemabinding.version2.Features) \r
+\r
+    /**\r
+     * Method setFeatures\r
+     * \r
+     * \r
+     * \r
+     * @param featuresArray\r
+     */\r
+    public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)\r
+    {\r
+        //-- copy array\r
+        _featuresList.removeAllElements();\r
+        for (int i = 0; i < featuresArray.length; i++) {\r
+            _featuresList.addElement(featuresArray[i]);\r
+        }\r
+    } //-- void setFeatures(jalview.schemabinding.version2.Features) \r
+\r
+    /**\r
+     * Sets the value of field 'hidden'.\r
+     * \r
+     * @param hidden the value of field 'hidden'.\r
+     */\r
+    public void setHidden(boolean hidden)\r
+    {\r
+        this._hidden = hidden;\r
+        this._has_hidden = true;\r
+    } //-- void setHidden(boolean) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void setHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void setHiddenSequences(int, int) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param hiddenSequencesArray\r
+     */\r
+    public void setHiddenSequences(int[] hiddenSequencesArray)\r
+    {\r
+        //-- copy array\r
+        _hiddenSequencesList.removeAllElements();\r
+        for (int i = 0; i < hiddenSequencesArray.length; i++) {\r
+            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));\r
+        }\r
+    } //-- void setHiddenSequences(int) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(int id)\r
+    {\r
+        this._id = id;\r
+        this._has_id = true;\r
+    } //-- void setId(int) \r
+\r
+    /**\r
+     * Method setPdbids\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vPdbids\r
+     */\r
+    public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _pdbidsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _pdbidsList.setElementAt(vPdbids, index);\r
+    } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) \r
+\r
+    /**\r
+     * Method setPdbids\r
+     * \r
+     * \r
+     * \r
+     * @param pdbidsArray\r
+     */\r
+    public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)\r
+    {\r
+        //-- copy array\r
+        _pdbidsList.removeAllElements();\r
+        for (int i = 0; i < pdbidsArray.length; i++) {\r
+            _pdbidsList.addElement(pdbidsArray[i]);\r
+        }\r
+    } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) \r
+\r
+    /**\r
+     * Sets the value of field 'start'.\r
+     * \r
+     * @param start the value of field 'start'.\r
+     */\r
+    public void setStart(int start)\r
+    {\r
+        this._start = start;\r
+        this._has_start = true;\r
+    } //-- void setStart(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JSeqDescriptor.java b/src/jalview/schemabinding/version2/JSeqDescriptor.java
index 9280390..eef74d2 100755 (executable)
--- a/src/jalview/schemabinding/version2/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/JSeqDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,566 +7,482 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class JSeqDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JSeqDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JSeqDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "JSeq";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _colour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_colour", "colour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        if (!target.hasColour())\r
-        {\r
-          return null;\r
+public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JSeqDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "JSeq";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _colour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteColour();\r
+                        return;\r
+                    }\r
+                    target.setColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        return new java.lang.Integer(target.getColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteColour();\r
-            return;\r
-          }\r
-          target.setColour( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _start\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasStart())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStart());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setStart( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _start\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _end\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _end\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _start\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_start", "start",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        if (!target.hasStart())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getStart());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setStart( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _id\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasId())\r
+                    return null;\r
+                return new java.lang.Integer(target.getId());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setId( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _id\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _hidden\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasHidden())\r
+                    return null;\r
+                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteHidden();\r
+                        return;\r
+                    }\r
+                    target.setHidden( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hidden\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _start\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _end\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        if (!target.hasEnd())\r
-        {\r
-          return null;\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _featuresList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                return target.getFeatures();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    target.addFeatures( (jalview.schemabinding.version2.Features) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Features();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _featuresList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        return new java.lang.Integer(target.getEnd());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setEnd( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _pdbidsList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                return target.getPdbids();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Pdbids();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _pdbidsList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _hiddenSequencesList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                return target.getHiddenSequences();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.addHiddenSequences( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hiddenSequencesList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _end\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _id\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.JSeqDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        if (!target.hasId())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getId());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setId( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _id\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _hidden\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_hidden", "hidden",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        if (!target.hasHidden())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getHidden() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteHidden();\r
-            return;\r
-          }\r
-          target.setHidden( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _hidden\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _featuresList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Features.class, "_featuresList", "features",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        return target.getFeatures();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          target.addFeatures( (jalview.schemabinding.version2.Features) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Features();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _featuresList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _pdbidsList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        return target.getPdbids();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Pdbids();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _pdbidsList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _hiddenSequencesList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_hiddenSequencesList", "hiddenSequences",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.JSeq.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JSeq target = (JSeq) object;\r
-        return target.getHiddenSequences();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JSeq target = (JSeq) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.addHiddenSequences( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _hiddenSequencesList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.JSeqDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.JSeq.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index 11f6e38..fe8deef 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,223 +7,221 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Date;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class JalviewModel.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewModel\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _creationDate\r
-   */\r
-  private java.util.Date _creationDate;\r
-\r
-  /**\r
-   * Field _version\r
-   */\r
-  private java.lang.String _version;\r
-\r
-  /**\r
-   * Field _vamsasModel\r
-   */\r
-  private jalview.schemabinding.version2.VamsasModel _vamsasModel;\r
-\r
-  /**\r
-   * Field _jalviewModelSequence\r
-   */\r
-  private jalview.schemabinding.version2.JalviewModelSequence\r
-      _jalviewModelSequence;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JalviewModel()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.JalviewModel()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'creationDate'.\r
-   *\r
-   * @return Date\r
-   * @return the value of field 'creationDate'.\r
-   */\r
-  public java.util.Date getCreationDate()\r
-  {\r
-    return this._creationDate;\r
-  } //-- java.util.Date getCreationDate()\r
-\r
-  /**\r
-   * Returns the value of field 'jalviewModelSequence'.\r
-   *\r
-   * @return JalviewModelSequence\r
-   * @return the value of field 'jalviewModelSequence'.\r
-   */\r
-  public jalview.schemabinding.version2.JalviewModelSequence\r
-      getJalviewModelSequence()\r
-  {\r
-    return this._jalviewModelSequence;\r
-  } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()\r
-\r
-  /**\r
-   * Returns the value of field 'vamsasModel'.\r
-   *\r
-   * @return VamsasModel\r
-   * @return the value of field 'vamsasModel'.\r
-   */\r
-  public jalview.schemabinding.version2.VamsasModel getVamsasModel()\r
-  {\r
-    return this._vamsasModel;\r
-  } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel()\r
-\r
-  /**\r
-   * Returns the value of field 'version'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'version'.\r
-   */\r
-  public java.lang.String getVersion()\r
-  {\r
-    return this._version;\r
-  } //-- java.lang.String getVersion()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class JalviewModel implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _creationDate\r
+     */\r
+    private java.util.Date _creationDate;\r
+\r
+    /**\r
+     * Field _version\r
+     */\r
+    private java.lang.String _version;\r
+\r
+    /**\r
+     * Field _vamsasModel\r
+     */\r
+    private jalview.schemabinding.version2.VamsasModel _vamsasModel;\r
+\r
+    /**\r
+     * Field _jalviewModelSequence\r
+     */\r
+    private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModel() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.JalviewModel()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'creationDate'.\r
+     * \r
+     * @return Date\r
+     * @return the value of field 'creationDate'.\r
+     */\r
+    public java.util.Date getCreationDate()\r
+    {\r
+        return this._creationDate;\r
+    } //-- java.util.Date getCreationDate() \r
+\r
+    /**\r
+     * Returns the value of field 'jalviewModelSequence'.\r
+     * \r
+     * @return JalviewModelSequence\r
+     * @return the value of field 'jalviewModelSequence'.\r
+     */\r
+    public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()\r
+    {\r
+        return this._jalviewModelSequence;\r
+    } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() \r
+\r
+    /**\r
+     * Returns the value of field 'vamsasModel'.\r
+     * \r
+     * @return VamsasModel\r
+     * @return the value of field 'vamsasModel'.\r
+     */\r
+    public jalview.schemabinding.version2.VamsasModel getVamsasModel()\r
+    {\r
+        return this._vamsasModel;\r
+    } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel() \r
+\r
+    /**\r
+     * Returns the value of field 'version'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'version'.\r
+     */\r
+    public java.lang.String getVersion()\r
+    {\r
+        return this._version;\r
+    } //-- java.lang.String getVersion() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'creationDate'.\r
+     * \r
+     * @param creationDate the value of field 'creationDate'.\r
+     */\r
+    public void setCreationDate(java.util.Date creationDate)\r
+    {\r
+        this._creationDate = creationDate;\r
+    } //-- void setCreationDate(java.util.Date) \r
+\r
+    /**\r
+     * Sets the value of field 'jalviewModelSequence'.\r
+     * \r
+     * @param jalviewModelSequence the value of field\r
+     * 'jalviewModelSequence'.\r
+     */\r
+    public void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)\r
+    {\r
+        this._jalviewModelSequence = jalviewModelSequence;\r
+    } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence) \r
+\r
+    /**\r
+     * Sets the value of field 'vamsasModel'.\r
+     * \r
+     * @param vamsasModel the value of field 'vamsasModel'.\r
+     */\r
+    public void setVamsasModel(jalview.schemabinding.version2.VamsasModel vamsasModel)\r
+    {\r
+        this._vamsasModel = vamsasModel;\r
+    } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel) \r
+\r
+    /**\r
+     * Sets the value of field 'version'.\r
+     * \r
+     * @param version the value of field 'version'.\r
+     */\r
+    public void setVersion(java.lang.String version)\r
+    {\r
+        this._version = version;\r
+    } //-- void setVersion(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'creationDate'.\r
-   *\r
-   * @param creationDate the value of field 'creationDate'.\r
-   */\r
-  public void setCreationDate(java.util.Date creationDate)\r
-  {\r
-    this._creationDate = creationDate;\r
-  } //-- void setCreationDate(java.util.Date)\r
-\r
-  /**\r
-   * Sets the value of field 'jalviewModelSequence'.\r
-   *\r
-   * @param jalviewModelSequence the value of field\r
-   * 'jalviewModelSequence'.\r
-   */\r
-  public void setJalviewModelSequence(jalview.schemabinding.version2.\r
-                                      JalviewModelSequence jalviewModelSequence)\r
-  {\r
-    this._jalviewModelSequence = jalviewModelSequence;\r
-  } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence)\r
-\r
-  /**\r
-   * Sets the value of field 'vamsasModel'.\r
-   *\r
-   * @param vamsasModel the value of field 'vamsasModel'.\r
-   */\r
-  public void setVamsasModel(jalview.schemabinding.version2.VamsasModel\r
-                             vamsasModel)\r
-  {\r
-    this._vamsasModel = vamsasModel;\r
-  } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel)\r
-\r
-  /**\r
-   * Sets the value of field 'version'.\r
-   *\r
-   * @param version the value of field 'version'.\r
-   */\r
-  public void setVersion(java.lang.String version)\r
-  {\r
-    this._version = version;\r
-  } //-- void setVersion(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.JalviewModel.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
index a9440e5..ad2dc13 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,350 +7,318 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class JalviewModelDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewModelDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JalviewModelDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "JalviewModel";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _creationDate\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class,\r
-        "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModel target = (JalviewModel) object;\r
-        return target.getCreationDate();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModel target = (JalviewModel) object;\r
-          target.setCreationDate( (java.util.Date) value);\r
+public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModelDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "JalviewModel";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _creationDate\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModel target = (JalviewModel) object;\r
+                return target.getCreationDate();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModel target = (JalviewModel) object;\r
+                    target.setCreationDate( (java.util.Date) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new java.util.Date();\r
+            }\r
+        } );\r
+        desc.setHandler( new org.exolab.castor.xml.handlers.DateFieldHandler(handler));\r
+        desc.setImmutable(true);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _creationDate\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _version\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModel target = (JalviewModel) object;\r
+                return target.getVersion();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModel target = (JalviewModel) object;\r
+                    target.setVersion( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _version\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new java.util.Date();\r
-      }\r
-    });\r
-    desc.setHandler(new org.exolab.castor.xml.handlers.DateFieldHandler(handler));\r
-    desc.setImmutable(true);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _creationDate\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _version\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_version", "version",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModel target = (JalviewModel) object;\r
-        return target.getVersion();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModel target = (JalviewModel) object;\r
-          target.setVersion( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _vamsasModel\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModel target = (JalviewModel) object;\r
+                return target.getVamsasModel();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModel target = (JalviewModel) object;\r
+                    target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.VamsasModel();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _vamsasModel\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _jalviewModelSequence\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModel target = (JalviewModel) object;\r
+                return target.getJalviewModelSequence();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModel target = (JalviewModel) object;\r
+                    target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.JalviewModelSequence();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setContainer(true);\r
+        desc.setClassDescriptor(new jalview.schemabinding.version2.JalviewModelSequenceDescriptor());\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _jalviewModelSequence\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.JalviewModelDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _version\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _vamsasModel\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModel target = (JalviewModel) object;\r
-        return target.getVamsasModel();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModel target = (JalviewModel) object;\r
-          target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel)\r
-                                value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.VamsasModel();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _vamsasModel\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _jalviewModelSequence\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.JalviewModelSequence.class,\r
-        "_jalviewModelSequence", "-error-if-this-is-used-",\r
-              org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModel target = (JalviewModel) object;\r
-        return target.getJalviewModelSequence();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModel target = (JalviewModel) object;\r
-          target.setJalviewModelSequence( (jalview.schemabinding.version2.\r
-                                           JalviewModelSequence) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.JalviewModelSequence();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setContainer(true);\r
-    desc.setClassDescriptor(new jalview.schemabinding.version2.\r
-                            JalviewModelSequenceDescriptor());\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _jalviewModelSequence\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.JalviewModelDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.JalviewModel.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.JalviewModel.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index ba0c4c8..45f486b 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,942 +7,898 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class JalviewModelSequence.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewModelSequence\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _JSeqList\r
-   */\r
-  private java.util.Vector _JSeqList;\r
-\r
-  /**\r
-   * Field _JGroupList\r
-   */\r
-  private java.util.Vector _JGroupList;\r
-\r
-  /**\r
-   * Field _viewportList\r
-   */\r
-  private java.util.Vector _viewportList;\r
-\r
-  /**\r
-   * Field _userColoursList\r
-   */\r
-  private java.util.Vector _userColoursList;\r
-\r
-  /**\r
-   * Field _treeList\r
-   */\r
-  private java.util.Vector _treeList;\r
-\r
-  /**\r
-   * Field _featureSettings\r
-   */\r
-  private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JalviewModelSequence()\r
-  {\r
-    super();\r
-    _JSeqList = new Vector();\r
-    _JGroupList = new Vector();\r
-    _viewportList = new Vector();\r
-    _userColoursList = new Vector();\r
-    _treeList = new Vector();\r
-  } //-- jalview.schemabinding.version2.JalviewModelSequence()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param vJGroup\r
-   */\r
-  public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _JGroupList.addElement(vJGroup);\r
-  } //-- void addJGroup(jalview.schemabinding.version2.JGroup)\r
-\r
-  /**\r
-   * Method addJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vJGroup\r
-   */\r
-  public void addJGroup(int index,\r
-                        jalview.schemabinding.version2.JGroup vJGroup)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _JGroupList.insertElementAt(vJGroup, index);\r
-  } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup)\r
-\r
-  /**\r
-   * Method addJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param vJSeq\r
-   */\r
-  public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _JSeqList.addElement(vJSeq);\r
-  } //-- void addJSeq(jalview.schemabinding.version2.JSeq)\r
-\r
-  /**\r
-   * Method addJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vJSeq\r
-   */\r
-  public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _JSeqList.insertElementAt(vJSeq, index);\r
-  } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq)\r
-\r
-  /**\r
-   * Method addTree\r
-   *\r
-   *\r
-   *\r
-   * @param vTree\r
-   */\r
-  public void addTree(jalview.schemabinding.version2.Tree vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _treeList.addElement(vTree);\r
-  } //-- void addTree(jalview.schemabinding.version2.Tree)\r
-\r
-  /**\r
-   * Method addTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vTree\r
-   */\r
-  public void addTree(int index, jalview.schemabinding.version2.Tree vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _treeList.insertElementAt(vTree, index);\r
-  } //-- void addTree(int, jalview.schemabinding.version2.Tree)\r
-\r
-  /**\r
-   * Method addUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param vUserColours\r
-   */\r
-  public void addUserColours(jalview.schemabinding.version2.UserColours\r
-                             vUserColours)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _userColoursList.addElement(vUserColours);\r
-  } //-- void addUserColours(jalview.schemabinding.version2.UserColours)\r
-\r
-  /**\r
-   * Method addUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vUserColours\r
-   */\r
-  public void addUserColours(int index,\r
-                             jalview.schemabinding.version2.UserColours\r
-                             vUserColours)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _userColoursList.insertElementAt(vUserColours, index);\r
-  } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours)\r
-\r
-  /**\r
-   * Method addViewport\r
-   *\r
-   *\r
-   *\r
-   * @param vViewport\r
-   */\r
-  public void addViewport(jalview.schemabinding.version2.Viewport vViewport)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _viewportList.addElement(vViewport);\r
-  } //-- void addViewport(jalview.schemabinding.version2.Viewport)\r
-\r
-  /**\r
-   * Method addViewport\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vViewport\r
-   */\r
-  public void addViewport(int index,\r
-                          jalview.schemabinding.version2.Viewport vViewport)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _viewportList.insertElementAt(vViewport, index);\r
-  } //-- void addViewport(int, jalview.schemabinding.version2.Viewport)\r
-\r
-  /**\r
-   * Method enumerateJGroup\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateJGroup()\r
-  {\r
-    return _JGroupList.elements();\r
-  } //-- java.util.Enumeration enumerateJGroup()\r
-\r
-  /**\r
-   * Method enumerateJSeq\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateJSeq()\r
-  {\r
-    return _JSeqList.elements();\r
-  } //-- java.util.Enumeration enumerateJSeq()\r
-\r
-  /**\r
-   * Method enumerateTree\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateTree()\r
-  {\r
-    return _treeList.elements();\r
-  } //-- java.util.Enumeration enumerateTree()\r
-\r
-  /**\r
-   * Method enumerateUserColours\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateUserColours()\r
-  {\r
-    return _userColoursList.elements();\r
-  } //-- java.util.Enumeration enumerateUserColours()\r
-\r
-  /**\r
-   * Method enumerateViewport\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateViewport()\r
-  {\r
-    return _viewportList.elements();\r
-  } //-- java.util.Enumeration enumerateViewport()\r
-\r
-  /**\r
-   * Returns the value of field 'featureSettings'.\r
-   *\r
-   * @return FeatureSettings\r
-   * @return the value of field 'featureSettings'.\r
-   */\r
-  public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
-  {\r
-    return this._featureSettings;\r
-  } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
-\r
-  /**\r
-   * Method getJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return JGroup\r
-   */\r
-  public jalview.schemabinding.version2.JGroup getJGroup(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _JGroupList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.JGroup getJGroup(int)\r
-\r
-  /**\r
-   * Method getJGroup\r
-   *\r
-   *\r
-   *\r
-   * @return JGroup\r
-   */\r
-  public jalview.schemabinding.version2.JGroup[] getJGroup()\r
-  {\r
-    int size = _JGroupList.size();\r
-    jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.\r
-        version2.JGroup[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.JGroup[] getJGroup()\r
-\r
-  /**\r
-   * Method getJGroupCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getJGroupCount()\r
-  {\r
-    return _JGroupList.size();\r
-  } //-- int getJGroupCount()\r
-\r
-  /**\r
-   * Method getJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return JSeq\r
-   */\r
-  public jalview.schemabinding.version2.JSeq getJSeq(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _JSeqList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.JSeq getJSeq(int)\r
-\r
-  /**\r
-   * Method getJSeq\r
-   *\r
-   *\r
-   *\r
-   * @return JSeq\r
-   */\r
-  public jalview.schemabinding.version2.JSeq[] getJSeq()\r
-  {\r
-    int size = _JSeqList.size();\r
-    jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.\r
-        version2.JSeq[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(\r
-          index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.JSeq[] getJSeq()\r
-\r
-  /**\r
-   * Method getJSeqCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getJSeqCount()\r
-  {\r
-    return _JSeqList.size();\r
-  } //-- int getJSeqCount()\r
-\r
-  /**\r
-   * Method getTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Tree\r
-   */\r
-  public jalview.schemabinding.version2.Tree getTree(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _treeList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.Tree getTree(int)\r
-\r
-  /**\r
-   * Method getTree\r
-   *\r
-   *\r
-   *\r
-   * @return Tree\r
-   */\r
-  public jalview.schemabinding.version2.Tree[] getTree()\r
-  {\r
-    int size = _treeList.size();\r
-    jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.\r
-        version2.Tree[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(\r
-          index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Tree[] getTree()\r
-\r
-  /**\r
-   * Method getTreeCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getTreeCount()\r
-  {\r
-    return _treeList.size();\r
-  } //-- int getTreeCount()\r
-\r
-  /**\r
-   * Method getUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return UserColours\r
-   */\r
-  public jalview.schemabinding.version2.UserColours getUserColours(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _userColoursList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.UserColours) _userColoursList.\r
-        elementAt(index);\r
-  } //-- jalview.schemabinding.version2.UserColours getUserColours(int)\r
-\r
-  /**\r
-   * Method getUserColours\r
-   *\r
-   *\r
-   *\r
-   * @return UserColours\r
-   */\r
-  public jalview.schemabinding.version2.UserColours[] getUserColours()\r
-  {\r
-    int size = _userColoursList.size();\r
-    jalview.schemabinding.version2.UserColours[] mArray = new jalview.\r
-        schemabinding.version2.UserColours[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.UserColours)\r
-          _userColoursList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.UserColours[] getUserColours()\r
-\r
-  /**\r
-   * Method getUserColoursCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getUserColoursCount()\r
-  {\r
-    return _userColoursList.size();\r
-  } //-- int getUserColoursCount()\r
-\r
-  /**\r
-   * Method getViewport\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Viewport\r
-   */\r
-  public jalview.schemabinding.version2.Viewport getViewport(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _viewportList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.Viewport getViewport(int)\r
-\r
-  /**\r
-   * Method getViewport\r
-   *\r
-   *\r
-   *\r
-   * @return Viewport\r
-   */\r
-  public jalview.schemabinding.version2.Viewport[] getViewport()\r
-  {\r
-    int size = _viewportList.size();\r
-    jalview.schemabinding.version2.Viewport[] mArray = new jalview.\r
-        schemabinding.version2.Viewport[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Viewport[] getViewport()\r
-\r
-  /**\r
-   * Method getViewportCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getViewportCount()\r
-  {\r
-    return _viewportList.size();\r
-  } //-- int getViewportCount()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllJGroup\r
-   *\r
-   */\r
-  public void removeAllJGroup()\r
-  {\r
-    _JGroupList.removeAllElements();\r
-  } //-- void removeAllJGroup()\r
-\r
-  /**\r
-   * Method removeAllJSeq\r
-   *\r
-   */\r
-  public void removeAllJSeq()\r
-  {\r
-    _JSeqList.removeAllElements();\r
-  } //-- void removeAllJSeq()\r
-\r
-  /**\r
-   * Method removeAllTree\r
-   *\r
-   */\r
-  public void removeAllTree()\r
-  {\r
-    _treeList.removeAllElements();\r
-  } //-- void removeAllTree()\r
-\r
-  /**\r
-   * Method removeAllUserColours\r
-   *\r
-   */\r
-  public void removeAllUserColours()\r
-  {\r
-    _userColoursList.removeAllElements();\r
-  } //-- void removeAllUserColours()\r
-\r
-  /**\r
-   * Method removeAllViewport\r
-   *\r
-   */\r
-  public void removeAllViewport()\r
-  {\r
-    _viewportList.removeAllElements();\r
-  } //-- void removeAllViewport()\r
-\r
-  /**\r
-   * Method removeJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return JGroup\r
-   */\r
-  public jalview.schemabinding.version2.JGroup removeJGroup(int index)\r
-  {\r
-    java.lang.Object obj = _JGroupList.elementAt(index);\r
-    _JGroupList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.JGroup) obj;\r
-  } //-- jalview.schemabinding.version2.JGroup removeJGroup(int)\r
-\r
-  /**\r
-   * Method removeJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return JSeq\r
-   */\r
-  public jalview.schemabinding.version2.JSeq removeJSeq(int index)\r
-  {\r
-    java.lang.Object obj = _JSeqList.elementAt(index);\r
-    _JSeqList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.JSeq) obj;\r
-  } //-- jalview.schemabinding.version2.JSeq removeJSeq(int)\r
-\r
-  /**\r
-   * Method removeTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Tree\r
-   */\r
-  public jalview.schemabinding.version2.Tree removeTree(int index)\r
-  {\r
-    java.lang.Object obj = _treeList.elementAt(index);\r
-    _treeList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Tree) obj;\r
-  } //-- jalview.schemabinding.version2.Tree removeTree(int)\r
-\r
-  /**\r
-   * Method removeUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return UserColours\r
-   */\r
-  public jalview.schemabinding.version2.UserColours removeUserColours(int index)\r
-  {\r
-    java.lang.Object obj = _userColoursList.elementAt(index);\r
-    _userColoursList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.UserColours) obj;\r
-  } //-- jalview.schemabinding.version2.UserColours removeUserColours(int)\r
-\r
-  /**\r
-   * Method removeViewport\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Viewport\r
-   */\r
-  public jalview.schemabinding.version2.Viewport removeViewport(int index)\r
-  {\r
-    java.lang.Object obj = _viewportList.elementAt(index);\r
-    _viewportList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Viewport) obj;\r
-  } //-- jalview.schemabinding.version2.Viewport removeViewport(int)\r
-\r
-  /**\r
-   * Sets the value of field 'featureSettings'.\r
-   *\r
-   * @param featureSettings the value of field 'featureSettings'.\r
-   */\r
-  public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings\r
-                                 featureSettings)\r
-  {\r
-    this._featureSettings = featureSettings;\r
-  } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings)\r
-\r
-  /**\r
-   * Method setJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vJGroup\r
-   */\r
-  public void setJGroup(int index,\r
-                        jalview.schemabinding.version2.JGroup vJGroup)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _JGroupList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _JGroupList.setElementAt(vJGroup, index);\r
-  } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup)\r
-\r
-  /**\r
-   * Method setJGroup\r
-   *\r
-   *\r
-   *\r
-   * @param JGroupArray\r
-   */\r
-  public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)\r
-  {\r
-    //-- copy array\r
-    _JGroupList.removeAllElements();\r
-    for (int i = 0; i < JGroupArray.length; i++)\r
-    {\r
-      _JGroupList.addElement(JGroupArray[i]);\r
-    }\r
-  } //-- void setJGroup(jalview.schemabinding.version2.JGroup)\r
-\r
-  /**\r
-   * Method setJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vJSeq\r
-   */\r
-  public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _JSeqList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _JSeqList.setElementAt(vJSeq, index);\r
-  } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq)\r
-\r
-  /**\r
-   * Method setJSeq\r
-   *\r
-   *\r
-   *\r
-   * @param JSeqArray\r
-   */\r
-  public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)\r
-  {\r
-    //-- copy array\r
-    _JSeqList.removeAllElements();\r
-    for (int i = 0; i < JSeqArray.length; i++)\r
-    {\r
-      _JSeqList.addElement(JSeqArray[i]);\r
-    }\r
-  } //-- void setJSeq(jalview.schemabinding.version2.JSeq)\r
-\r
-  /**\r
-   * Method setTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vTree\r
-   */\r
-  public void setTree(int index, jalview.schemabinding.version2.Tree vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _treeList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _treeList.setElementAt(vTree, index);\r
-  } //-- void setTree(int, jalview.schemabinding.version2.Tree)\r
-\r
-  /**\r
-   * Method setTree\r
-   *\r
-   *\r
-   *\r
-   * @param treeArray\r
-   */\r
-  public void setTree(jalview.schemabinding.version2.Tree[] treeArray)\r
-  {\r
-    //-- copy array\r
-    _treeList.removeAllElements();\r
-    for (int i = 0; i < treeArray.length; i++)\r
-    {\r
-      _treeList.addElement(treeArray[i]);\r
-    }\r
-  } //-- void setTree(jalview.schemabinding.version2.Tree)\r
-\r
-  /**\r
-   * Method setUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vUserColours\r
-   */\r
-  public void setUserColours(int index,\r
-                             jalview.schemabinding.version2.UserColours\r
-                             vUserColours)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _userColoursList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _userColoursList.setElementAt(vUserColours, index);\r
-  } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours)\r
-\r
-  /**\r
-   * Method setUserColours\r
-   *\r
-   *\r
-   *\r
-   * @param userColoursArray\r
-   */\r
-  public void setUserColours(jalview.schemabinding.version2.UserColours[]\r
-                             userColoursArray)\r
-  {\r
-    //-- copy array\r
-    _userColoursList.removeAllElements();\r
-    for (int i = 0; i < userColoursArray.length; i++)\r
-    {\r
-      _userColoursList.addElement(userColoursArray[i]);\r
-    }\r
-  } //-- void setUserColours(jalview.schemabinding.version2.UserColours)\r
-\r
-  /**\r
-   * Method setViewport\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vViewport\r
-   */\r
-  public void setViewport(int index,\r
-                          jalview.schemabinding.version2.Viewport vViewport)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _viewportList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _viewportList.setElementAt(vViewport, index);\r
-  } //-- void setViewport(int, jalview.schemabinding.version2.Viewport)\r
-\r
-  /**\r
-   * Method setViewport\r
-   *\r
-   *\r
-   *\r
-   * @param viewportArray\r
-   */\r
-  public void setViewport(jalview.schemabinding.version2.Viewport[]\r
-                          viewportArray)\r
-  {\r
-    //-- copy array\r
-    _viewportList.removeAllElements();\r
-    for (int i = 0; i < viewportArray.length; i++)\r
-    {\r
-      _viewportList.addElement(viewportArray[i]);\r
-    }\r
-  } //-- void setViewport(jalview.schemabinding.version2.Viewport)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class,\r
-                  reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class JalviewModelSequence implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _JSeqList\r
+     */\r
+    private java.util.Vector _JSeqList;\r
+\r
+    /**\r
+     * Field _JGroupList\r
+     */\r
+    private java.util.Vector _JGroupList;\r
+\r
+    /**\r
+     * Field _viewportList\r
+     */\r
+    private java.util.Vector _viewportList;\r
+\r
+    /**\r
+     * Field _userColoursList\r
+     */\r
+    private java.util.Vector _userColoursList;\r
+\r
+    /**\r
+     * Field _treeList\r
+     */\r
+    private java.util.Vector _treeList;\r
+\r
+    /**\r
+     * Field _featureSettings\r
+     */\r
+    private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModelSequence() {\r
+        super();\r
+        _JSeqList = new Vector();\r
+        _JGroupList = new Vector();\r
+        _viewportList = new Vector();\r
+        _userColoursList = new Vector();\r
+        _treeList = new Vector();\r
+    } //-- jalview.schemabinding.version2.JalviewModelSequence()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param vJGroup\r
+     */\r
+    public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _JGroupList.addElement(vJGroup);\r
+    } //-- void addJGroup(jalview.schemabinding.version2.JGroup) \r
+\r
+    /**\r
+     * Method addJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJGroup\r
+     */\r
+    public void addJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _JGroupList.insertElementAt(vJGroup, index);\r
+    } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup) \r
+\r
+    /**\r
+     * Method addJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param vJSeq\r
+     */\r
+    public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _JSeqList.addElement(vJSeq);\r
+    } //-- void addJSeq(jalview.schemabinding.version2.JSeq) \r
+\r
+    /**\r
+     * Method addJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJSeq\r
+     */\r
+    public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _JSeqList.insertElementAt(vJSeq, index);\r
+    } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq) \r
+\r
+    /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param vTree\r
+     */\r
+    public void addTree(jalview.schemabinding.version2.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.addElement(vTree);\r
+    } //-- void addTree(jalview.schemabinding.version2.Tree) \r
+\r
+    /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void addTree(int index, jalview.schemabinding.version2.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.insertElementAt(vTree, index);\r
+    } //-- void addTree(int, jalview.schemabinding.version2.Tree) \r
+\r
+    /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(jalview.schemabinding.version2.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.addElement(vUserColours);\r
+    } //-- void addUserColours(jalview.schemabinding.version2.UserColours) \r
+\r
+    /**\r
+     * Method addUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void addUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _userColoursList.insertElementAt(vUserColours, index);\r
+    } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours) \r
+\r
+    /**\r
+     * Method addViewport\r
+     * \r
+     * \r
+     * \r
+     * @param vViewport\r
+     */\r
+    public void addViewport(jalview.schemabinding.version2.Viewport vViewport)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _viewportList.addElement(vViewport);\r
+    } //-- void addViewport(jalview.schemabinding.version2.Viewport) \r
+\r
+    /**\r
+     * Method addViewport\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vViewport\r
+     */\r
+    public void addViewport(int index, jalview.schemabinding.version2.Viewport vViewport)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _viewportList.insertElementAt(vViewport, index);\r
+    } //-- void addViewport(int, jalview.schemabinding.version2.Viewport) \r
+\r
+    /**\r
+     * Method enumerateJGroup\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateJGroup()\r
+    {\r
+        return _JGroupList.elements();\r
+    } //-- java.util.Enumeration enumerateJGroup() \r
+\r
+    /**\r
+     * Method enumerateJSeq\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateJSeq()\r
+    {\r
+        return _JSeqList.elements();\r
+    } //-- java.util.Enumeration enumerateJSeq() \r
+\r
+    /**\r
+     * Method enumerateTree\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateTree()\r
+    {\r
+        return _treeList.elements();\r
+    } //-- java.util.Enumeration enumerateTree() \r
+\r
+    /**\r
+     * Method enumerateUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateUserColours()\r
+    {\r
+        return _userColoursList.elements();\r
+    } //-- java.util.Enumeration enumerateUserColours() \r
+\r
+    /**\r
+     * Method enumerateViewport\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateViewport()\r
+    {\r
+        return _viewportList.elements();\r
+    } //-- java.util.Enumeration enumerateViewport() \r
+\r
+    /**\r
+     * Returns the value of field 'featureSettings'.\r
+     * \r
+     * @return FeatureSettings\r
+     * @return the value of field 'featureSettings'.\r
+     */\r
+    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
+    {\r
+        return this._featureSettings;\r
+    } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings() \r
+\r
+    /**\r
+     * Method getJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JGroup\r
+     */\r
+    public jalview.schemabinding.version2.JGroup getJGroup(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _JGroupList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.JGroup getJGroup(int) \r
+\r
+    /**\r
+     * Method getJGroup\r
+     * \r
+     * \r
+     * \r
+     * @return JGroup\r
+     */\r
+    public jalview.schemabinding.version2.JGroup[] getJGroup()\r
+    {\r
+        int size = _JGroupList.size();\r
+        jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.version2.JGroup[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.JGroup[] getJGroup() \r
+\r
+    /**\r
+     * Method getJGroupCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getJGroupCount()\r
+    {\r
+        return _JGroupList.size();\r
+    } //-- int getJGroupCount() \r
+\r
+    /**\r
+     * Method getJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JSeq\r
+     */\r
+    public jalview.schemabinding.version2.JSeq getJSeq(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _JSeqList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.JSeq getJSeq(int) \r
+\r
+    /**\r
+     * Method getJSeq\r
+     * \r
+     * \r
+     * \r
+     * @return JSeq\r
+     */\r
+    public jalview.schemabinding.version2.JSeq[] getJSeq()\r
+    {\r
+        int size = _JSeqList.size();\r
+        jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.version2.JSeq[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.JSeq[] getJSeq() \r
+\r
+    /**\r
+     * Method getJSeqCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getJSeqCount()\r
+    {\r
+        return _JSeqList.size();\r
+    } //-- int getJSeqCount() \r
+\r
+    /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Tree\r
+     */\r
+    public jalview.schemabinding.version2.Tree getTree(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Tree getTree(int) \r
+\r
+    /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @return Tree\r
+     */\r
+    public jalview.schemabinding.version2.Tree[] getTree()\r
+    {\r
+        int size = _treeList.size();\r
+        jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.version2.Tree[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Tree[] getTree() \r
+\r
+    /**\r
+     * Method getTreeCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getTreeCount()\r
+    {\r
+        return _treeList.size();\r
+    } //-- int getTreeCount() \r
+\r
+    /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.schemabinding.version2.UserColours getUserColours(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.UserColours getUserColours(int) \r
+\r
+    /**\r
+     * Method getUserColours\r
+     * \r
+     * \r
+     * \r
+     * @return UserColours\r
+     */\r
+    public jalview.schemabinding.version2.UserColours[] getUserColours()\r
+    {\r
+        int size = _userColoursList.size();\r
+        jalview.schemabinding.version2.UserColours[] mArray = new jalview.schemabinding.version2.UserColours[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.UserColours[] getUserColours() \r
+\r
+    /**\r
+     * Method getUserColoursCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getUserColoursCount()\r
+    {\r
+        return _userColoursList.size();\r
+    } //-- int getUserColoursCount() \r
+\r
+    /**\r
+     * Method getViewport\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Viewport\r
+     */\r
+    public jalview.schemabinding.version2.Viewport getViewport(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _viewportList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Viewport getViewport(int) \r
+\r
+    /**\r
+     * Method getViewport\r
+     * \r
+     * \r
+     * \r
+     * @return Viewport\r
+     */\r
+    public jalview.schemabinding.version2.Viewport[] getViewport()\r
+    {\r
+        int size = _viewportList.size();\r
+        jalview.schemabinding.version2.Viewport[] mArray = new jalview.schemabinding.version2.Viewport[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Viewport[] getViewport() \r
+\r
+    /**\r
+     * Method getViewportCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getViewportCount()\r
+    {\r
+        return _viewportList.size();\r
+    } //-- int getViewportCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllJGroup\r
+     * \r
+     */\r
+    public void removeAllJGroup()\r
+    {\r
+        _JGroupList.removeAllElements();\r
+    } //-- void removeAllJGroup() \r
+\r
+    /**\r
+     * Method removeAllJSeq\r
+     * \r
+     */\r
+    public void removeAllJSeq()\r
+    {\r
+        _JSeqList.removeAllElements();\r
+    } //-- void removeAllJSeq() \r
+\r
+    /**\r
+     * Method removeAllTree\r
+     * \r
+     */\r
+    public void removeAllTree()\r
+    {\r
+        _treeList.removeAllElements();\r
+    } //-- void removeAllTree() \r
+\r
+    /**\r
+     * Method removeAllUserColours\r
+     * \r
+     */\r
+    public void removeAllUserColours()\r
+    {\r
+        _userColoursList.removeAllElements();\r
+    } //-- void removeAllUserColours() \r
+\r
+    /**\r
+     * Method removeAllViewport\r
+     * \r
+     */\r
+    public void removeAllViewport()\r
+    {\r
+        _viewportList.removeAllElements();\r
+    } //-- void removeAllViewport() \r
+\r
+    /**\r
+     * Method removeJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JGroup\r
+     */\r
+    public jalview.schemabinding.version2.JGroup removeJGroup(int index)\r
+    {\r
+        java.lang.Object obj = _JGroupList.elementAt(index);\r
+        _JGroupList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.JGroup) obj;\r
+    } //-- jalview.schemabinding.version2.JGroup removeJGroup(int) \r
+\r
+    /**\r
+     * Method removeJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return JSeq\r
+     */\r
+    public jalview.schemabinding.version2.JSeq removeJSeq(int index)\r
+    {\r
+        java.lang.Object obj = _JSeqList.elementAt(index);\r
+        _JSeqList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.JSeq) obj;\r
+    } //-- jalview.schemabinding.version2.JSeq removeJSeq(int) \r
+\r
+    /**\r
+     * Method removeTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Tree\r
+     */\r
+    public jalview.schemabinding.version2.Tree removeTree(int index)\r
+    {\r
+        java.lang.Object obj = _treeList.elementAt(index);\r
+        _treeList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Tree) obj;\r
+    } //-- jalview.schemabinding.version2.Tree removeTree(int) \r
+\r
+    /**\r
+     * Method removeUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return UserColours\r
+     */\r
+    public jalview.schemabinding.version2.UserColours removeUserColours(int index)\r
+    {\r
+        java.lang.Object obj = _userColoursList.elementAt(index);\r
+        _userColoursList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.UserColours) obj;\r
+    } //-- jalview.schemabinding.version2.UserColours removeUserColours(int) \r
+\r
+    /**\r
+     * Method removeViewport\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Viewport\r
+     */\r
+    public jalview.schemabinding.version2.Viewport removeViewport(int index)\r
+    {\r
+        java.lang.Object obj = _viewportList.elementAt(index);\r
+        _viewportList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Viewport) obj;\r
+    } //-- jalview.schemabinding.version2.Viewport removeViewport(int) \r
+\r
+    /**\r
+     * Sets the value of field 'featureSettings'.\r
+     * \r
+     * @param featureSettings the value of field 'featureSettings'.\r
+     */\r
+    public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings featureSettings)\r
+    {\r
+        this._featureSettings = featureSettings;\r
+    } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings) \r
+\r
+    /**\r
+     * Method setJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJGroup\r
+     */\r
+    public void setJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _JGroupList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _JGroupList.setElementAt(vJGroup, index);\r
+    } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup) \r
+\r
+    /**\r
+     * Method setJGroup\r
+     * \r
+     * \r
+     * \r
+     * @param JGroupArray\r
+     */\r
+    public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)\r
+    {\r
+        //-- copy array\r
+        _JGroupList.removeAllElements();\r
+        for (int i = 0; i < JGroupArray.length; i++) {\r
+            _JGroupList.addElement(JGroupArray[i]);\r
+        }\r
+    } //-- void setJGroup(jalview.schemabinding.version2.JGroup) \r
+\r
+    /**\r
+     * Method setJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vJSeq\r
+     */\r
+    public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _JSeqList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _JSeqList.setElementAt(vJSeq, index);\r
+    } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq) \r
+\r
+    /**\r
+     * Method setJSeq\r
+     * \r
+     * \r
+     * \r
+     * @param JSeqArray\r
+     */\r
+    public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)\r
+    {\r
+        //-- copy array\r
+        _JSeqList.removeAllElements();\r
+        for (int i = 0; i < JSeqArray.length; i++) {\r
+            _JSeqList.addElement(JSeqArray[i]);\r
+        }\r
+    } //-- void setJSeq(jalview.schemabinding.version2.JSeq) \r
+\r
+    /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void setTree(int index, jalview.schemabinding.version2.Tree vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _treeList.setElementAt(vTree, index);\r
+    } //-- void setTree(int, jalview.schemabinding.version2.Tree) \r
+\r
+    /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param treeArray\r
+     */\r
+    public void setTree(jalview.schemabinding.version2.Tree[] treeArray)\r
+    {\r
+        //-- copy array\r
+        _treeList.removeAllElements();\r
+        for (int i = 0; i < treeArray.length; i++) {\r
+            _treeList.addElement(treeArray[i]);\r
+        }\r
+    } //-- void setTree(jalview.schemabinding.version2.Tree) \r
+\r
+    /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vUserColours\r
+     */\r
+    public void setUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _userColoursList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _userColoursList.setElementAt(vUserColours, index);\r
+    } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours) \r
+\r
+    /**\r
+     * Method setUserColours\r
+     * \r
+     * \r
+     * \r
+     * @param userColoursArray\r
+     */\r
+    public void setUserColours(jalview.schemabinding.version2.UserColours[] userColoursArray)\r
+    {\r
+        //-- copy array\r
+        _userColoursList.removeAllElements();\r
+        for (int i = 0; i < userColoursArray.length; i++) {\r
+            _userColoursList.addElement(userColoursArray[i]);\r
+        }\r
+    } //-- void setUserColours(jalview.schemabinding.version2.UserColours) \r
+\r
+    /**\r
+     * Method setViewport\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vViewport\r
+     */\r
+    public void setViewport(int index, jalview.schemabinding.version2.Viewport vViewport)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _viewportList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _viewportList.setElementAt(vViewport, index);\r
+    } //-- void setViewport(int, jalview.schemabinding.version2.Viewport) \r
+\r
+    /**\r
+     * Method setViewport\r
+     * \r
+     * \r
+     * \r
+     * @param viewportArray\r
+     */\r
+    public void setViewport(jalview.schemabinding.version2.Viewport[] viewportArray)\r
+    {\r
+        //-- copy array\r
+        _viewportList.removeAllElements();\r
+        for (int i = 0; i < viewportArray.length; i++) {\r
+            _viewportList.addElement(viewportArray[i]);\r
+        }\r
+    } //-- void setViewport(jalview.schemabinding.version2.Viewport) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
index 557b8fe..7f5bd43 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,424 +7,377 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class JalviewModelSequenceDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewModelSequenceDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JalviewModelSequenceDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _JSeqList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.JSeq.class, "_JSeqList", "JSeq",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getJSeq();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.addJSeq( (jalview.schemabinding.version2.JSeq) value);\r
+public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewModelSequenceDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _JSeqList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getJSeq();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.addJSeq( (jalview.schemabinding.version2.JSeq) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.JSeq();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _JSeqList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _JGroupList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getJGroup();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.addJGroup( (jalview.schemabinding.version2.JGroup) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.JGroup();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _JGroupList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.JSeq();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _JSeqList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _JGroupList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.JGroup.class, "_JGroupList", "JGroup",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getJGroup();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.addJGroup( (jalview.schemabinding.version2.JGroup) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _viewportList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getViewport();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.addViewport( (jalview.schemabinding.version2.Viewport) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Viewport();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _viewportList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _userColoursList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getUserColours();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.addUserColours( (jalview.schemabinding.version2.UserColours) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.UserColours();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _userColoursList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.JGroup();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _JGroupList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _viewportList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Viewport.class, "_viewportList", "Viewport",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getViewport();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.addViewport( (jalview.schemabinding.version2.Viewport) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _treeList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getTree();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.addTree( (jalview.schemabinding.version2.Tree) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Tree();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _treeList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _featureSettings\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewModelSequence target = (JalviewModelSequence) object;\r
+                return target.getFeatureSettings();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewModelSequence target = (JalviewModelSequence) object;\r
+                    target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.FeatureSettings();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _featureSettings\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Viewport();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _viewportList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _userColoursList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.UserColours.class, "_userColoursList",\r
-        "UserColours", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.JalviewModelSequenceDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getUserColours();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.addUserColours( (jalview.schemabinding.version2.UserColours)\r
-                                value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.UserColours();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _userColoursList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _treeList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Tree.class, "_treeList", "tree",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getTree();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.addTree( (jalview.schemabinding.version2.Tree) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Tree();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _treeList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _featureSettings\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.FeatureSettings.class, "_featureSettings",\r
-        "FeatureSettings", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewModelSequence target = (JalviewModelSequence) object;\r
-        return target.getFeatureSettings();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewModelSequence target = (JalviewModelSequence) object;\r
-          target.setFeatureSettings( (jalview.schemabinding.version2.\r
-                                      FeatureSettings) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.FeatureSettings();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _featureSettings\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.JalviewModelSequenceDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.JalviewModelSequence.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.JalviewModelSequence.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 5b4fb76..7963596 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,302 +7,294 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class JalviewUserColours.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewUserColours\r
-    implements java.io.Serializable\r
-{\r
+public class JalviewUserColours implements java.io.Serializable {\r
 \r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
 \r
-  /**\r
-   * Field _schemeName\r
-   */\r
-  private java.lang.String _schemeName;\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
 \r
-  /**\r
-   * Field _colourList\r
-   */\r
-  private java.util.Vector _colourList;\r
+    /**\r
+     * Field _schemeName\r
+     */\r
+    private java.lang.String _schemeName;\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
+    /**\r
+     * Field _colourList\r
+     */\r
+    private java.util.Vector _colourList;\r
 \r
-  public JalviewUserColours()\r
-  {\r
-    super();\r
-    _colourList = new Vector();\r
-  } //-- jalview.schemabinding.version2.JalviewUserColours()\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  /**\r
-   * Method addColour\r
-   *\r
-   *\r
-   *\r
-   * @param vColour\r
-   */\r
-  public void addColour(jalview.schemabinding.version2.Colour vColour)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _colourList.addElement(vColour);\r
-  } //-- void addColour(jalview.schemabinding.version2.Colour)\r
+    public JalviewUserColours() {\r
+        super();\r
+        _colourList = new Vector();\r
+    } //-- jalview.schemabinding.version2.JalviewUserColours()\r
 \r
-  /**\r
-   * Method addColour\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vColour\r
-   */\r
-  public void addColour(int index,\r
-                        jalview.schemabinding.version2.Colour vColour)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _colourList.insertElementAt(vColour, index);\r
-  } //-- void addColour(int, jalview.schemabinding.version2.Colour)\r
 \r
-  /**\r
-   * Method enumerateColour\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateColour()\r
-  {\r
-    return _colourList.elements();\r
-  } //-- java.util.Enumeration enumerateColour()\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-  /**\r
-   * Method getColour\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Colour\r
-   */\r
-  public jalview.schemabinding.version2.Colour getColour(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _colourList.size()))\r
+    /**\r
+     * Method addColour\r
+     * \r
+     * \r
+     * \r
+     * @param vColour\r
+     */\r
+    public void addColour(jalview.schemabinding.version2.Colour vColour)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.Colour getColour(int)\r
-\r
-  /**\r
-   * Method getColour\r
-   *\r
-   *\r
-   *\r
-   * @return Colour\r
-   */\r
-  public jalview.schemabinding.version2.Colour[] getColour()\r
-  {\r
-    int size = _colourList.size();\r
-    jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.\r
-        version2.Colour[size];\r
-    for (int index = 0; index < size; index++)\r
+        _colourList.addElement(vColour);\r
+    } //-- void addColour(jalview.schemabinding.version2.Colour) \r
+\r
+    /**\r
+     * Method addColour\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vColour\r
+     */\r
+    public void addColour(int index, jalview.schemabinding.version2.Colour vColour)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Colour[] getColour()\r
-\r
-  /**\r
-   * Method getColourCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getColourCount()\r
-  {\r
-    return _colourList.size();\r
-  } //-- int getColourCount()\r
-\r
-  /**\r
-   * Returns the value of field 'schemeName'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'schemeName'.\r
-   */\r
-  public java.lang.String getSchemeName()\r
-  {\r
-    return this._schemeName;\r
-  } //-- java.lang.String getSchemeName()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+        _colourList.insertElementAt(vColour, index);\r
+    } //-- void addColour(int, jalview.schemabinding.version2.Colour) \r
+\r
+    /**\r
+     * Method enumerateColour\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateColour()\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return _colourList.elements();\r
+    } //-- java.util.Enumeration enumerateColour() \r
+\r
+    /**\r
+     * Method getColour\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Colour\r
+     */\r
+    public jalview.schemabinding.version2.Colour getColour(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllColour\r
-   *\r
-   */\r
-  public void removeAllColour()\r
-  {\r
-    _colourList.removeAllElements();\r
-  } //-- void removeAllColour()\r
-\r
-  /**\r
-   * Method removeColour\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Colour\r
-   */\r
-  public jalview.schemabinding.version2.Colour removeColour(int index)\r
-  {\r
-    java.lang.Object obj = _colourList.elementAt(index);\r
-    _colourList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Colour) obj;\r
-  } //-- jalview.schemabinding.version2.Colour removeColour(int)\r
-\r
-  /**\r
-   * Method setColour\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vColour\r
-   */\r
-  public void setColour(int index,\r
-                        jalview.schemabinding.version2.Colour vColour)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _colourList.size()))\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _colourList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Colour getColour(int) \r
+\r
+    /**\r
+     * Method getColour\r
+     * \r
+     * \r
+     * \r
+     * @return Colour\r
+     */\r
+    public jalview.schemabinding.version2.Colour[] getColour()\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _colourList.setElementAt(vColour, index);\r
-  } //-- void setColour(int, jalview.schemabinding.version2.Colour)\r
-\r
-  /**\r
-   * Method setColour\r
-   *\r
-   *\r
-   *\r
-   * @param colourArray\r
-   */\r
-  public void setColour(jalview.schemabinding.version2.Colour[] colourArray)\r
-  {\r
-    //-- copy array\r
-    _colourList.removeAllElements();\r
-    for (int i = 0; i < colourArray.length; i++)\r
+        int size = _colourList.size();\r
+        jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.version2.Colour[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Colour[] getColour() \r
+\r
+    /**\r
+     * Method getColourCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getColourCount()\r
     {\r
-      _colourList.addElement(colourArray[i]);\r
-    }\r
-  } //-- void setColour(jalview.schemabinding.version2.Colour)\r
-\r
-  /**\r
-   * Sets the value of field 'schemeName'.\r
-   *\r
-   * @param schemeName the value of field 'schemeName'.\r
-   */\r
-  public void setSchemeName(java.lang.String schemeName)\r
-  {\r
-    this._schemeName = schemeName;\r
-  } //-- void setSchemeName(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.JalviewUserColours.class,\r
-                  reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        return _colourList.size();\r
+    } //-- int getColourCount() \r
+\r
+    /**\r
+     * Returns the value of field 'schemeName'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'schemeName'.\r
+     */\r
+    public java.lang.String getSchemeName()\r
+    {\r
+        return this._schemeName;\r
+    } //-- java.lang.String getSchemeName() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllColour\r
+     * \r
+     */\r
+    public void removeAllColour()\r
+    {\r
+        _colourList.removeAllElements();\r
+    } //-- void removeAllColour() \r
+\r
+    /**\r
+     * Method removeColour\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Colour\r
+     */\r
+    public jalview.schemabinding.version2.Colour removeColour(int index)\r
+    {\r
+        java.lang.Object obj = _colourList.elementAt(index);\r
+        _colourList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Colour) obj;\r
+    } //-- jalview.schemabinding.version2.Colour removeColour(int) \r
+\r
+    /**\r
+     * Method setColour\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vColour\r
+     */\r
+    public void setColour(int index, jalview.schemabinding.version2.Colour vColour)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _colourList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _colourList.setElementAt(vColour, index);\r
+    } //-- void setColour(int, jalview.schemabinding.version2.Colour) \r
+\r
+    /**\r
+     * Method setColour\r
+     * \r
+     * \r
+     * \r
+     * @param colourArray\r
+     */\r
+    public void setColour(jalview.schemabinding.version2.Colour[] colourArray)\r
+    {\r
+        //-- copy array\r
+        _colourList.removeAllElements();\r
+        for (int i = 0; i < colourArray.length; i++) {\r
+            _colourList.addElement(colourArray[i]);\r
+        }\r
+    } //-- void setColour(jalview.schemabinding.version2.Colour) \r
+\r
+    /**\r
+     * Sets the value of field 'schemeName'.\r
+     * \r
+     * @param schemeName the value of field 'schemeName'.\r
+     */\r
+    public void setSchemeName(java.lang.String schemeName)\r
+    {\r
+        this._schemeName = schemeName;\r
+    } //-- void setSchemeName(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
index b726902..661d102 100755 (executable)
--- a/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,251 +7,238 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class JalviewUserColoursDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class JalviewUserColoursDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public JalviewUserColoursDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org/colours";\r
-    xmlName = "JalviewUserColours";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _schemeName\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_schemeName", "schemeName",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewUserColours target = (JalviewUserColours) object;\r
-        return target.getSchemeName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewUserColours target = (JalviewUserColours) object;\r
-          target.setSchemeName( (java.lang.String) value);\r
+public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public JalviewUserColoursDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org/colours";\r
+        xmlName = "JalviewUserColours";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _schemeName\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewUserColours target = (JalviewUserColours) object;\r
+                return target.getSchemeName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewUserColours target = (JalviewUserColours) object;\r
+                    target.setSchemeName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _schemeName\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _colourList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JalviewUserColours target = (JalviewUserColours) object;\r
+                return target.getColour();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JalviewUserColours target = (JalviewUserColours) object;\r
+                    target.addColour( (jalview.schemabinding.version2.Colour) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Colour();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colourList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.JalviewUserColoursDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _schemeName\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _colourList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Colour.class, "_colourList", "colour",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        JalviewUserColours target = (JalviewUserColours) object;\r
-        return target.getColour();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          JalviewUserColours target = (JalviewUserColours) object;\r
-          target.addColour( (jalview.schemabinding.version2.Colour) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Colour();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colourList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.JalviewUserColoursDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.JalviewUserColours.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.JalviewUserColours.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 7bf72de..47423eb 100644 (file)
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,166 +7,167 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class OtherData.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class OtherData\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _key\r
-   */\r
-  private java.lang.String _key;\r
-\r
-  /**\r
-   * Field _value\r
-   */\r
-  private java.lang.String _value;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public OtherData()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.OtherData()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'key'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'key'.\r
-   */\r
-  public java.lang.String getKey()\r
-  {\r
-    return this._key;\r
-  } //-- java.lang.String getKey()\r
-\r
-  /**\r
-   * Returns the value of field 'value'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'value'.\r
-   */\r
-  public java.lang.String getValue()\r
-  {\r
-    return this._value;\r
-  } //-- java.lang.String getValue()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class OtherData implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _key\r
+     */\r
+    private java.lang.String _key;\r
+\r
+    /**\r
+     * Field _value\r
+     */\r
+    private java.lang.String _value;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public OtherData() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.OtherData()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'key'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'key'.\r
+     */\r
+    public java.lang.String getKey()\r
+    {\r
+        return this._key;\r
+    } //-- java.lang.String getKey() \r
+\r
+    /**\r
+     * Returns the value of field 'value'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'value'.\r
+     */\r
+    public java.lang.String getValue()\r
+    {\r
+        return this._value;\r
+    } //-- java.lang.String getValue() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'key'.\r
+     * \r
+     * @param key the value of field 'key'.\r
+     */\r
+    public void setKey(java.lang.String key)\r
+    {\r
+        this._key = key;\r
+    } //-- void setKey(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'value'.\r
+     * \r
+     * @param value the value of field 'value'.\r
+     */\r
+    public void setValue(java.lang.String value)\r
+    {\r
+        this._value = value;\r
+    } //-- void setValue(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'key'.\r
-   *\r
-   * @param key the value of field 'key'.\r
-   */\r
-  public void setKey(java.lang.String key)\r
-  {\r
-    this._key = key;\r
-  } //-- void setKey(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'value'.\r
-   *\r
-   * @param value the value of field 'value'.\r
-   */\r
-  public void setValue(java.lang.String value)\r
-  {\r
-    this._value = value;\r
-  } //-- void setValue(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.OtherData.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
index f39c05d..f6ec794 100644 (file)
--- a/src/jalview/schemabinding/version2/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,252 +7,240 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class OtherDataDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class OtherDataDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public OtherDataDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "otherData";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _key\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        OtherData target = (OtherData) object;\r
-        return target.getKey();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          OtherData target = (OtherData) object;\r
-          target.setKey( (java.lang.String) value);\r
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public OtherDataDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "otherData";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _key\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                OtherData target = (OtherData) object;\r
+                return target.getKey();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    OtherData target = (OtherData) object;\r
+                    target.setKey( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _key\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _value\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                OtherData target = (OtherData) object;\r
+                return target.getValue();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    OtherData target = (OtherData) object;\r
+                    target.setValue( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _value\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.OtherDataDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _key\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _value\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_value", "value",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        OtherData target = (OtherData) object;\r
-        return target.getValue();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          OtherData target = (OtherData) object;\r
-          target.setValue( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _value\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.OtherDataDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.OtherData.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.OtherData.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index f4fa4fe..93c2748 100755 (executable)
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,358 +7,346 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Pdbentry.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Pdbentry\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private java.lang.String _id;\r
-\r
-  /**\r
-   * Field _type\r
-   */\r
-  private java.lang.String _type;\r
-\r
-  /**\r
-   * Field _file\r
-   */\r
-  private java.lang.String _file;\r
-\r
-  /**\r
-   * Field _items\r
-   */\r
-  private java.util.Vector _items;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Pdbentry()\r
-  {\r
-    super();\r
-    _items = new Vector();\r
-  } //-- jalview.schemabinding.version2.Pdbentry()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param vPdbentryItem\r
-   */\r
-  public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem\r
-                              vPdbentryItem)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _items.addElement(vPdbentryItem);\r
-  } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem)\r
-\r
-  /**\r
-   * Method addPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vPdbentryItem\r
-   */\r
-  public void addPdbentryItem(int index,\r
-                              jalview.schemabinding.version2.PdbentryItem\r
-                              vPdbentryItem)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _items.insertElementAt(vPdbentryItem, index);\r
-  } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)\r
-\r
-  /**\r
-   * Method enumeratePdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumeratePdbentryItem()\r
-  {\r
-    return _items.elements();\r
-  } //-- java.util.Enumeration enumeratePdbentryItem()\r
-\r
-  /**\r
-   * Returns the value of field 'file'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'file'.\r
-   */\r
-  public java.lang.String getFile()\r
-  {\r
-    return this._file;\r
-  } //-- java.lang.String getFile()\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'id'.\r
-   */\r
-  public java.lang.String getId()\r
-  {\r
-    return this._id;\r
-  } //-- java.lang.String getId()\r
-\r
-  /**\r
-   * Method getPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return PdbentryItem\r
-   */\r
-  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _items.size()))\r
+public class Pdbentry implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _type\r
+     */\r
+    private java.lang.String _type;\r
+\r
+    /**\r
+     * Field _file\r
+     */\r
+    private java.lang.String _file;\r
+\r
+    /**\r
+     * Field _items\r
+     */\r
+    private java.util.Vector _items;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Pdbentry() {\r
+        super();\r
+        _items = new Vector();\r
+    } //-- jalview.schemabinding.version2.Pdbentry()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param vPdbentryItem\r
+     */\r
+    public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _items.addElement(vPdbentryItem);\r
+    } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem) \r
+\r
+    /**\r
+     * Method addPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vPdbentryItem\r
+     */\r
+    public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _items.insertElementAt(vPdbentryItem, index);\r
+    } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) \r
+\r
+    /**\r
+     * Method enumeratePdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumeratePdbentryItem()\r
+    {\r
+        return _items.elements();\r
+    } //-- java.util.Enumeration enumeratePdbentryItem() \r
+\r
+    /**\r
+     * Returns the value of field 'file'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'file'.\r
+     */\r
+    public java.lang.String getFile()\r
+    {\r
+        return this._file;\r
+    } //-- java.lang.String getFile() \r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'id'.\r
+     */\r
+    public java.lang.String getId()\r
+    {\r
+        return this._id;\r
+    } //-- java.lang.String getId() \r
+\r
+    /**\r
+     * Method getPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return PdbentryItem\r
+     */\r
+    public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _items.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int) \r
+\r
+    /**\r
+     * Method getPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @return PdbentryItem\r
+     */\r
+    public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()\r
+    {\r
+        int size = _items.size();\r
+        jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.schemabinding.version2.PdbentryItem[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() \r
+\r
+    /**\r
+     * Method getPdbentryItemCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getPdbentryItemCount()\r
+    {\r
+        return _items.size();\r
+    } //-- int getPdbentryItemCount() \r
+\r
+    /**\r
+     * Returns the value of field 'type'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'type'.\r
+     */\r
+    public java.lang.String getType()\r
+    {\r
+        return this._type;\r
+    } //-- java.lang.String getType() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllPdbentryItem\r
+     * \r
+     */\r
+    public void removeAllPdbentryItem()\r
+    {\r
+        _items.removeAllElements();\r
+    } //-- void removeAllPdbentryItem() \r
+\r
+    /**\r
+     * Method removePdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return PdbentryItem\r
+     */\r
+    public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int index)\r
+    {\r
+        java.lang.Object obj = _items.elementAt(index);\r
+        _items.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.PdbentryItem) obj;\r
+    } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int) \r
+\r
+    /**\r
+     * Sets the value of field 'file'.\r
+     * \r
+     * @param file the value of field 'file'.\r
+     */\r
+    public void setFile(java.lang.String file)\r
+    {\r
+        this._file = file;\r
+    } //-- void setFile(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(java.lang.String id)\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int)\r
-\r
-  /**\r
-   * Method getPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @return PdbentryItem\r
-   */\r
-  public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()\r
-  {\r
-    int size = _items.size();\r
-    jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.\r
-        schemabinding.version2.PdbentryItem[size];\r
-    for (int index = 0; index < size; index++)\r
+        this._id = id;\r
+    } //-- void setId(java.lang.String) \r
+\r
+    /**\r
+     * Method setPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vPdbentryItem\r
+     */\r
+    public void setPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()\r
-\r
-  /**\r
-   * Method getPdbentryItemCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getPdbentryItemCount()\r
-  {\r
-    return _items.size();\r
-  } //-- int getPdbentryItemCount()\r
-\r
-  /**\r
-   * Returns the value of field 'type'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'type'.\r
-   */\r
-  public java.lang.String getType()\r
-  {\r
-    return this._type;\r
-  } //-- java.lang.String getType()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _items.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _items.setElementAt(vPdbentryItem, index);\r
+    } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) \r
+\r
+    /**\r
+     * Method setPdbentryItem\r
+     * \r
+     * \r
+     * \r
+     * @param pdbentryItemArray\r
+     */\r
+    public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray)\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        //-- copy array\r
+        _items.removeAllElements();\r
+        for (int i = 0; i < pdbentryItemArray.length; i++) {\r
+            _items.addElement(pdbentryItemArray[i]);\r
+        }\r
+    } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem) \r
+\r
+    /**\r
+     * Sets the value of field 'type'.\r
+     * \r
+     * @param type the value of field 'type'.\r
+     */\r
+    public void setType(java.lang.String type)\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllPdbentryItem\r
-   *\r
-   */\r
-  public void removeAllPdbentryItem()\r
-  {\r
-    _items.removeAllElements();\r
-  } //-- void removeAllPdbentryItem()\r
-\r
-  /**\r
-   * Method removePdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return PdbentryItem\r
-   */\r
-  public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int\r
-      index)\r
-  {\r
-    java.lang.Object obj = _items.elementAt(index);\r
-    _items.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.PdbentryItem) obj;\r
-  } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int)\r
-\r
-  /**\r
-   * Sets the value of field 'file'.\r
-   *\r
-   * @param file the value of field 'file'.\r
-   */\r
-  public void setFile(java.lang.String file)\r
-  {\r
-    this._file = file;\r
-  } //-- void setFile(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(java.lang.String id)\r
-  {\r
-    this._id = id;\r
-  } //-- void setId(java.lang.String)\r
-\r
-  /**\r
-   * Method setPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vPdbentryItem\r
-   */\r
-  public void setPdbentryItem(int index,\r
-                              jalview.schemabinding.version2.PdbentryItem\r
-                              vPdbentryItem)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _items.size()))\r
+        this._type = type;\r
+    } //-- void setType(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _items.setElementAt(vPdbentryItem, index);\r
-  } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)\r
-\r
-  /**\r
-   * Method setPdbentryItem\r
-   *\r
-   *\r
-   *\r
-   * @param pdbentryItemArray\r
-   */\r
-  public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[]\r
-                              pdbentryItemArray)\r
-  {\r
-    //-- copy array\r
-    _items.removeAllElements();\r
-    for (int i = 0; i < pdbentryItemArray.length; i++)\r
+        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      _items.addElement(pdbentryItemArray[i]);\r
-    }\r
-  } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem)\r
-\r
-  /**\r
-   * Sets the value of field 'type'.\r
-   *\r
-   * @param type the value of field 'type'.\r
-   */\r
-  public void setType(java.lang.String type)\r
-  {\r
-    this._type = type;\r
-  } //-- void setType(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Pdbentry.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
index e6fa0e1..61a9eda 100755 (executable)
--- a/src/jalview/schemabinding/version2/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,337 +7,309 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class PdbentryDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class PdbentryDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public PdbentryDescriptor()\r
-  {\r
-    super();\r
-    xmlName = "pdbentry";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _id\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Pdbentry target = (Pdbentry) object;\r
-        return target.getId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Pdbentry target = (Pdbentry) object;\r
-          target.setId( (java.lang.String) value);\r
+public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbentryDescriptor() {\r
+        super();\r
+        xmlName = "pdbentry";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _id\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Pdbentry target = (Pdbentry) object;\r
+                return target.getId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Pdbentry target = (Pdbentry) object;\r
+                    target.setId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _id\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _type\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Pdbentry target = (Pdbentry) object;\r
+                return target.getType();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Pdbentry target = (Pdbentry) object;\r
+                    target.setType( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _type\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _id\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _type\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Pdbentry target = (Pdbentry) object;\r
-        return target.getType();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Pdbentry target = (Pdbentry) object;\r
-          target.setType( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- _file\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Pdbentry target = (Pdbentry) object;\r
+                return target.getFile();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Pdbentry target = (Pdbentry) object;\r
+                    target.setFile( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _file\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _items\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Pdbentry target = (Pdbentry) object;\r
+                return target.getPdbentryItem();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Pdbentry target = (Pdbentry) object;\r
+                    target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.PdbentryItem();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setContainer(true);\r
+        desc.setClassDescriptor(new jalview.schemabinding.version2.PdbentryItemDescriptor());\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _items\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.PdbentryDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _type\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _file\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Pdbentry target = (Pdbentry) object;\r
-        return target.getFile();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Pdbentry target = (Pdbentry) object;\r
-          target.setFile( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _file\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _items\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.PdbentryItem.class, "_items", (String)null,\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Pdbentry target = (Pdbentry) object;\r
-        return target.getPdbentryItem();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Pdbentry target = (Pdbentry) object;\r
-          target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem)\r
-                                 value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.PdbentryItem();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setContainer(true);\r
-    desc.setClassDescriptor(new jalview.schemabinding.version2.\r
-                            PdbentryItemDescriptor());\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _items\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.PdbentryDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Pdbentry.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Pdbentry.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 527f5ab..6f64036 100755 (executable)
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,197 +7,191 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import java.util.*;\r
+import java.io.Serializable;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
 \r
 /**\r
  * Class PdbentryItem.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class PdbentryItem\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _propertyList\r
-   */\r
-  private java.util.Vector _propertyList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public PdbentryItem()\r
-  {\r
-    super();\r
-    _propertyList = new Vector();\r
-  } //-- jalview.schemabinding.version2.PdbentryItem()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addProperty\r
-   *\r
-   *\r
-   *\r
-   * @param vProperty\r
-   */\r
-  public void addProperty(jalview.schemabinding.version2.Property vProperty)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _propertyList.addElement(vProperty);\r
-  } //-- void addProperty(jalview.schemabinding.version2.Property)\r
-\r
-  /**\r
-   * Method addProperty\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vProperty\r
-   */\r
-  public void addProperty(int index,\r
-                          jalview.schemabinding.version2.Property vProperty)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _propertyList.insertElementAt(vProperty, index);\r
-  } //-- void addProperty(int, jalview.schemabinding.version2.Property)\r
-\r
-  /**\r
-   * Method enumerateProperty\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateProperty()\r
-  {\r
-    return _propertyList.elements();\r
-  } //-- java.util.Enumeration enumerateProperty()\r
-\r
-  /**\r
-   * Method getProperty\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Property\r
-   */\r
-  public jalview.schemabinding.version2.Property getProperty(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _propertyList.size()))\r
+public class PdbentryItem implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _propertyList\r
+     */\r
+    private java.util.Vector _propertyList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbentryItem() {\r
+        super();\r
+        _propertyList = new Vector();\r
+    } //-- jalview.schemabinding.version2.PdbentryItem()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addProperty\r
+     * \r
+     * \r
+     * \r
+     * @param vProperty\r
+     */\r
+    public void addProperty(jalview.schemabinding.version2.Property vProperty)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _propertyList.addElement(vProperty);\r
+    } //-- void addProperty(jalview.schemabinding.version2.Property) \r
+\r
+    /**\r
+     * Method addProperty\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vProperty\r
+     */\r
+    public void addProperty(int index, jalview.schemabinding.version2.Property vProperty)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _propertyList.insertElementAt(vProperty, index);\r
+    } //-- void addProperty(int, jalview.schemabinding.version2.Property) \r
+\r
+    /**\r
+     * Method enumerateProperty\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateProperty()\r
+    {\r
+        return _propertyList.elements();\r
+    } //-- java.util.Enumeration enumerateProperty() \r
+\r
+    /**\r
+     * Method getProperty\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Property\r
+     */\r
+    public jalview.schemabinding.version2.Property getProperty(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _propertyList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Property getProperty(int) \r
+\r
+    /**\r
+     * Method getProperty\r
+     * \r
+     * \r
+     * \r
+     * @return Property\r
+     */\r
+    public jalview.schemabinding.version2.Property[] getProperty()\r
+    {\r
+        int size = _propertyList.size();\r
+        jalview.schemabinding.version2.Property[] mArray = new jalview.schemabinding.version2.Property[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Property[] getProperty() \r
+\r
+    /**\r
+     * Method getPropertyCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getPropertyCount()\r
+    {\r
+        return _propertyList.size();\r
+    } //-- int getPropertyCount() \r
+\r
+    /**\r
+     * Method removeAllProperty\r
+     * \r
+     */\r
+    public void removeAllProperty()\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Property) _propertyList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.Property getProperty(int)\r
-\r
-  /**\r
-   * Method getProperty\r
-   *\r
-   *\r
-   *\r
-   * @return Property\r
-   */\r
-  public jalview.schemabinding.version2.Property[] getProperty()\r
-  {\r
-    int size = _propertyList.size();\r
-    jalview.schemabinding.version2.Property[] mArray = new jalview.\r
-        schemabinding.version2.Property[size];\r
-    for (int index = 0; index < size; index++)\r
+        _propertyList.removeAllElements();\r
+    } //-- void removeAllProperty() \r
+\r
+    /**\r
+     * Method removeProperty\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Property\r
+     */\r
+    public jalview.schemabinding.version2.Property removeProperty(int index)\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Property[] getProperty()\r
-\r
-  /**\r
-   * Method getPropertyCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getPropertyCount()\r
-  {\r
-    return _propertyList.size();\r
-  } //-- int getPropertyCount()\r
-\r
-  /**\r
-   * Method removeAllProperty\r
-   *\r
-   */\r
-  public void removeAllProperty()\r
-  {\r
-    _propertyList.removeAllElements();\r
-  } //-- void removeAllProperty()\r
-\r
-  /**\r
-   * Method removeProperty\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Property\r
-   */\r
-  public jalview.schemabinding.version2.Property removeProperty(int index)\r
-  {\r
-    java.lang.Object obj = _propertyList.elementAt(index);\r
-    _propertyList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Property) obj;\r
-  } //-- jalview.schemabinding.version2.Property removeProperty(int)\r
-\r
-  /**\r
-   * Method setProperty\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vProperty\r
-   */\r
-  public void setProperty(int index,\r
-                          jalview.schemabinding.version2.Property vProperty)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _propertyList.size()))\r
+        java.lang.Object obj = _propertyList.elementAt(index);\r
+        _propertyList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Property) obj;\r
+    } //-- jalview.schemabinding.version2.Property removeProperty(int) \r
+\r
+    /**\r
+     * Method setProperty\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vProperty\r
+     */\r
+    public void setProperty(int index, jalview.schemabinding.version2.Property vProperty)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _propertyList.setElementAt(vProperty, index);\r
-  } //-- void setProperty(int, jalview.schemabinding.version2.Property)\r
-\r
-  /**\r
-   * Method setProperty\r
-   *\r
-   *\r
-   *\r
-   * @param propertyArray\r
-   */\r
-  public void setProperty(jalview.schemabinding.version2.Property[]\r
-                          propertyArray)\r
-  {\r
-    //-- copy array\r
-    _propertyList.removeAllElements();\r
-    for (int i = 0; i < propertyArray.length; i++)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _propertyList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _propertyList.setElementAt(vProperty, index);\r
+    } //-- void setProperty(int, jalview.schemabinding.version2.Property) \r
+\r
+    /**\r
+     * Method setProperty\r
+     * \r
+     * \r
+     * \r
+     * @param propertyArray\r
+     */\r
+    public void setProperty(jalview.schemabinding.version2.Property[] propertyArray)\r
     {\r
-      _propertyList.addElement(propertyArray[i]);\r
-    }\r
-  } //-- void setProperty(jalview.schemabinding.version2.Property)\r
+        //-- copy array\r
+        _propertyList.removeAllElements();\r
+        for (int i = 0; i < propertyArray.length; i++) {\r
+            _propertyList.addElement(propertyArray[i]);\r
+        }\r
+    } //-- void setProperty(jalview.schemabinding.version2.Property) \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
index 7c1b0d4..d9d36c0 100755 (executable)
--- a/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,207 +7,202 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class PdbentryItemDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class PdbentryItemDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public PdbentryItemDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "pdbentry";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _propertyList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Property.class, "_propertyList", "property",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        PdbentryItem target = (PdbentryItem) object;\r
-        return target.getProperty();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          PdbentryItem target = (PdbentryItem) object;\r
-          target.addProperty( (jalview.schemabinding.version2.Property) value);\r
+public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbentryItemDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "pdbentry";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _propertyList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                PdbentryItem target = (PdbentryItem) object;\r
+                return target.getProperty();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    PdbentryItem target = (PdbentryItem) object;\r
+                    target.addProperty( (jalview.schemabinding.version2.Property) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Property();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _propertyList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Property();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _propertyList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.PdbentryItemDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.PdbentryItem.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.PdbentryItemDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.PdbentryItem.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 8625b88..347ff35 100755 (executable)
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,110 +7,270 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Pdbids.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Pdbids\r
-    extends Pdbentry implements java.io.Serializable\r
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry \r
+implements java.io.Serializable\r
 {\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Pdbids()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Pdbids()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _structureStateList\r
+     */\r
+    private java.util.Vector _structureStateList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Pdbids() {\r
+        super();\r
+        _structureStateList = new Vector();\r
+    } //-- jalview.schemabinding.version2.Pdbids()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param vStructureState\r
+     */\r
+    public void addStructureState(jalview.schemabinding.version2.StructureState vStructureState)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _structureStateList.addElement(vStructureState);\r
+    } //-- void addStructureState(jalview.schemabinding.version2.StructureState) \r
+\r
+    /**\r
+     * Method addStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vStructureState\r
+     */\r
+    public void addStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _structureStateList.insertElementAt(vStructureState, index);\r
+    } //-- void addStructureState(int, jalview.schemabinding.version2.StructureState) \r
+\r
+    /**\r
+     * Method enumerateStructureState\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateStructureState()\r
+    {\r
+        return _structureStateList.elements();\r
+    } //-- java.util.Enumeration enumerateStructureState() \r
+\r
+    /**\r
+     * Method getStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return StructureState\r
+     */\r
+    public jalview.schemabinding.version2.StructureState getStructureState(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _structureStateList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.StructureState getStructureState(int) \r
+\r
+    /**\r
+     * Method getStructureState\r
+     * \r
+     * \r
+     * \r
+     * @return StructureState\r
+     */\r
+    public jalview.schemabinding.version2.StructureState[] getStructureState()\r
+    {\r
+        int size = _structureStateList.size();\r
+        jalview.schemabinding.version2.StructureState[] mArray = new jalview.schemabinding.version2.StructureState[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.StructureState[] getStructureState() \r
+\r
+    /**\r
+     * Method getStructureStateCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getStructureStateCount()\r
+    {\r
+        return _structureStateList.size();\r
+    } //-- int getStructureStateCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllStructureState\r
+     * \r
+     */\r
+    public void removeAllStructureState()\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        _structureStateList.removeAllElements();\r
+    } //-- void removeAllStructureState() \r
+\r
+    /**\r
+     * Method removeStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return StructureState\r
+     */\r
+    public jalview.schemabinding.version2.StructureState removeStructureState(int index)\r
+    {\r
+        java.lang.Object obj = _structureStateList.elementAt(index);\r
+        _structureStateList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.StructureState) obj;\r
+    } //-- jalview.schemabinding.version2.StructureState removeStructureState(int) \r
+\r
+    /**\r
+     * Method setStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vStructureState\r
+     */\r
+    public void setStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _structureStateList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _structureStateList.setElementAt(vStructureState, index);\r
+    } //-- void setStructureState(int, jalview.schemabinding.version2.StructureState) \r
+\r
+    /**\r
+     * Method setStructureState\r
+     * \r
+     * \r
+     * \r
+     * @param structureStateArray\r
+     */\r
+    public void setStructureState(jalview.schemabinding.version2.StructureState[] structureStateArray)\r
+    {\r
+        //-- copy array\r
+        _structureStateList.removeAllElements();\r
+        for (int i = 0; i < structureStateArray.length; i++) {\r
+            _structureStateList.addElement(structureStateArray[i]);\r
+        }\r
+    } //-- void setStructureState(jalview.schemabinding.version2.StructureState) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Pdbids.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
index 2d539c9..d96b776 100755 (executable)
--- a/src/jalview/schemabinding/version2/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,159 +7,205 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class PdbidsDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class PdbidsDescriptor\r
-    extends PdbentryDescriptor\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public PdbidsDescriptor()\r
-  {\r
-    super();\r
-    setExtendsWithoutFlatten(new PdbentryDescriptor());\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "pdbids";\r
-  } //-- jalview.schemabinding.version2.PdbidsDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return super.getExtends();\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    if (identity == null)\r
+public class PdbidsDescriptor extends jalview.schemabinding.version2.PdbentryDescriptor {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbidsDescriptor() {\r
+        super();\r
+        setExtendsWithoutFlatten(new jalview.schemabinding.version2.PdbentryDescriptor());\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "pdbids";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _structureStateList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Pdbids target = (Pdbids) object;\r
+                return target.getStructureState();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Pdbids target = (Pdbids) object;\r
+                    target.addStructureState( (jalview.schemabinding.version2.StructureState) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.StructureState();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _structureStateList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.PdbidsDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return super.getExtends();\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        if (identity == null)\r
+            return super.getIdentity();\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Pdbids.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      return super.getIdentity();\r
-    }\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Pdbids.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PdbidsItem.java b/src/jalview/schemabinding/version2/PdbidsItem.java
new file mode 100644 (file)
index 0000000..0c5c10f
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbidsItem.java
@@ -0,0 +1,70 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.Serializable;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class PdbidsItem.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbidsItem implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _structureState\r
+     */\r
+    private jalview.schemabinding.version2.StructureState _structureState;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbidsItem() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.PdbidsItem()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'structureState'.\r
+     * \r
+     * @return StructureState\r
+     * @return the value of field 'structureState'.\r
+     */\r
+    public jalview.schemabinding.version2.StructureState getStructureState()\r
+    {\r
+        return this._structureState;\r
+    } //-- jalview.schemabinding.version2.StructureState getStructureState() \r
+\r
+    /**\r
+     * Sets the value of field 'structureState'.\r
+     * \r
+     * @param structureState the value of field 'structureState'.\r
+     */\r
+    public void setStructureState(jalview.schemabinding.version2.StructureState structureState)\r
+    {\r
+        this._structureState = structureState;\r
+    } //-- void setStructureState(jalview.schemabinding.version2.StructureState) \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java b/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java
new file mode 100644 (file)
index 0000000..9128920
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java
@@ -0,0 +1,207 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class PdbidsItemDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbidsItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PdbidsItemDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "pdbids";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _structureState\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureState", "structureState", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                PdbidsItem target = (PdbidsItem) object;\r
+                return target.getStructureState();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    PdbidsItem target = (PdbidsItem) object;\r
+                    target.setStructureState( (jalview.schemabinding.version2.StructureState) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.StructureState();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _structureState\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.PdbidsItemDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.PdbidsItem.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index 4059340..338dd90 100755 (executable)
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,166 +7,167 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Property.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Property\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _name\r
-   */\r
-  private java.lang.String _name;\r
-\r
-  /**\r
-   * Field _value\r
-   */\r
-  private java.lang.String _value;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Property()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Property()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'name'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'name'.\r
-   */\r
-  public java.lang.String getName()\r
-  {\r
-    return this._name;\r
-  } //-- java.lang.String getName()\r
-\r
-  /**\r
-   * Returns the value of field 'value'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'value'.\r
-   */\r
-  public java.lang.String getValue()\r
-  {\r
-    return this._value;\r
-  } //-- java.lang.String getValue()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class Property implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+    /**\r
+     * Field _value\r
+     */\r
+    private java.lang.String _value;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Property() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.Property()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'value'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'value'.\r
+     */\r
+    public java.lang.String getValue()\r
+    {\r
+        return this._value;\r
+    } //-- java.lang.String getValue() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'value'.\r
+     * \r
+     * @param value the value of field 'value'.\r
+     */\r
+    public void setValue(java.lang.String value)\r
+    {\r
+        this._value = value;\r
+    } //-- void setValue(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'name'.\r
-   *\r
-   * @param name the value of field 'name'.\r
-   */\r
-  public void setName(java.lang.String name)\r
-  {\r
-    this._name = name;\r
-  } //-- void setName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'value'.\r
-   *\r
-   * @param value the value of field 'value'.\r
-   */\r
-  public void setValue(java.lang.String value)\r
-  {\r
-    this._value = value;\r
-  } //-- void setValue(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Property.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/PropertyDescriptor.java b/src/jalview/schemabinding/version2/PropertyDescriptor.java
index 9d0eafa..e22704c 100755 (executable)
--- a/src/jalview/schemabinding/version2/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/PropertyDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,252 +7,240 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class PropertyDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class PropertyDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public PropertyDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "property";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _name\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Property target = (Property) object;\r
-        return target.getName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Property target = (Property) object;\r
-          target.setName( (java.lang.String) value);\r
+public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public PropertyDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "property";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _name\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Property target = (Property) object;\r
+                return target.getName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Property target = (Property) object;\r
+                    target.setName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _name\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _value\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Property target = (Property) object;\r
+                return target.getValue();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Property target = (Property) object;\r
+                    target.setValue( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _value\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.PropertyDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _name\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _value\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_value", "value",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Property target = (Property) object;\r
-        return target.getValue();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Property target = (Property) object;\r
-          target.setValue( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _value\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.PropertyDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Property.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Property.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 372a2c5..993ad23 100755 (executable)
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,274 +7,270 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Sequence.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Sequence\r
-    extends jalview.schemabinding.version2.SequenceType implements java.io.\r
-    Serializable\r
+public class Sequence extends jalview.schemabinding.version2.SequenceType \r
+implements java.io.Serializable\r
 {\r
 \r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
 \r
-  /**\r
-   * Field _DBRefList\r
-   */\r
-  private java.util.Vector _DBRefList;\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
+    /**\r
+     * Field _DBRefList\r
+     */\r
+    private java.util.Vector _DBRefList;\r
 \r
-  public Sequence()\r
-  {\r
-    super();\r
-    _DBRefList = new Vector();\r
-  } //-- jalview.schemabinding.version2.Sequence()\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  /**\r
-   * Method addDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param vDBRef\r
-   */\r
-  public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _DBRefList.addElement(vDBRef);\r
-  } //-- void addDBRef(jalview.schemabinding.version2.DBRef)\r
+    public Sequence() {\r
+        super();\r
+        _DBRefList = new Vector();\r
+    } //-- jalview.schemabinding.version2.Sequence()\r
 \r
-  /**\r
-   * Method addDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vDBRef\r
-   */\r
-  public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _DBRefList.insertElementAt(vDBRef, index);\r
-  } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef)\r
 \r
-  /**\r
-   * Method enumerateDBRef\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateDBRef()\r
-  {\r
-    return _DBRefList.elements();\r
-  } //-- java.util.Enumeration enumerateDBRef()\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-  /**\r
-   * Method getDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return DBRef\r
-   */\r
-  public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _DBRefList.size()))\r
+    /**\r
+     * Method addDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param vDBRef\r
+     */\r
+    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
+        _DBRefList.addElement(vDBRef);\r
+    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) \r
 \r
-    return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
-  } //-- jalview.schemabinding.version2.DBRef getDBRef(int)\r
-\r
-  /**\r
-   * Method getDBRef\r
-   *\r
-   *\r
-   *\r
-   * @return DBRef\r
-   */\r
-  public jalview.schemabinding.version2.DBRef[] getDBRef()\r
-  {\r
-    int size = _DBRefList.size();\r
-    jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.\r
-        version2.DBRef[size];\r
-    for (int index = 0; index < size; index++)\r
+    /**\r
+     * Method addDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vDBRef\r
+     */\r
+    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.DBRef[] getDBRef()\r
+        _DBRefList.insertElementAt(vDBRef, index);\r
+    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) \r
 \r
-  /**\r
-   * Method getDBRefCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getDBRefCount()\r
-  {\r
-    return _DBRefList.size();\r
-  } //-- int getDBRefCount()\r
+    /**\r
+     * Method enumerateDBRef\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateDBRef()\r
+    {\r
+        return _DBRefList.elements();\r
+    } //-- java.util.Enumeration enumerateDBRef() \r
 \r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+    /**\r
+     * Method getDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _DBRefList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) \r
+\r
+    /**\r
+     * Method getDBRef\r
+     * \r
+     * \r
+     * \r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef[] getDBRef()\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
+        int size = _DBRefList.size();\r
+        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method getDBRefCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getDBRefCount()\r
+    {\r
+        return _DBRefList.size();\r
+    } //-- int getDBRefCount() \r
 \r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
 \r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
-  /**\r
-   * Method removeAllDBRef\r
-   *\r
-   */\r
-  public void removeAllDBRef()\r
-  {\r
-    _DBRefList.removeAllElements();\r
-  } //-- void removeAllDBRef()\r
+    /**\r
+     * Method removeAllDBRef\r
+     * \r
+     */\r
+    public void removeAllDBRef()\r
+    {\r
+        _DBRefList.removeAllElements();\r
+    } //-- void removeAllDBRef() \r
 \r
-  /**\r
-   * Method removeDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return DBRef\r
-   */\r
-  public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
-  {\r
-    java.lang.Object obj = _DBRefList.elementAt(index);\r
-    _DBRefList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.DBRef) obj;\r
-  } //-- jalview.schemabinding.version2.DBRef removeDBRef(int)\r
+    /**\r
+     * Method removeDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
+    {\r
+        java.lang.Object obj = _DBRefList.elementAt(index);\r
+        _DBRefList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.DBRef) obj;\r
+    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) \r
 \r
-  /**\r
-   * Method setDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vDBRef\r
-   */\r
-  public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _DBRefList.size()))\r
+    /**\r
+     * Method setDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vDBRef\r
+     */\r
+    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _DBRefList.setElementAt(vDBRef, index);\r
-  } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _DBRefList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _DBRefList.setElementAt(vDBRef, index);\r
+    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) \r
 \r
-  /**\r
-   * Method setDBRef\r
-   *\r
-   *\r
-   *\r
-   * @param DBRefArray\r
-   */\r
-  public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
-  {\r
-    //-- copy array\r
-    _DBRefList.removeAllElements();\r
-    for (int i = 0; i < DBRefArray.length; i++)\r
+    /**\r
+     * Method setDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param DBRefArray\r
+     */\r
+    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
     {\r
-      _DBRefList.addElement(DBRefArray[i]);\r
-    }\r
-  } //-- void setDBRef(jalview.schemabinding.version2.DBRef)\r
+        //-- copy array\r
+        _DBRefList.removeAllElements();\r
+        for (int i = 0; i < DBRefArray.length; i++) {\r
+            _DBRefList.addElement(DBRefArray[i]);\r
+        }\r
+    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) \r
 \r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Sequence.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SequenceDescriptor.java b/src/jalview/schemabinding/version2/SequenceDescriptor.java
index 8c621ca..555284a 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,213 +7,205 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class SequenceDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceDescriptor\r
-    extends jalview.schemabinding.version2.SequenceTypeDescriptor\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SequenceDescriptor()\r
-  {\r
-    super();\r
-    setExtendsWithoutFlatten(new jalview.schemabinding.version2.\r
-                             SequenceTypeDescriptor());\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "Sequence";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _DBRefList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.DBRef.class, "_DBRefList", "DBRef",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Sequence target = (Sequence) object;\r
-        return target.getDBRef();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Sequence target = (Sequence) object;\r
-          target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+public class SequenceDescriptor extends jalview.schemabinding.version2.SequenceTypeDescriptor {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SequenceDescriptor() {\r
+        super();\r
+        setExtendsWithoutFlatten(new jalview.schemabinding.version2.SequenceTypeDescriptor());\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "Sequence";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _DBRefList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Sequence target = (Sequence) object;\r
+                return target.getDBRef();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Sequence target = (Sequence) object;\r
+                    target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.DBRef();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _DBRefList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.DBRef();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _DBRefList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.SequenceDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return super.getExtends();\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    if (identity == null)\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.SequenceDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return super.getExtends();\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        if (identity == null)\r
+            return super.getIdentity();\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Sequence.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      return super.getIdentity();\r
-    }\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Sequence.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 020cbb9..6f0342b 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,467 +7,445 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class SequenceSet.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceSet\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _gapChar\r
-   */\r
-  private java.lang.String _gapChar;\r
-\r
-  /**\r
-   * Field _sequenceList\r
-   */\r
-  private java.util.Vector _sequenceList;\r
-\r
-  /**\r
-   * Field _annotationList\r
-   */\r
-  private java.util.Vector _annotationList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SequenceSet()\r
-  {\r
-    super();\r
-    _sequenceList = new Vector();\r
-    _annotationList = new Vector();\r
-  } //-- jalview.schemabinding.version2.SequenceSet()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param vAnnotation\r
-   */\r
-  public void addAnnotation(jalview.schemabinding.version2.Annotation\r
-                            vAnnotation)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _annotationList.addElement(vAnnotation);\r
-  } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)\r
-\r
-  /**\r
-   * Method addAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vAnnotation\r
-   */\r
-  public void addAnnotation(int index,\r
-                            jalview.schemabinding.version2.Annotation\r
-                            vAnnotation)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _annotationList.insertElementAt(vAnnotation, index);\r
-  } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)\r
-\r
-  /**\r
-   * Method addSequence\r
-   *\r
-   *\r
-   *\r
-   * @param vSequence\r
-   */\r
-  public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _sequenceList.addElement(vSequence);\r
-  } //-- void addSequence(jalview.schemabinding.version2.Sequence)\r
-\r
-  /**\r
-   * Method addSequence\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSequence\r
-   */\r
-  public void addSequence(int index,\r
-                          jalview.schemabinding.version2.Sequence vSequence)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _sequenceList.insertElementAt(vSequence, index);\r
-  } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)\r
-\r
-  /**\r
-   * Method enumerateAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateAnnotation()\r
-  {\r
-    return _annotationList.elements();\r
-  } //-- java.util.Enumeration enumerateAnnotation()\r
-\r
-  /**\r
-   * Method enumerateSequence\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateSequence()\r
-  {\r
-    return _sequenceList.elements();\r
-  } //-- java.util.Enumeration enumerateSequence()\r
-\r
-  /**\r
-   * Method getAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Annotation\r
-   */\r
-  public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _annotationList.size()))\r
+public class SequenceSet implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _gapChar\r
+     */\r
+    private java.lang.String _gapChar;\r
+\r
+    /**\r
+     * Field _sequenceList\r
+     */\r
+    private java.util.Vector _sequenceList;\r
+\r
+    /**\r
+     * Field _annotationList\r
+     */\r
+    private java.util.Vector _annotationList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SequenceSet() {\r
+        super();\r
+        _sequenceList = new Vector();\r
+        _annotationList = new Vector();\r
+    } //-- jalview.schemabinding.version2.SequenceSet()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param vAnnotation\r
+     */\r
+    public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _annotationList.addElement(vAnnotation);\r
+    } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) \r
+\r
+    /**\r
+     * Method addAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vAnnotation\r
+     */\r
+    public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _annotationList.insertElementAt(vAnnotation, index);\r
+    } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) \r
+\r
+    /**\r
+     * Method addSequence\r
+     * \r
+     * \r
+     * \r
+     * @param vSequence\r
+     */\r
+    public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _sequenceList.addElement(vSequence);\r
+    } //-- void addSequence(jalview.schemabinding.version2.Sequence) \r
+\r
+    /**\r
+     * Method addSequence\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSequence\r
+     */\r
+    public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _sequenceList.insertElementAt(vSequence, index);\r
+    } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) \r
+\r
+    /**\r
+     * Method enumerateAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateAnnotation()\r
+    {\r
+        return _annotationList.elements();\r
+    } //-- java.util.Enumeration enumerateAnnotation() \r
+\r
+    /**\r
+     * Method enumerateSequence\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateSequence()\r
+    {\r
+        return _sequenceList.elements();\r
+    } //-- java.util.Enumeration enumerateSequence() \r
+\r
+    /**\r
+     * Method getAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Annotation\r
+     */\r
+    public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _annotationList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) \r
+\r
+    /**\r
+     * Method getAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @return Annotation\r
+     */\r
+    public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
+    {\r
+        int size = _annotationList.size();\r
+        jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() \r
+\r
+    /**\r
+     * Method getAnnotationCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getAnnotationCount()\r
+    {\r
+        return _annotationList.size();\r
+    } //-- int getAnnotationCount() \r
+\r
+    /**\r
+     * Returns the value of field 'gapChar'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'gapChar'.\r
+     */\r
+    public java.lang.String getGapChar()\r
+    {\r
+        return this._gapChar;\r
+    } //-- java.lang.String getGapChar() \r
+\r
+    /**\r
+     * Method getSequence\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Sequence\r
+     */\r
+    public jalview.schemabinding.version2.Sequence getSequence(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.Sequence getSequence(int) \r
+\r
+    /**\r
+     * Method getSequence\r
+     * \r
+     * \r
+     * \r
+     * @return Sequence\r
+     */\r
+    public jalview.schemabinding.version2.Sequence[] getSequence()\r
+    {\r
+        int size = _sequenceList.size();\r
+        jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.Sequence[] getSequence() \r
+\r
+    /**\r
+     * Method getSequenceCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSequenceCount()\r
+    {\r
+        return _sequenceList.size();\r
+    } //-- int getSequenceCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllAnnotation\r
+     * \r
+     */\r
+    public void removeAllAnnotation()\r
+    {\r
+        _annotationList.removeAllElements();\r
+    } //-- void removeAllAnnotation() \r
+\r
+    /**\r
+     * Method removeAllSequence\r
+     * \r
+     */\r
+    public void removeAllSequence()\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Annotation) _annotationList.\r
-        elementAt(index);\r
-  } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)\r
-\r
-  /**\r
-   * Method getAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @return Annotation\r
-   */\r
-  public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
-  {\r
-    int size = _annotationList.size();\r
-    jalview.schemabinding.version2.Annotation[] mArray = new jalview.\r
-        schemabinding.version2.Annotation[size];\r
-    for (int index = 0; index < size; index++)\r
+        _sequenceList.removeAllElements();\r
+    } //-- void removeAllSequence() \r
+\r
+    /**\r
+     * Method removeAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Annotation\r
+     */\r
+    public jalview.schemabinding.version2.Annotation removeAnnotation(int index)\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.Annotation)\r
-          _annotationList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Annotation[] getAnnotation()\r
-\r
-  /**\r
-   * Method getAnnotationCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getAnnotationCount()\r
-  {\r
-    return _annotationList.size();\r
-  } //-- int getAnnotationCount()\r
-\r
-  /**\r
-   * Returns the value of field 'gapChar'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'gapChar'.\r
-   */\r
-  public java.lang.String getGapChar()\r
-  {\r
-    return this._gapChar;\r
-  } //-- java.lang.String getGapChar()\r
-\r
-  /**\r
-   * Method getSequence\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Sequence\r
-   */\r
-  public jalview.schemabinding.version2.Sequence getSequence(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _sequenceList.size()))\r
+        java.lang.Object obj = _annotationList.elementAt(index);\r
+        _annotationList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Annotation) obj;\r
+    } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int) \r
+\r
+    /**\r
+     * Method removeSequence\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Sequence\r
+     */\r
+    public jalview.schemabinding.version2.Sequence removeSequence(int index)\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(\r
-        index);\r
-  } //-- jalview.schemabinding.version2.Sequence getSequence(int)\r
-\r
-  /**\r
-   * Method getSequence\r
-   *\r
-   *\r
-   *\r
-   * @return Sequence\r
-   */\r
-  public jalview.schemabinding.version2.Sequence[] getSequence()\r
-  {\r
-    int size = _sequenceList.size();\r
-    jalview.schemabinding.version2.Sequence[] mArray = new jalview.\r
-        schemabinding.version2.Sequence[size];\r
-    for (int index = 0; index < size; index++)\r
+        java.lang.Object obj = _sequenceList.elementAt(index);\r
+        _sequenceList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.Sequence) obj;\r
+    } //-- jalview.schemabinding.version2.Sequence removeSequence(int) \r
+\r
+    /**\r
+     * Method setAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vAnnotation\r
+     */\r
+    public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.\r
-          elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.Sequence[] getSequence()\r
-\r
-  /**\r
-   * Method getSequenceCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getSequenceCount()\r
-  {\r
-    return _sequenceList.size();\r
-  } //-- int getSequenceCount()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _annotationList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _annotationList.setElementAt(vAnnotation, index);\r
+    } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation) \r
+\r
+    /**\r
+     * Method setAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @param annotationArray\r
+     */\r
+    public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        //-- copy array\r
+        _annotationList.removeAllElements();\r
+        for (int i = 0; i < annotationArray.length; i++) {\r
+            _annotationList.addElement(annotationArray[i]);\r
+        }\r
+    } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) \r
+\r
+    /**\r
+     * Sets the value of field 'gapChar'.\r
+     * \r
+     * @param gapChar the value of field 'gapChar'.\r
+     */\r
+    public void setGapChar(java.lang.String gapChar)\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllAnnotation\r
-   *\r
-   */\r
-  public void removeAllAnnotation()\r
-  {\r
-    _annotationList.removeAllElements();\r
-  } //-- void removeAllAnnotation()\r
-\r
-  /**\r
-   * Method removeAllSequence\r
-   *\r
-   */\r
-  public void removeAllSequence()\r
-  {\r
-    _sequenceList.removeAllElements();\r
-  } //-- void removeAllSequence()\r
-\r
-  /**\r
-   * Method removeAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Annotation\r
-   */\r
-  public jalview.schemabinding.version2.Annotation removeAnnotation(int index)\r
-  {\r
-    java.lang.Object obj = _annotationList.elementAt(index);\r
-    _annotationList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Annotation) obj;\r
-  } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)\r
-\r
-  /**\r
-   * Method removeSequence\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return Sequence\r
-   */\r
-  public jalview.schemabinding.version2.Sequence removeSequence(int index)\r
-  {\r
-    java.lang.Object obj = _sequenceList.elementAt(index);\r
-    _sequenceList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.Sequence) obj;\r
-  } //-- jalview.schemabinding.version2.Sequence removeSequence(int)\r
-\r
-  /**\r
-   * Method setAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vAnnotation\r
-   */\r
-  public void setAnnotation(int index,\r
-                            jalview.schemabinding.version2.Annotation\r
-                            vAnnotation)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _annotationList.size()))\r
+        this._gapChar = gapChar;\r
+    } //-- void setGapChar(java.lang.String) \r
+\r
+    /**\r
+     * Method setSequence\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSequence\r
+     */\r
+    public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _annotationList.setElementAt(vAnnotation, index);\r
-  } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation)\r
-\r
-  /**\r
-   * Method setAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @param annotationArray\r
-   */\r
-  public void setAnnotation(jalview.schemabinding.version2.Annotation[]\r
-                            annotationArray)\r
-  {\r
-    //-- copy array\r
-    _annotationList.removeAllElements();\r
-    for (int i = 0; i < annotationArray.length; i++)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _sequenceList.setElementAt(vSequence, index);\r
+    } //-- void setSequence(int, jalview.schemabinding.version2.Sequence) \r
+\r
+    /**\r
+     * Method setSequence\r
+     * \r
+     * \r
+     * \r
+     * @param sequenceArray\r
+     */\r
+    public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)\r
     {\r
-      _annotationList.addElement(annotationArray[i]);\r
-    }\r
-  } //-- void setAnnotation(jalview.schemabinding.version2.Annotation)\r
-\r
-  /**\r
-   * Sets the value of field 'gapChar'.\r
-   *\r
-   * @param gapChar the value of field 'gapChar'.\r
-   */\r
-  public void setGapChar(java.lang.String gapChar)\r
-  {\r
-    this._gapChar = gapChar;\r
-  } //-- void setGapChar(java.lang.String)\r
-\r
-  /**\r
-   * Method setSequence\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSequence\r
-   */\r
-  public void setSequence(int index,\r
-                          jalview.schemabinding.version2.Sequence vSequence)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _sequenceList.size()))\r
+        //-- copy array\r
+        _sequenceList.removeAllElements();\r
+        for (int i = 0; i < sequenceArray.length; i++) {\r
+            _sequenceList.addElement(sequenceArray[i]);\r
+        }\r
+    } //-- void setSequence(jalview.schemabinding.version2.Sequence) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _sequenceList.setElementAt(vSequence, index);\r
-  } //-- void setSequence(int, jalview.schemabinding.version2.Sequence)\r
-\r
-  /**\r
-   * Method setSequence\r
-   *\r
-   *\r
-   *\r
-   * @param sequenceArray\r
-   */\r
-  public void setSequence(jalview.schemabinding.version2.Sequence[]\r
-                          sequenceArray)\r
-  {\r
-    //-- copy array\r
-    _sequenceList.removeAllElements();\r
-    for (int i = 0; i < sequenceArray.length; i++)\r
+        return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      _sequenceList.addElement(sequenceArray[i]);\r
-    }\r
-  } //-- void setSequence(jalview.schemabinding.version2.Sequence)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.SequenceSet.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 938f1ed..70ad2dc 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,297 +7,275 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class SequenceSetDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceSetDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SequenceSetDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "SequenceSet";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _gapChar\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_gapChar", "gapChar",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceSet target = (SequenceSet) object;\r
-        return target.getGapChar();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceSet target = (SequenceSet) object;\r
-          target.setGapChar( (java.lang.String) value);\r
+public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SequenceSetDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "SequenceSet";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _gapChar\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceSet target = (SequenceSet) object;\r
+                return target.getGapChar();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceSet target = (SequenceSet) object;\r
+                    target.setGapChar( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _gapChar\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _sequenceList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceSet target = (SequenceSet) object;\r
+                return target.getSequence();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceSet target = (SequenceSet) object;\r
+                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Sequence();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequenceList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- _annotationList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceSet target = (SequenceSet) object;\r
+                return target.getAnnotation();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceSet target = (SequenceSet) object;\r
+                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.Annotation();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _annotationList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.SequenceSetDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _gapChar\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _sequenceList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Sequence.class, "_sequenceList", "Sequence",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceSet target = (SequenceSet) object;\r
-        return target.getSequence();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceSet target = (SequenceSet) object;\r
-          target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Sequence();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _sequenceList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _annotationList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.Annotation.class, "_annotationList",\r
-        "Annotation", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceSet target = (SequenceSet) object;\r
-        return target.getAnnotation();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceSet target = (SequenceSet) object;\r
-          target.addAnnotation( (jalview.schemabinding.version2.Annotation)\r
-                               value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.Annotation();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _annotationList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.SequenceSetDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.SequenceSet.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.SequenceSet.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index 4c60f87..d413e2d 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,218 +7,219 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class SequenceType.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceType\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private java.lang.String _id;\r
-\r
-  /**\r
-   * Field _description\r
-   */\r
-  private java.lang.String _description;\r
-\r
-  /**\r
-   * Field _sequence\r
-   */\r
-  private java.lang.String _sequence;\r
-\r
-  /**\r
-   * Field _name\r
-   */\r
-  private java.lang.String _name;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SequenceType()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.SequenceType()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'description'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'description'.\r
-   */\r
-  public java.lang.String getDescription()\r
-  {\r
-    return this._description;\r
-  } //-- java.lang.String getDescription()\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'id'.\r
-   */\r
-  public java.lang.String getId()\r
-  {\r
-    return this._id;\r
-  } //-- java.lang.String getId()\r
-\r
-  /**\r
-   * Returns the value of field 'name'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'name'.\r
-   */\r
-  public java.lang.String getName()\r
-  {\r
-    return this._name;\r
-  } //-- java.lang.String getName()\r
-\r
-  /**\r
-   * Returns the value of field 'sequence'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'sequence'.\r
-   */\r
-  public java.lang.String getSequence()\r
-  {\r
-    return this._sequence;\r
-  } //-- java.lang.String getSequence()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class SequenceType implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _description\r
+     */\r
+    private java.lang.String _description;\r
+\r
+    /**\r
+     * Field _sequence\r
+     */\r
+    private java.lang.String _sequence;\r
+\r
+    /**\r
+     * Field _name\r
+     */\r
+    private java.lang.String _name;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SequenceType() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.SequenceType()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'description'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'description'.\r
+     */\r
+    public java.lang.String getDescription()\r
+    {\r
+        return this._description;\r
+    } //-- java.lang.String getDescription() \r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'id'.\r
+     */\r
+    public java.lang.String getId()\r
+    {\r
+        return this._id;\r
+    } //-- java.lang.String getId() \r
+\r
+    /**\r
+     * Returns the value of field 'name'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'name'.\r
+     */\r
+    public java.lang.String getName()\r
+    {\r
+        return this._name;\r
+    } //-- java.lang.String getName() \r
+\r
+    /**\r
+     * Returns the value of field 'sequence'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'sequence'.\r
+     */\r
+    public java.lang.String getSequence()\r
+    {\r
+        return this._sequence;\r
+    } //-- java.lang.String getSequence() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'description'.\r
+     * \r
+     * @param description the value of field 'description'.\r
+     */\r
+    public void setDescription(java.lang.String description)\r
+    {\r
+        this._description = description;\r
+    } //-- void setDescription(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(java.lang.String id)\r
+    {\r
+        this._id = id;\r
+    } //-- void setId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'name'.\r
+     * \r
+     * @param name the value of field 'name'.\r
+     */\r
+    public void setName(java.lang.String name)\r
+    {\r
+        this._name = name;\r
+    } //-- void setName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'sequence'.\r
+     * \r
+     * @param sequence the value of field 'sequence'.\r
+     */\r
+    public void setSequence(java.lang.String sequence)\r
+    {\r
+        this._sequence = sequence;\r
+    } //-- void setSequence(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'description'.\r
-   *\r
-   * @param description the value of field 'description'.\r
-   */\r
-  public void setDescription(java.lang.String description)\r
-  {\r
-    this._description = description;\r
-  } //-- void setDescription(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(java.lang.String id)\r
-  {\r
-    this._id = id;\r
-  } //-- void setId(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'name'.\r
-   *\r
-   * @param name the value of field 'name'.\r
-   */\r
-  public void setName(java.lang.String name)\r
-  {\r
-    this._name = name;\r
-  } //-- void setName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'sequence'.\r
-   *\r
-   * @param sequence the value of field 'sequence'.\r
-   */\r
-  public void setSequence(java.lang.String sequence)\r
-  {\r
-    this._sequence = sequence;\r
-  } //-- void setSequence(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.SequenceType.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
index 2910786..ef6c636 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,342 +7,315 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class SequenceTypeDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceTypeDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SequenceTypeDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "SequenceType";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _id\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceType target = (SequenceType) object;\r
-        return target.getId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceType target = (SequenceType) object;\r
-          target.setId( (java.lang.String) value);\r
+public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SequenceTypeDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "SequenceType";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _id\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceType target = (SequenceType) object;\r
+                return target.getId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceType target = (SequenceType) object;\r
+                    target.setId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _id\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _description\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceType target = (SequenceType) object;\r
+                return target.getDescription();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceType target = (SequenceType) object;\r
+                    target.setDescription( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _description\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _id\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _description\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_description", "description",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceType target = (SequenceType) object;\r
-        return target.getDescription();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceType target = (SequenceType) object;\r
-          target.setDescription( (java.lang.String) value);\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _sequence\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceType target = (SequenceType) object;\r
+                return target.getSequence();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceType target = (SequenceType) object;\r
+                    target.setSequence( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequence\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _name\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                SequenceType target = (SequenceType) object;\r
+                return target.getName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    SequenceType target = (SequenceType) object;\r
+                    target.setName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _name\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _description\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _sequence\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_sequence", "sequence",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.SequenceTypeDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceType target = (SequenceType) object;\r
-        return target.getSequence();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceType target = (SequenceType) object;\r
-          target.setSequence( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _sequence\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _name\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        SequenceType target = (SequenceType) object;\r
-        return target.getName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          SequenceType target = (SequenceType) object;\r
-          target.setName( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _name\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.SequenceTypeDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.SequenceType.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.SequenceType.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 4f85d33..668ef9d 100755 (executable)
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,246 +7,247 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Setting.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Setting\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _type\r
-   */\r
-  private java.lang.String _type;\r
-\r
-  /**\r
-   * Field _colour\r
-   */\r
-  private int _colour;\r
-\r
-  /**\r
-   * keeps track of state for field: _colour\r
-   */\r
-  private boolean _has_colour;\r
-\r
-  /**\r
-   * Field _display\r
-   */\r
-  private boolean _display;\r
-\r
-  /**\r
-   * keeps track of state for field: _display\r
-   */\r
-  private boolean _has_display;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Setting()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Setting()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteColour\r
-   *\r
-   */\r
-  public void deleteColour()\r
-  {\r
-    this._has_colour = false;\r
-  } //-- void deleteColour()\r
-\r
-  /**\r
-   * Method deleteDisplay\r
-   *\r
-   */\r
-  public void deleteDisplay()\r
-  {\r
-    this._has_display = false;\r
-  } //-- void deleteDisplay()\r
-\r
-  /**\r
-   * Returns the value of field 'colour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'colour'.\r
-   */\r
-  public int getColour()\r
-  {\r
-    return this._colour;\r
-  } //-- int getColour()\r
-\r
-  /**\r
-   * Returns the value of field 'display'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'display'.\r
-   */\r
-  public boolean getDisplay()\r
-  {\r
-    return this._display;\r
-  } //-- boolean getDisplay()\r
-\r
-  /**\r
-   * Returns the value of field 'type'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'type'.\r
-   */\r
-  public java.lang.String getType()\r
-  {\r
-    return this._type;\r
-  } //-- java.lang.String getType()\r
-\r
-  /**\r
-   * Method hasColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasColour()\r
-  {\r
-    return this._has_colour;\r
-  } //-- boolean hasColour()\r
-\r
-  /**\r
-   * Method hasDisplay\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasDisplay()\r
-  {\r
-    return this._has_display;\r
-  } //-- boolean hasDisplay()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class Setting implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _type\r
+     */\r
+    private java.lang.String _type;\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private int _colour;\r
+\r
+    /**\r
+     * keeps track of state for field: _colour\r
+     */\r
+    private boolean _has_colour;\r
+\r
+    /**\r
+     * Field _display\r
+     */\r
+    private boolean _display;\r
+\r
+    /**\r
+     * keeps track of state for field: _display\r
+     */\r
+    private boolean _has_display;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Setting() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.Setting()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteColour\r
+     * \r
+     */\r
+    public void deleteColour()\r
+    {\r
+        this._has_colour= false;\r
+    } //-- void deleteColour() \r
+\r
+    /**\r
+     * Method deleteDisplay\r
+     * \r
+     */\r
+    public void deleteDisplay()\r
+    {\r
+        this._has_display= false;\r
+    } //-- void deleteDisplay() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public int getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- int getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'display'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'display'.\r
+     */\r
+    public boolean getDisplay()\r
+    {\r
+        return this._display;\r
+    } //-- boolean getDisplay() \r
+\r
+    /**\r
+     * Returns the value of field 'type'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'type'.\r
+     */\r
+    public java.lang.String getType()\r
+    {\r
+        return this._type;\r
+    } //-- java.lang.String getType() \r
+\r
+    /**\r
+     * Method hasColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColour()\r
+    {\r
+        return this._has_colour;\r
+    } //-- boolean hasColour() \r
+\r
+    /**\r
+     * Method hasDisplay\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasDisplay()\r
+    {\r
+        return this._has_display;\r
+    } //-- boolean hasDisplay() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(int colour)\r
+    {\r
+        this._colour = colour;\r
+        this._has_colour = true;\r
+    } //-- void setColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'display'.\r
+     * \r
+     * @param display the value of field 'display'.\r
+     */\r
+    public void setDisplay(boolean display)\r
+    {\r
+        this._display = display;\r
+        this._has_display = true;\r
+    } //-- void setDisplay(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'type'.\r
+     * \r
+     * @param type the value of field 'type'.\r
+     */\r
+    public void setType(java.lang.String type)\r
+    {\r
+        this._type = type;\r
+    } //-- void setType(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'colour'.\r
-   *\r
-   * @param colour the value of field 'colour'.\r
-   */\r
-  public void setColour(int colour)\r
-  {\r
-    this._colour = colour;\r
-    this._has_colour = true;\r
-  } //-- void setColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'display'.\r
-   *\r
-   * @param display the value of field 'display'.\r
-   */\r
-  public void setDisplay(boolean display)\r
-  {\r
-    this._display = display;\r
-    this._has_display = true;\r
-  } //-- void setDisplay(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'type'.\r
-   *\r
-   * @param type the value of field 'type'.\r
-   */\r
-  public void setType(java.lang.String type)\r
-  {\r
-    this._type = type;\r
-  } //-- void setType(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Setting.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/SettingDescriptor.java b/src/jalview/schemabinding/version2/SettingDescriptor.java
index 9e19f65..6cadc16 100755 (executable)
--- a/src/jalview/schemabinding/version2/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/SettingDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,315 +7,284 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class SettingDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SettingDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public SettingDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "setting";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _type\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Setting target = (Setting) object;\r
-        return target.getType();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Setting target = (Setting) object;\r
-          target.setType( (java.lang.String) value);\r
+public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public SettingDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "setting";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _type\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Setting target = (Setting) object;\r
+                return target.getType();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Setting target = (Setting) object;\r
+                    target.setType( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _type\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Setting target = (Setting) object;\r
+                if(!target.hasColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Setting target = (Setting) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _type\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_colour", "colour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Setting target = (Setting) object;\r
-        if (!target.hasColour())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Setting target = (Setting) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setColour( ( (java.lang.Integer) value).intValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _display\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Setting target = (Setting) object;\r
+                if(!target.hasDisplay())\r
+                    return null;\r
+                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Setting target = (Setting) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setDisplay( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setRequired(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _display\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.SettingDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _display\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_display", "display",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Setting target = (Setting) object;\r
-        if (!target.hasDisplay())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getDisplay() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Setting target = (Setting) object;\r
-          // ignore null values for non optional primitives\r
-          if (value == null)\r
-          {\r
-            return;\r
-          }\r
-\r
-          target.setDisplay( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setRequired(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _display\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.SettingDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Setting.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.Setting.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
new file mode 100644 (file)
index 0000000..be826fc
--- /dev/null
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -0,0 +1,415 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class StructureState.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class StructureState implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * internal content storage\r
+     */\r
+    private java.lang.String _content = "";\r
+\r
+    /**\r
+     * Field _visible\r
+     */\r
+    private boolean _visible;\r
+\r
+    /**\r
+     * keeps track of state for field: _visible\r
+     */\r
+    private boolean _has_visible;\r
+\r
+    /**\r
+     * Field _xpos\r
+     */\r
+    private int _xpos;\r
+\r
+    /**\r
+     * keeps track of state for field: _xpos\r
+     */\r
+    private boolean _has_xpos;\r
+\r
+    /**\r
+     * Field _ypos\r
+     */\r
+    private int _ypos;\r
+\r
+    /**\r
+     * keeps track of state for field: _ypos\r
+     */\r
+    private boolean _has_ypos;\r
+\r
+    /**\r
+     * Field _width\r
+     */\r
+    private int _width;\r
+\r
+    /**\r
+     * keeps track of state for field: _width\r
+     */\r
+    private boolean _has_width;\r
+\r
+    /**\r
+     * Field _height\r
+     */\r
+    private int _height;\r
+\r
+    /**\r
+     * keeps track of state for field: _height\r
+     */\r
+    private boolean _has_height;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public StructureState() {\r
+        super();\r
+        setContent("");\r
+    } //-- jalview.schemabinding.version2.StructureState()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteHeight\r
+     * \r
+     */\r
+    public void deleteHeight()\r
+    {\r
+        this._has_height= false;\r
+    } //-- void deleteHeight() \r
+\r
+    /**\r
+     * Method deleteVisible\r
+     * \r
+     */\r
+    public void deleteVisible()\r
+    {\r
+        this._has_visible= false;\r
+    } //-- void deleteVisible() \r
+\r
+    /**\r
+     * Method deleteWidth\r
+     * \r
+     */\r
+    public void deleteWidth()\r
+    {\r
+        this._has_width= false;\r
+    } //-- void deleteWidth() \r
+\r
+    /**\r
+     * Method deleteXpos\r
+     * \r
+     */\r
+    public void deleteXpos()\r
+    {\r
+        this._has_xpos= false;\r
+    } //-- void deleteXpos() \r
+\r
+    /**\r
+     * Method deleteYpos\r
+     * \r
+     */\r
+    public void deleteYpos()\r
+    {\r
+        this._has_ypos= false;\r
+    } //-- void deleteYpos() \r
+\r
+    /**\r
+     * Returns the value of field 'content'. The field 'content'\r
+     * has the following description: internal content storage\r
+     * \r
+     * @return String\r
+     * @return the value of field 'content'.\r
+     */\r
+    public java.lang.String getContent()\r
+    {\r
+        return this._content;\r
+    } //-- java.lang.String getContent() \r
+\r
+    /**\r
+     * Returns the value of field 'height'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'height'.\r
+     */\r
+    public int getHeight()\r
+    {\r
+        return this._height;\r
+    } //-- int getHeight() \r
+\r
+    /**\r
+     * Returns the value of field 'visible'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'visible'.\r
+     */\r
+    public boolean getVisible()\r
+    {\r
+        return this._visible;\r
+    } //-- boolean getVisible() \r
+\r
+    /**\r
+     * Returns the value of field 'width'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'width'.\r
+     */\r
+    public int getWidth()\r
+    {\r
+        return this._width;\r
+    } //-- int getWidth() \r
+\r
+    /**\r
+     * Returns the value of field 'xpos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'xpos'.\r
+     */\r
+    public int getXpos()\r
+    {\r
+        return this._xpos;\r
+    } //-- int getXpos() \r
+\r
+    /**\r
+     * Returns the value of field 'ypos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'ypos'.\r
+     */\r
+    public int getYpos()\r
+    {\r
+        return this._ypos;\r
+    } //-- int getYpos() \r
+\r
+    /**\r
+     * Method hasHeight\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHeight()\r
+    {\r
+        return this._has_height;\r
+    } //-- boolean hasHeight() \r
+\r
+    /**\r
+     * Method hasVisible\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasVisible()\r
+    {\r
+        return this._has_visible;\r
+    } //-- boolean hasVisible() \r
+\r
+    /**\r
+     * Method hasWidth\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasWidth()\r
+    {\r
+        return this._has_width;\r
+    } //-- boolean hasWidth() \r
+\r
+    /**\r
+     * Method hasXpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasXpos()\r
+    {\r
+        return this._has_xpos;\r
+    } //-- boolean hasXpos() \r
+\r
+    /**\r
+     * Method hasYpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasYpos()\r
+    {\r
+        return this._has_ypos;\r
+    } //-- boolean hasYpos() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'content'. The field 'content' has\r
+     * the following description: internal content storage\r
+     * \r
+     * @param content the value of field 'content'.\r
+     */\r
+    public void setContent(java.lang.String content)\r
+    {\r
+        this._content = content;\r
+    } //-- void setContent(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'height'.\r
+     * \r
+     * @param height the value of field 'height'.\r
+     */\r
+    public void setHeight(int height)\r
+    {\r
+        this._height = height;\r
+        this._has_height = true;\r
+    } //-- void setHeight(int) \r
+\r
+    /**\r
+     * Sets the value of field 'visible'.\r
+     * \r
+     * @param visible the value of field 'visible'.\r
+     */\r
+    public void setVisible(boolean visible)\r
+    {\r
+        this._visible = visible;\r
+        this._has_visible = true;\r
+    } //-- void setVisible(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'width'.\r
+     * \r
+     * @param width the value of field 'width'.\r
+     */\r
+    public void setWidth(int width)\r
+    {\r
+        this._width = width;\r
+        this._has_width = true;\r
+    } //-- void setWidth(int) \r
+\r
+    /**\r
+     * Sets the value of field 'xpos'.\r
+     * \r
+     * @param xpos the value of field 'xpos'.\r
+     */\r
+    public void setXpos(int xpos)\r
+    {\r
+        this._xpos = xpos;\r
+        this._has_xpos = true;\r
+    } //-- void setXpos(int) \r
+\r
+    /**\r
+     * Sets the value of field 'ypos'.\r
+     * \r
+     * @param ypos the value of field 'ypos'.\r
+     */\r
+    public void setYpos(int ypos)\r
+    {\r
+        this._ypos = ypos;\r
+        this._has_ypos = true;\r
+    } //-- void setYpos(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/StructureStateDescriptor.java
new file mode 100644 (file)
index 0000000..998d373
--- /dev/null
+++ b/src/jalview/schemabinding/version2/StructureStateDescriptor.java
@@ -0,0 +1,411 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class StructureStateDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public StructureStateDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "structureState";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- _content\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                return target.getContent();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    target.setContent( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _content\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _visible\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                if(!target.hasVisible())\r
+                    return null;\r
+                return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteVisible();\r
+                        return;\r
+                    }\r
+                    target.setVisible( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _visible\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _xpos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                if(!target.hasXpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getXpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteXpos();\r
+                        return;\r
+                    }\r
+                    target.setXpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _xpos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _ypos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                if(!target.hasYpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getYpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteYpos();\r
+                        return;\r
+                    }\r
+                    target.setYpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _ypos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _width\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                if(!target.hasWidth())\r
+                    return null;\r
+                return new java.lang.Integer(target.getWidth());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteWidth();\r
+                        return;\r
+                    }\r
+                    target.setWidth( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _width\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _height\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                StructureState target = (StructureState) object;\r
+                if(!target.hasHeight())\r
+                    return null;\r
+                return new java.lang.Integer(target.getHeight());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    StructureState target = (StructureState) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteHeight();\r
+                        return;\r
+                    }\r
+                    target.setHeight( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _height\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.StructureStateDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.StructureState.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index ca6d5de..85854c1 100755 (executable)
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,246 +7,247 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class ThresholdLine.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class ThresholdLine\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _label\r
-   */\r
-  private java.lang.String _label;\r
-\r
-  /**\r
-   * Field _value\r
-   */\r
-  private float _value;\r
-\r
-  /**\r
-   * keeps track of state for field: _value\r
-   */\r
-  private boolean _has_value;\r
-\r
-  /**\r
-   * Field _colour\r
-   */\r
-  private int _colour;\r
-\r
-  /**\r
-   * keeps track of state for field: _colour\r
-   */\r
-  private boolean _has_colour;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public ThresholdLine()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.ThresholdLine()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteColour\r
-   *\r
-   */\r
-  public void deleteColour()\r
-  {\r
-    this._has_colour = false;\r
-  } //-- void deleteColour()\r
-\r
-  /**\r
-   * Method deleteValue\r
-   *\r
-   */\r
-  public void deleteValue()\r
-  {\r
-    this._has_value = false;\r
-  } //-- void deleteValue()\r
-\r
-  /**\r
-   * Returns the value of field 'colour'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'colour'.\r
-   */\r
-  public int getColour()\r
-  {\r
-    return this._colour;\r
-  } //-- int getColour()\r
-\r
-  /**\r
-   * Returns the value of field 'label'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'label'.\r
-   */\r
-  public java.lang.String getLabel()\r
-  {\r
-    return this._label;\r
-  } //-- java.lang.String getLabel()\r
-\r
-  /**\r
-   * Returns the value of field 'value'.\r
-   *\r
-   * @return float\r
-   * @return the value of field 'value'.\r
-   */\r
-  public float getValue()\r
-  {\r
-    return this._value;\r
-  } //-- float getValue()\r
-\r
-  /**\r
-   * Method hasColour\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasColour()\r
-  {\r
-    return this._has_colour;\r
-  } //-- boolean hasColour()\r
-\r
-  /**\r
-   * Method hasValue\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasValue()\r
-  {\r
-    return this._has_value;\r
-  } //-- boolean hasValue()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class ThresholdLine implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _label\r
+     */\r
+    private java.lang.String _label;\r
+\r
+    /**\r
+     * Field _value\r
+     */\r
+    private float _value;\r
+\r
+    /**\r
+     * keeps track of state for field: _value\r
+     */\r
+    private boolean _has_value;\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private int _colour;\r
+\r
+    /**\r
+     * keeps track of state for field: _colour\r
+     */\r
+    private boolean _has_colour;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public ThresholdLine() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.ThresholdLine()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteColour\r
+     * \r
+     */\r
+    public void deleteColour()\r
+    {\r
+        this._has_colour= false;\r
+    } //-- void deleteColour() \r
+\r
+    /**\r
+     * Method deleteValue\r
+     * \r
+     */\r
+    public void deleteValue()\r
+    {\r
+        this._has_value= false;\r
+    } //-- void deleteValue() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public int getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- int getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'label'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'label'.\r
+     */\r
+    public java.lang.String getLabel()\r
+    {\r
+        return this._label;\r
+    } //-- java.lang.String getLabel() \r
+\r
+    /**\r
+     * Returns the value of field 'value'.\r
+     * \r
+     * @return float\r
+     * @return the value of field 'value'.\r
+     */\r
+    public float getValue()\r
+    {\r
+        return this._value;\r
+    } //-- float getValue() \r
+\r
+    /**\r
+     * Method hasColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColour()\r
+    {\r
+        return this._has_colour;\r
+    } //-- boolean hasColour() \r
+\r
+    /**\r
+     * Method hasValue\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasValue()\r
+    {\r
+        return this._has_value;\r
+    } //-- boolean hasValue() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(int colour)\r
+    {\r
+        this._colour = colour;\r
+        this._has_colour = true;\r
+    } //-- void setColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'label'.\r
+     * \r
+     * @param label the value of field 'label'.\r
+     */\r
+    public void setLabel(java.lang.String label)\r
+    {\r
+        this._label = label;\r
+    } //-- void setLabel(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'value'.\r
+     * \r
+     * @param value the value of field 'value'.\r
+     */\r
+    public void setValue(float value)\r
+    {\r
+        this._value = value;\r
+        this._has_value = true;\r
+    } //-- void setValue(float) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'colour'.\r
-   *\r
-   * @param colour the value of field 'colour'.\r
-   */\r
-  public void setColour(int colour)\r
-  {\r
-    this._colour = colour;\r
-    this._has_colour = true;\r
-  } //-- void setColour(int)\r
-\r
-  /**\r
-   * Sets the value of field 'label'.\r
-   *\r
-   * @param label the value of field 'label'.\r
-   */\r
-  public void setLabel(java.lang.String label)\r
-  {\r
-    this._label = label;\r
-  } //-- void setLabel(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'value'.\r
-   *\r
-   * @param value the value of field 'value'.\r
-   */\r
-  public void setValue(float value)\r
-  {\r
-    this._value = value;\r
-    this._has_value = true;\r
-  } //-- void setValue(float)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
index a4cf76f..9241003 100755 (executable)
--- a/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,308 +7,282 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class ThresholdLineDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class ThresholdLineDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public ThresholdLineDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "thresholdLine";\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _label\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_label", "label",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        ThresholdLine target = (ThresholdLine) object;\r
-        return target.getLabel();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          ThresholdLine target = (ThresholdLine) object;\r
-          target.setLabel( (java.lang.String) value);\r
+public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public ThresholdLineDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "thresholdLine";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _label\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                ThresholdLine target = (ThresholdLine) object;\r
+                return target.getLabel();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    ThresholdLine target = (ThresholdLine) object;\r
+                    target.setLabel( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _label\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _value\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                ThresholdLine target = (ThresholdLine) object;\r
+                if(!target.hasValue())\r
+                    return null;\r
+                return new java.lang.Float(target.getValue());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    ThresholdLine target = (ThresholdLine) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteValue();\r
+                        return;\r
+                    }\r
+                    target.setValue( ((java.lang.Float)value).floatValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _value\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            FloatValidator typeValidator = new FloatValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _label\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _value\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,\r
-        "_value", "value", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        ThresholdLine target = (ThresholdLine) object;\r
-        if (!target.hasValue())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Float(target.getValue());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          ThresholdLine target = (ThresholdLine) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteValue();\r
-            return;\r
-          }\r
-          target.setValue( ( (java.lang.Float) value).floatValue());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _colour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                ThresholdLine target = (ThresholdLine) object;\r
+                if(!target.hasColour())\r
+                    return null;\r
+                return new java.lang.Integer(target.getColour());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    ThresholdLine target = (ThresholdLine) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteColour();\r
+                        return;\r
+                    }\r
+                    target.setColour( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _colour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.ThresholdLineDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _value\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      FloatValidator typeValidator = new FloatValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _colour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_colour", "colour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        ThresholdLine target = (ThresholdLine) object;\r
-        if (!target.hasColour())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getColour());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          ThresholdLine target = (ThresholdLine) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteColour();\r
-            return;\r
-          }\r
-          target.setColour( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _colour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-  } //-- jalview.schemabinding.version2.ThresholdLineDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.ThresholdLine.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.ThresholdLine.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index 3f9098a..96b2e18 100755 (executable)
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,828 +7,829 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Tree.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Tree\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _width\r
-   */\r
-  private int _width;\r
-\r
-  /**\r
-   * keeps track of state for field: _width\r
-   */\r
-  private boolean _has_width;\r
-\r
-  /**\r
-   * Field _height\r
-   */\r
-  private int _height;\r
-\r
-  /**\r
-   * keeps track of state for field: _height\r
-   */\r
-  private boolean _has_height;\r
-\r
-  /**\r
-   * Field _xpos\r
-   */\r
-  private int _xpos;\r
-\r
-  /**\r
-   * keeps track of state for field: _xpos\r
-   */\r
-  private boolean _has_xpos;\r
-\r
-  /**\r
-   * Field _ypos\r
-   */\r
-  private int _ypos;\r
-\r
-  /**\r
-   * keeps track of state for field: _ypos\r
-   */\r
-  private boolean _has_ypos;\r
-\r
-  /**\r
-   * Field _fontName\r
-   */\r
-  private java.lang.String _fontName;\r
-\r
-  /**\r
-   * Field _fontSize\r
-   */\r
-  private int _fontSize;\r
-\r
-  /**\r
-   * keeps track of state for field: _fontSize\r
-   */\r
-  private boolean _has_fontSize;\r
-\r
-  /**\r
-   * Field _fontStyle\r
-   */\r
-  private int _fontStyle;\r
-\r
-  /**\r
-   * keeps track of state for field: _fontStyle\r
-   */\r
-  private boolean _has_fontStyle;\r
-\r
-  /**\r
-   * Field _threshold\r
-   */\r
-  private float _threshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _threshold\r
-   */\r
-  private boolean _has_threshold;\r
-\r
-  /**\r
-   * Field _showBootstrap\r
-   */\r
-  private boolean _showBootstrap;\r
-\r
-  /**\r
-   * keeps track of state for field: _showBootstrap\r
-   */\r
-  private boolean _has_showBootstrap;\r
-\r
-  /**\r
-   * Field _showDistances\r
-   */\r
-  private boolean _showDistances;\r
-\r
-  /**\r
-   * keeps track of state for field: _showDistances\r
-   */\r
-  private boolean _has_showDistances;\r
-\r
-  /**\r
-   * Field _markUnlinked\r
-   */\r
-  private boolean _markUnlinked;\r
-\r
-  /**\r
-   * keeps track of state for field: _markUnlinked\r
-   */\r
-  private boolean _has_markUnlinked;\r
-\r
-  /**\r
-   * Field _fitToWindow\r
-   */\r
-  private boolean _fitToWindow;\r
-\r
-  /**\r
-   * keeps track of state for field: _fitToWindow\r
-   */\r
-  private boolean _has_fitToWindow;\r
-\r
-  /**\r
-   * Field _currentTree\r
-   */\r
-  private boolean _currentTree;\r
-\r
-  /**\r
-   * keeps track of state for field: _currentTree\r
-   */\r
-  private boolean _has_currentTree;\r
-\r
-  /**\r
-   * Field _title\r
-   */\r
-  private java.lang.String _title;\r
-\r
-  /**\r
-   * Field _newick\r
-   */\r
-  private java.lang.String _newick;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Tree()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.Tree()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteCurrentTree\r
-   *\r
-   */\r
-  public void deleteCurrentTree()\r
-  {\r
-    this._has_currentTree = false;\r
-  } //-- void deleteCurrentTree()\r
-\r
-  /**\r
-   * Method deleteFitToWindow\r
-   *\r
-   */\r
-  public void deleteFitToWindow()\r
-  {\r
-    this._has_fitToWindow = false;\r
-  } //-- void deleteFitToWindow()\r
-\r
-  /**\r
-   * Method deleteFontSize\r
-   *\r
-   */\r
-  public void deleteFontSize()\r
-  {\r
-    this._has_fontSize = false;\r
-  } //-- void deleteFontSize()\r
-\r
-  /**\r
-   * Method deleteFontStyle\r
-   *\r
-   */\r
-  public void deleteFontStyle()\r
-  {\r
-    this._has_fontStyle = false;\r
-  } //-- void deleteFontStyle()\r
-\r
-  /**\r
-   * Method deleteHeight\r
-   *\r
-   */\r
-  public void deleteHeight()\r
-  {\r
-    this._has_height = false;\r
-  } //-- void deleteHeight()\r
-\r
-  /**\r
-   * Method deleteMarkUnlinked\r
-   *\r
-   */\r
-  public void deleteMarkUnlinked()\r
-  {\r
-    this._has_markUnlinked = false;\r
-  } //-- void deleteMarkUnlinked()\r
-\r
-  /**\r
-   * Method deleteShowBootstrap\r
-   *\r
-   */\r
-  public void deleteShowBootstrap()\r
-  {\r
-    this._has_showBootstrap = false;\r
-  } //-- void deleteShowBootstrap()\r
-\r
-  /**\r
-   * Method deleteShowDistances\r
-   *\r
-   */\r
-  public void deleteShowDistances()\r
-  {\r
-    this._has_showDistances = false;\r
-  } //-- void deleteShowDistances()\r
-\r
-  /**\r
-   * Method deleteThreshold\r
-   *\r
-   */\r
-  public void deleteThreshold()\r
-  {\r
-    this._has_threshold = false;\r
-  } //-- void deleteThreshold()\r
-\r
-  /**\r
-   * Method deleteWidth\r
-   *\r
-   */\r
-  public void deleteWidth()\r
-  {\r
-    this._has_width = false;\r
-  } //-- void deleteWidth()\r
-\r
-  /**\r
-   * Method deleteXpos\r
-   *\r
-   */\r
-  public void deleteXpos()\r
-  {\r
-    this._has_xpos = false;\r
-  } //-- void deleteXpos()\r
-\r
-  /**\r
-   * Method deleteYpos\r
-   *\r
-   */\r
-  public void deleteYpos()\r
-  {\r
-    this._has_ypos = false;\r
-  } //-- void deleteYpos()\r
-\r
-  /**\r
-   * Returns the value of field 'currentTree'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'currentTree'.\r
-   */\r
-  public boolean getCurrentTree()\r
-  {\r
-    return this._currentTree;\r
-  } //-- boolean getCurrentTree()\r
-\r
-  /**\r
-   * Returns the value of field 'fitToWindow'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'fitToWindow'.\r
-   */\r
-  public boolean getFitToWindow()\r
-  {\r
-    return this._fitToWindow;\r
-  } //-- boolean getFitToWindow()\r
-\r
-  /**\r
-   * Returns the value of field 'fontName'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'fontName'.\r
-   */\r
-  public java.lang.String getFontName()\r
-  {\r
-    return this._fontName;\r
-  } //-- java.lang.String getFontName()\r
-\r
-  /**\r
-   * Returns the value of field 'fontSize'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'fontSize'.\r
-   */\r
-  public int getFontSize()\r
-  {\r
-    return this._fontSize;\r
-  } //-- int getFontSize()\r
-\r
-  /**\r
-   * Returns the value of field 'fontStyle'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'fontStyle'.\r
-   */\r
-  public int getFontStyle()\r
-  {\r
-    return this._fontStyle;\r
-  } //-- int getFontStyle()\r
-\r
-  /**\r
-   * Returns the value of field 'height'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'height'.\r
-   */\r
-  public int getHeight()\r
-  {\r
-    return this._height;\r
-  } //-- int getHeight()\r
-\r
-  /**\r
-   * Returns the value of field 'markUnlinked'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'markUnlinked'.\r
-   */\r
-  public boolean getMarkUnlinked()\r
-  {\r
-    return this._markUnlinked;\r
-  } //-- boolean getMarkUnlinked()\r
-\r
-  /**\r
-   * Returns the value of field 'newick'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'newick'.\r
-   */\r
-  public java.lang.String getNewick()\r
-  {\r
-    return this._newick;\r
-  } //-- java.lang.String getNewick()\r
-\r
-  /**\r
-   * Returns the value of field 'showBootstrap'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showBootstrap'.\r
-   */\r
-  public boolean getShowBootstrap()\r
-  {\r
-    return this._showBootstrap;\r
-  } //-- boolean getShowBootstrap()\r
-\r
-  /**\r
-   * Returns the value of field 'showDistances'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showDistances'.\r
-   */\r
-  public boolean getShowDistances()\r
-  {\r
-    return this._showDistances;\r
-  } //-- boolean getShowDistances()\r
-\r
-  /**\r
-   * Returns the value of field 'threshold'.\r
-   *\r
-   * @return float\r
-   * @return the value of field 'threshold'.\r
-   */\r
-  public float getThreshold()\r
-  {\r
-    return this._threshold;\r
-  } //-- float getThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'title'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'title'.\r
-   */\r
-  public java.lang.String getTitle()\r
-  {\r
-    return this._title;\r
-  } //-- java.lang.String getTitle()\r
-\r
-  /**\r
-   * Returns the value of field 'width'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'width'.\r
-   */\r
-  public int getWidth()\r
-  {\r
-    return this._width;\r
-  } //-- int getWidth()\r
-\r
-  /**\r
-   * Returns the value of field 'xpos'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'xpos'.\r
-   */\r
-  public int getXpos()\r
-  {\r
-    return this._xpos;\r
-  } //-- int getXpos()\r
-\r
-  /**\r
-   * Returns the value of field 'ypos'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'ypos'.\r
-   */\r
-  public int getYpos()\r
-  {\r
-    return this._ypos;\r
-  } //-- int getYpos()\r
-\r
-  /**\r
-   * Method hasCurrentTree\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasCurrentTree()\r
-  {\r
-    return this._has_currentTree;\r
-  } //-- boolean hasCurrentTree()\r
-\r
-  /**\r
-   * Method hasFitToWindow\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasFitToWindow()\r
-  {\r
-    return this._has_fitToWindow;\r
-  } //-- boolean hasFitToWindow()\r
-\r
-  /**\r
-   * Method hasFontSize\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasFontSize()\r
-  {\r
-    return this._has_fontSize;\r
-  } //-- boolean hasFontSize()\r
-\r
-  /**\r
-   * Method hasFontStyle\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasFontStyle()\r
-  {\r
-    return this._has_fontStyle;\r
-  } //-- boolean hasFontStyle()\r
-\r
-  /**\r
-   * Method hasHeight\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasHeight()\r
-  {\r
-    return this._has_height;\r
-  } //-- boolean hasHeight()\r
-\r
-  /**\r
-   * Method hasMarkUnlinked\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasMarkUnlinked()\r
-  {\r
-    return this._has_markUnlinked;\r
-  } //-- boolean hasMarkUnlinked()\r
-\r
-  /**\r
-   * Method hasShowBootstrap\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowBootstrap()\r
-  {\r
-    return this._has_showBootstrap;\r
-  } //-- boolean hasShowBootstrap()\r
-\r
-  /**\r
-   * Method hasShowDistances\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowDistances()\r
-  {\r
-    return this._has_showDistances;\r
-  } //-- boolean hasShowDistances()\r
-\r
-  /**\r
-   * Method hasThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasThreshold()\r
-  {\r
-    return this._has_threshold;\r
-  } //-- boolean hasThreshold()\r
-\r
-  /**\r
-   * Method hasWidth\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasWidth()\r
-  {\r
-    return this._has_width;\r
-  } //-- boolean hasWidth()\r
-\r
-  /**\r
-   * Method hasXpos\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasXpos()\r
-  {\r
-    return this._has_xpos;\r
-  } //-- boolean hasXpos()\r
-\r
-  /**\r
-   * Method hasYpos\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasYpos()\r
-  {\r
-    return this._has_ypos;\r
-  } //-- boolean hasYpos()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'currentTree'.\r
-   *\r
-   * @param currentTree the value of field 'currentTree'.\r
-   */\r
-  public void setCurrentTree(boolean currentTree)\r
-  {\r
-    this._currentTree = currentTree;\r
-    this._has_currentTree = true;\r
-  } //-- void setCurrentTree(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'fitToWindow'.\r
-   *\r
-   * @param fitToWindow the value of field 'fitToWindow'.\r
-   */\r
-  public void setFitToWindow(boolean fitToWindow)\r
-  {\r
-    this._fitToWindow = fitToWindow;\r
-    this._has_fitToWindow = true;\r
-  } //-- void setFitToWindow(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'fontName'.\r
-   *\r
-   * @param fontName the value of field 'fontName'.\r
-   */\r
-  public void setFontName(java.lang.String fontName)\r
-  {\r
-    this._fontName = fontName;\r
-  } //-- void setFontName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'fontSize'.\r
-   *\r
-   * @param fontSize the value of field 'fontSize'.\r
-   */\r
-  public void setFontSize(int fontSize)\r
-  {\r
-    this._fontSize = fontSize;\r
-    this._has_fontSize = true;\r
-  } //-- void setFontSize(int)\r
-\r
-  /**\r
-   * Sets the value of field 'fontStyle'.\r
-   *\r
-   * @param fontStyle the value of field 'fontStyle'.\r
-   */\r
-  public void setFontStyle(int fontStyle)\r
-  {\r
-    this._fontStyle = fontStyle;\r
-    this._has_fontStyle = true;\r
-  } //-- void setFontStyle(int)\r
-\r
-  /**\r
-   * Sets the value of field 'height'.\r
-   *\r
-   * @param height the value of field 'height'.\r
-   */\r
-  public void setHeight(int height)\r
-  {\r
-    this._height = height;\r
-    this._has_height = true;\r
-  } //-- void setHeight(int)\r
-\r
-  /**\r
-   * Sets the value of field 'markUnlinked'.\r
-   *\r
-   * @param markUnlinked the value of field 'markUnlinked'.\r
-   */\r
-  public void setMarkUnlinked(boolean markUnlinked)\r
-  {\r
-    this._markUnlinked = markUnlinked;\r
-    this._has_markUnlinked = true;\r
-  } //-- void setMarkUnlinked(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'newick'.\r
-   *\r
-   * @param newick the value of field 'newick'.\r
-   */\r
-  public void setNewick(java.lang.String newick)\r
-  {\r
-    this._newick = newick;\r
-  } //-- void setNewick(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'showBootstrap'.\r
-   *\r
-   * @param showBootstrap the value of field 'showBootstrap'.\r
-   */\r
-  public void setShowBootstrap(boolean showBootstrap)\r
-  {\r
-    this._showBootstrap = showBootstrap;\r
-    this._has_showBootstrap = true;\r
-  } //-- void setShowBootstrap(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showDistances'.\r
-   *\r
-   * @param showDistances the value of field 'showDistances'.\r
-   */\r
-  public void setShowDistances(boolean showDistances)\r
-  {\r
-    this._showDistances = showDistances;\r
-    this._has_showDistances = true;\r
-  } //-- void setShowDistances(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'threshold'.\r
-   *\r
-   * @param threshold the value of field 'threshold'.\r
-   */\r
-  public void setThreshold(float threshold)\r
-  {\r
-    this._threshold = threshold;\r
-    this._has_threshold = true;\r
-  } //-- void setThreshold(float)\r
-\r
-  /**\r
-   * Sets the value of field 'title'.\r
-   *\r
-   * @param title the value of field 'title'.\r
-   */\r
-  public void setTitle(java.lang.String title)\r
-  {\r
-    this._title = title;\r
-  } //-- void setTitle(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'width'.\r
-   *\r
-   * @param width the value of field 'width'.\r
-   */\r
-  public void setWidth(int width)\r
-  {\r
-    this._width = width;\r
-    this._has_width = true;\r
-  } //-- void setWidth(int)\r
-\r
-  /**\r
-   * Sets the value of field 'xpos'.\r
-   *\r
-   * @param xpos the value of field 'xpos'.\r
-   */\r
-  public void setXpos(int xpos)\r
-  {\r
-    this._xpos = xpos;\r
-    this._has_xpos = true;\r
-  } //-- void setXpos(int)\r
-\r
-  /**\r
-   * Sets the value of field 'ypos'.\r
-   *\r
-   * @param ypos the value of field 'ypos'.\r
-   */\r
-  public void setYpos(int ypos)\r
-  {\r
-    this._ypos = ypos;\r
-    this._has_ypos = true;\r
-  } //-- void setYpos(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.\r
-        schemabinding.version2.Tree.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class Tree implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _width\r
+     */\r
+    private int _width;\r
+\r
+    /**\r
+     * keeps track of state for field: _width\r
+     */\r
+    private boolean _has_width;\r
+\r
+    /**\r
+     * Field _height\r
+     */\r
+    private int _height;\r
+\r
+    /**\r
+     * keeps track of state for field: _height\r
+     */\r
+    private boolean _has_height;\r
+\r
+    /**\r
+     * Field _xpos\r
+     */\r
+    private int _xpos;\r
+\r
+    /**\r
+     * keeps track of state for field: _xpos\r
+     */\r
+    private boolean _has_xpos;\r
+\r
+    /**\r
+     * Field _ypos\r
+     */\r
+    private int _ypos;\r
+\r
+    /**\r
+     * keeps track of state for field: _ypos\r
+     */\r
+    private boolean _has_ypos;\r
+\r
+    /**\r
+     * Field _fontName\r
+     */\r
+    private java.lang.String _fontName;\r
+\r
+    /**\r
+     * Field _fontSize\r
+     */\r
+    private int _fontSize;\r
+\r
+    /**\r
+     * keeps track of state for field: _fontSize\r
+     */\r
+    private boolean _has_fontSize;\r
+\r
+    /**\r
+     * Field _fontStyle\r
+     */\r
+    private int _fontStyle;\r
+\r
+    /**\r
+     * keeps track of state for field: _fontStyle\r
+     */\r
+    private boolean _has_fontStyle;\r
+\r
+    /**\r
+     * Field _threshold\r
+     */\r
+    private float _threshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _threshold\r
+     */\r
+    private boolean _has_threshold;\r
+\r
+    /**\r
+     * Field _showBootstrap\r
+     */\r
+    private boolean _showBootstrap;\r
+\r
+    /**\r
+     * keeps track of state for field: _showBootstrap\r
+     */\r
+    private boolean _has_showBootstrap;\r
+\r
+    /**\r
+     * Field _showDistances\r
+     */\r
+    private boolean _showDistances;\r
+\r
+    /**\r
+     * keeps track of state for field: _showDistances\r
+     */\r
+    private boolean _has_showDistances;\r
+\r
+    /**\r
+     * Field _markUnlinked\r
+     */\r
+    private boolean _markUnlinked;\r
+\r
+    /**\r
+     * keeps track of state for field: _markUnlinked\r
+     */\r
+    private boolean _has_markUnlinked;\r
+\r
+    /**\r
+     * Field _fitToWindow\r
+     */\r
+    private boolean _fitToWindow;\r
+\r
+    /**\r
+     * keeps track of state for field: _fitToWindow\r
+     */\r
+    private boolean _has_fitToWindow;\r
+\r
+    /**\r
+     * Field _currentTree\r
+     */\r
+    private boolean _currentTree;\r
+\r
+    /**\r
+     * keeps track of state for field: _currentTree\r
+     */\r
+    private boolean _has_currentTree;\r
+\r
+    /**\r
+     * Field _title\r
+     */\r
+    private java.lang.String _title;\r
+\r
+    /**\r
+     * Field _newick\r
+     */\r
+    private java.lang.String _newick;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Tree() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.Tree()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteCurrentTree\r
+     * \r
+     */\r
+    public void deleteCurrentTree()\r
+    {\r
+        this._has_currentTree= false;\r
+    } //-- void deleteCurrentTree() \r
+\r
+    /**\r
+     * Method deleteFitToWindow\r
+     * \r
+     */\r
+    public void deleteFitToWindow()\r
+    {\r
+        this._has_fitToWindow= false;\r
+    } //-- void deleteFitToWindow() \r
+\r
+    /**\r
+     * Method deleteFontSize\r
+     * \r
+     */\r
+    public void deleteFontSize()\r
+    {\r
+        this._has_fontSize= false;\r
+    } //-- void deleteFontSize() \r
+\r
+    /**\r
+     * Method deleteFontStyle\r
+     * \r
+     */\r
+    public void deleteFontStyle()\r
+    {\r
+        this._has_fontStyle= false;\r
+    } //-- void deleteFontStyle() \r
+\r
+    /**\r
+     * Method deleteHeight\r
+     * \r
+     */\r
+    public void deleteHeight()\r
+    {\r
+        this._has_height= false;\r
+    } //-- void deleteHeight() \r
+\r
+    /**\r
+     * Method deleteMarkUnlinked\r
+     * \r
+     */\r
+    public void deleteMarkUnlinked()\r
+    {\r
+        this._has_markUnlinked= false;\r
+    } //-- void deleteMarkUnlinked() \r
+\r
+    /**\r
+     * Method deleteShowBootstrap\r
+     * \r
+     */\r
+    public void deleteShowBootstrap()\r
+    {\r
+        this._has_showBootstrap= false;\r
+    } //-- void deleteShowBootstrap() \r
+\r
+    /**\r
+     * Method deleteShowDistances\r
+     * \r
+     */\r
+    public void deleteShowDistances()\r
+    {\r
+        this._has_showDistances= false;\r
+    } //-- void deleteShowDistances() \r
+\r
+    /**\r
+     * Method deleteThreshold\r
+     * \r
+     */\r
+    public void deleteThreshold()\r
+    {\r
+        this._has_threshold= false;\r
+    } //-- void deleteThreshold() \r
+\r
+    /**\r
+     * Method deleteWidth\r
+     * \r
+     */\r
+    public void deleteWidth()\r
+    {\r
+        this._has_width= false;\r
+    } //-- void deleteWidth() \r
+\r
+    /**\r
+     * Method deleteXpos\r
+     * \r
+     */\r
+    public void deleteXpos()\r
+    {\r
+        this._has_xpos= false;\r
+    } //-- void deleteXpos() \r
+\r
+    /**\r
+     * Method deleteYpos\r
+     * \r
+     */\r
+    public void deleteYpos()\r
+    {\r
+        this._has_ypos= false;\r
+    } //-- void deleteYpos() \r
+\r
+    /**\r
+     * Returns the value of field 'currentTree'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'currentTree'.\r
+     */\r
+    public boolean getCurrentTree()\r
+    {\r
+        return this._currentTree;\r
+    } //-- boolean getCurrentTree() \r
+\r
+    /**\r
+     * Returns the value of field 'fitToWindow'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'fitToWindow'.\r
+     */\r
+    public boolean getFitToWindow()\r
+    {\r
+        return this._fitToWindow;\r
+    } //-- boolean getFitToWindow() \r
+\r
+    /**\r
+     * Returns the value of field 'fontName'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'fontName'.\r
+     */\r
+    public java.lang.String getFontName()\r
+    {\r
+        return this._fontName;\r
+    } //-- java.lang.String getFontName() \r
+\r
+    /**\r
+     * Returns the value of field 'fontSize'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'fontSize'.\r
+     */\r
+    public int getFontSize()\r
+    {\r
+        return this._fontSize;\r
+    } //-- int getFontSize() \r
+\r
+    /**\r
+     * Returns the value of field 'fontStyle'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'fontStyle'.\r
+     */\r
+    public int getFontStyle()\r
+    {\r
+        return this._fontStyle;\r
+    } //-- int getFontStyle() \r
+\r
+    /**\r
+     * Returns the value of field 'height'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'height'.\r
+     */\r
+    public int getHeight()\r
+    {\r
+        return this._height;\r
+    } //-- int getHeight() \r
+\r
+    /**\r
+     * Returns the value of field 'markUnlinked'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'markUnlinked'.\r
+     */\r
+    public boolean getMarkUnlinked()\r
+    {\r
+        return this._markUnlinked;\r
+    } //-- boolean getMarkUnlinked() \r
+\r
+    /**\r
+     * Returns the value of field 'newick'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'newick'.\r
+     */\r
+    public java.lang.String getNewick()\r
+    {\r
+        return this._newick;\r
+    } //-- java.lang.String getNewick() \r
+\r
+    /**\r
+     * Returns the value of field 'showBootstrap'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showBootstrap'.\r
+     */\r
+    public boolean getShowBootstrap()\r
+    {\r
+        return this._showBootstrap;\r
+    } //-- boolean getShowBootstrap() \r
+\r
+    /**\r
+     * Returns the value of field 'showDistances'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showDistances'.\r
+     */\r
+    public boolean getShowDistances()\r
+    {\r
+        return this._showDistances;\r
+    } //-- boolean getShowDistances() \r
+\r
+    /**\r
+     * Returns the value of field 'threshold'.\r
+     * \r
+     * @return float\r
+     * @return the value of field 'threshold'.\r
+     */\r
+    public float getThreshold()\r
+    {\r
+        return this._threshold;\r
+    } //-- float getThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'title'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'title'.\r
+     */\r
+    public java.lang.String getTitle()\r
+    {\r
+        return this._title;\r
+    } //-- java.lang.String getTitle() \r
+\r
+    /**\r
+     * Returns the value of field 'width'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'width'.\r
+     */\r
+    public int getWidth()\r
+    {\r
+        return this._width;\r
+    } //-- int getWidth() \r
+\r
+    /**\r
+     * Returns the value of field 'xpos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'xpos'.\r
+     */\r
+    public int getXpos()\r
+    {\r
+        return this._xpos;\r
+    } //-- int getXpos() \r
+\r
+    /**\r
+     * Returns the value of field 'ypos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'ypos'.\r
+     */\r
+    public int getYpos()\r
+    {\r
+        return this._ypos;\r
+    } //-- int getYpos() \r
+\r
+    /**\r
+     * Method hasCurrentTree\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasCurrentTree()\r
+    {\r
+        return this._has_currentTree;\r
+    } //-- boolean hasCurrentTree() \r
+\r
+    /**\r
+     * Method hasFitToWindow\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasFitToWindow()\r
+    {\r
+        return this._has_fitToWindow;\r
+    } //-- boolean hasFitToWindow() \r
+\r
+    /**\r
+     * Method hasFontSize\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasFontSize()\r
+    {\r
+        return this._has_fontSize;\r
+    } //-- boolean hasFontSize() \r
+\r
+    /**\r
+     * Method hasFontStyle\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasFontStyle()\r
+    {\r
+        return this._has_fontStyle;\r
+    } //-- boolean hasFontStyle() \r
+\r
+    /**\r
+     * Method hasHeight\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHeight()\r
+    {\r
+        return this._has_height;\r
+    } //-- boolean hasHeight() \r
+\r
+    /**\r
+     * Method hasMarkUnlinked\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasMarkUnlinked()\r
+    {\r
+        return this._has_markUnlinked;\r
+    } //-- boolean hasMarkUnlinked() \r
+\r
+    /**\r
+     * Method hasShowBootstrap\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowBootstrap()\r
+    {\r
+        return this._has_showBootstrap;\r
+    } //-- boolean hasShowBootstrap() \r
+\r
+    /**\r
+     * Method hasShowDistances\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowDistances()\r
+    {\r
+        return this._has_showDistances;\r
+    } //-- boolean hasShowDistances() \r
+\r
+    /**\r
+     * Method hasThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasThreshold()\r
+    {\r
+        return this._has_threshold;\r
+    } //-- boolean hasThreshold() \r
+\r
+    /**\r
+     * Method hasWidth\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasWidth()\r
+    {\r
+        return this._has_width;\r
+    } //-- boolean hasWidth() \r
+\r
+    /**\r
+     * Method hasXpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasXpos()\r
+    {\r
+        return this._has_xpos;\r
+    } //-- boolean hasXpos() \r
+\r
+    /**\r
+     * Method hasYpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasYpos()\r
+    {\r
+        return this._has_ypos;\r
+    } //-- boolean hasYpos() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'currentTree'.\r
+     * \r
+     * @param currentTree the value of field 'currentTree'.\r
+     */\r
+    public void setCurrentTree(boolean currentTree)\r
+    {\r
+        this._currentTree = currentTree;\r
+        this._has_currentTree = true;\r
+    } //-- void setCurrentTree(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'fitToWindow'.\r
+     * \r
+     * @param fitToWindow the value of field 'fitToWindow'.\r
+     */\r
+    public void setFitToWindow(boolean fitToWindow)\r
+    {\r
+        this._fitToWindow = fitToWindow;\r
+        this._has_fitToWindow = true;\r
+    } //-- void setFitToWindow(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'fontName'.\r
+     * \r
+     * @param fontName the value of field 'fontName'.\r
+     */\r
+    public void setFontName(java.lang.String fontName)\r
+    {\r
+        this._fontName = fontName;\r
+    } //-- void setFontName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'fontSize'.\r
+     * \r
+     * @param fontSize the value of field 'fontSize'.\r
+     */\r
+    public void setFontSize(int fontSize)\r
+    {\r
+        this._fontSize = fontSize;\r
+        this._has_fontSize = true;\r
+    } //-- void setFontSize(int) \r
+\r
+    /**\r
+     * Sets the value of field 'fontStyle'.\r
+     * \r
+     * @param fontStyle the value of field 'fontStyle'.\r
+     */\r
+    public void setFontStyle(int fontStyle)\r
+    {\r
+        this._fontStyle = fontStyle;\r
+        this._has_fontStyle = true;\r
+    } //-- void setFontStyle(int) \r
+\r
+    /**\r
+     * Sets the value of field 'height'.\r
+     * \r
+     * @param height the value of field 'height'.\r
+     */\r
+    public void setHeight(int height)\r
+    {\r
+        this._height = height;\r
+        this._has_height = true;\r
+    } //-- void setHeight(int) \r
+\r
+    /**\r
+     * Sets the value of field 'markUnlinked'.\r
+     * \r
+     * @param markUnlinked the value of field 'markUnlinked'.\r
+     */\r
+    public void setMarkUnlinked(boolean markUnlinked)\r
+    {\r
+        this._markUnlinked = markUnlinked;\r
+        this._has_markUnlinked = true;\r
+    } //-- void setMarkUnlinked(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'newick'.\r
+     * \r
+     * @param newick the value of field 'newick'.\r
+     */\r
+    public void setNewick(java.lang.String newick)\r
+    {\r
+        this._newick = newick;\r
+    } //-- void setNewick(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'showBootstrap'.\r
+     * \r
+     * @param showBootstrap the value of field 'showBootstrap'.\r
+     */\r
+    public void setShowBootstrap(boolean showBootstrap)\r
+    {\r
+        this._showBootstrap = showBootstrap;\r
+        this._has_showBootstrap = true;\r
+    } //-- void setShowBootstrap(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showDistances'.\r
+     * \r
+     * @param showDistances the value of field 'showDistances'.\r
+     */\r
+    public void setShowDistances(boolean showDistances)\r
+    {\r
+        this._showDistances = showDistances;\r
+        this._has_showDistances = true;\r
+    } //-- void setShowDistances(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'threshold'.\r
+     * \r
+     * @param threshold the value of field 'threshold'.\r
+     */\r
+    public void setThreshold(float threshold)\r
+    {\r
+        this._threshold = threshold;\r
+        this._has_threshold = true;\r
+    } //-- void setThreshold(float) \r
+\r
+    /**\r
+     * Sets the value of field 'title'.\r
+     * \r
+     * @param title the value of field 'title'.\r
+     */\r
+    public void setTitle(java.lang.String title)\r
+    {\r
+        this._title = title;\r
+    } //-- void setTitle(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'width'.\r
+     * \r
+     * @param width the value of field 'width'.\r
+     */\r
+    public void setWidth(int width)\r
+    {\r
+        this._width = width;\r
+        this._has_width = true;\r
+    } //-- void setWidth(int) \r
+\r
+    /**\r
+     * Sets the value of field 'xpos'.\r
+     * \r
+     * @param xpos the value of field 'xpos'.\r
+     */\r
+    public void setXpos(int xpos)\r
+    {\r
+        this._xpos = xpos;\r
+        this._has_xpos = true;\r
+    } //-- void setXpos(int) \r
+\r
+    /**\r
+     * Sets the value of field 'ypos'.\r
+     * \r
+     * @param ypos the value of field 'ypos'.\r
+     */\r
+    public void setYpos(int ypos)\r
+    {\r
+        this._ypos = ypos;\r
+        this._has_ypos = true;\r
+    } //-- void setYpos(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/TreeDescriptor.java b/src/jalview/schemabinding/version2/TreeDescriptor.java
index 1b7065e..5232c12 100755 (executable)
--- a/src/jalview/schemabinding/version2/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/TreeDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,925 +7,771 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class TreeDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class TreeDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public TreeDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "tree";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _width\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_width", "width",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasWidth())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getWidth());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteWidth();\r
-            return;\r
-          }\r
-          target.setWidth( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _width\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _height\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_height", "height",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public TreeDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "tree";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _width\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasWidth())\r
+                    return null;\r
+                return new java.lang.Integer(target.getWidth());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteWidth();\r
+                        return;\r
+                    }\r
+                    target.setWidth( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _width\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _height\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasHeight())\r
+                    return null;\r
+                return new java.lang.Integer(target.getHeight());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteHeight();\r
+                        return;\r
+                    }\r
+                    target.setHeight( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _height\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _xpos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasXpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getXpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteXpos();\r
+                        return;\r
+                    }\r
+                    target.setXpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _xpos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _ypos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasYpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getYpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteYpos();\r
+                        return;\r
+                    }\r
+                    target.setYpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _ypos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontName\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                return target.getFontName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    target.setFontName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontName\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontSize\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasFontSize())\r
+                    return null;\r
+                return new java.lang.Integer(target.getFontSize());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteFontSize();\r
+                        return;\r
+                    }\r
+                    target.setFontSize( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontSize\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontStyle\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasFontStyle())\r
+                    return null;\r
+                return new java.lang.Integer(target.getFontStyle());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteFontStyle();\r
+                        return;\r
+                    }\r
+                    target.setFontStyle( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontStyle\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _threshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasThreshold())\r
+                    return null;\r
+                return new java.lang.Float(target.getThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteThreshold();\r
+                        return;\r
+                    }\r
+                    target.setThreshold( ((java.lang.Float)value).floatValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _threshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            FloatValidator typeValidator = new FloatValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showBootstrap\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasShowBootstrap())\r
+                    return null;\r
+                return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowBootstrap();\r
+                        return;\r
+                    }\r
+                    target.setShowBootstrap( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showBootstrap\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showDistances\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasShowDistances())\r
+                    return null;\r
+                return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowDistances();\r
+                        return;\r
+                    }\r
+                    target.setShowDistances( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showDistances\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _markUnlinked\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasMarkUnlinked())\r
+                    return null;\r
+                return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteMarkUnlinked();\r
+                        return;\r
+                    }\r
+                    target.setMarkUnlinked( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _markUnlinked\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fitToWindow\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasFitToWindow())\r
+                    return null;\r
+                return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteFitToWindow();\r
+                        return;\r
+                    }\r
+                    target.setFitToWindow( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fitToWindow\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _currentTree\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                if(!target.hasCurrentTree())\r
+                    return null;\r
+                return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteCurrentTree();\r
+                        return;\r
+                    }\r
+                    target.setCurrentTree( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _currentTree\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _title\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                return target.getTitle();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    target.setTitle( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _title\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _newick\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Tree target = (Tree) object;\r
+                return target.getNewick();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Tree target = (Tree) object;\r
+                    target.setNewick( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _newick\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.TreeDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasHeight())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getHeight());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteHeight();\r
-            return;\r
-          }\r
-          target.setHeight( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _height\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _xpos\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasXpos())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getXpos());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteXpos();\r
-            return;\r
-          }\r
-          target.setXpos( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _xpos\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _ypos\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasYpos())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getYpos());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteYpos();\r
-            return;\r
-          }\r
-          target.setYpos( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _ypos\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontName\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_fontName", "fontName",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        return target.getFontName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          target.setFontName( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontName\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontSize\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_fontSize", "fontSize",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.Tree.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasFontSize())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getFontSize());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteFontSize();\r
-            return;\r
-          }\r
-          target.setFontSize( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontSize\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontStyle\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_fontStyle", "fontStyle",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasFontStyle())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getFontStyle());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteFontStyle();\r
-            return;\r
-          }\r
-          target.setFontStyle( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontStyle\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _threshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,\r
-        "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Float(target.getThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteThreshold();\r
-            return;\r
-          }\r
-          target.setThreshold( ( (java.lang.Float) value).floatValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _threshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      FloatValidator typeValidator = new FloatValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showBootstrap\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showBootstrap", "showBootstrap",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasShowBootstrap())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowBootstrap() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowBootstrap();\r
-            return;\r
-          }\r
-          target.setShowBootstrap( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showBootstrap\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showDistances\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showDistances", "showDistances",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasShowDistances())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowDistances() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowDistances();\r
-            return;\r
-          }\r
-          target.setShowDistances( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showDistances\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _markUnlinked\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_markUnlinked", "markUnlinked",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasMarkUnlinked())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteMarkUnlinked();\r
-            return;\r
-          }\r
-          target.setMarkUnlinked( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _markUnlinked\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fitToWindow\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_fitToWindow", "fitToWindow",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasFitToWindow())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getFitToWindow() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteFitToWindow();\r
-            return;\r
-          }\r
-          target.setFitToWindow( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fitToWindow\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _currentTree\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_currentTree", "currentTree",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        if (!target.hasCurrentTree())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getCurrentTree() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteCurrentTree();\r
-            return;\r
-          }\r
-          target.setCurrentTree( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _currentTree\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _title\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        return target.getTitle();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          target.setTitle( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _title\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _newick\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_newick", "newick",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Tree target = (Tree) object;\r
-        return target.getNewick();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Tree target = (Tree) object;\r
-          target.setNewick( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _newick\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.TreeDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Tree.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index d186608..00bc181 100755 (executable)
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,110 +7,112 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class UserColourScheme.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class UserColourScheme\r
-    extends JalviewUserColours implements java.io.Serializable\r
+public class UserColourScheme extends JalviewUserColours \r
+implements java.io.Serializable\r
 {\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
 \r
-  public UserColourScheme()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.UserColourScheme()\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+    public UserColourScheme() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.UserColourScheme()\r
 \r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
 \r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.\r
-        unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
index adcb59b..cf86a11 100755 (executable)
--- a/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,159 +7,160 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class UserColourSchemeDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class UserColourSchemeDescriptor\r
-    extends JalviewUserColoursDescriptor\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public UserColourSchemeDescriptor()\r
-  {\r
-    super();\r
-    setExtendsWithoutFlatten(new JalviewUserColoursDescriptor());\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "UserColourScheme";\r
-  } //-- jalview.schemabinding.version2.UserColourSchemeDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return super.getExtends();\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    if (identity == null)\r
+public class UserColourSchemeDescriptor extends JalviewUserColoursDescriptor {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColourSchemeDescriptor() {\r
+        super();\r
+        setExtendsWithoutFlatten(new JalviewUserColoursDescriptor());\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "UserColourScheme";\r
+    } //-- jalview.schemabinding.version2.UserColourSchemeDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return super.getExtends();\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        if (identity == null)\r
+            return super.getIdentity();\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.UserColourScheme.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      return super.getIdentity();\r
-    }\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.UserColourScheme.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index fe77948..28f2b39 100755 (executable)
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,167 +7,167 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class UserColours.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class UserColours\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private java.lang.String _id;\r
-\r
-  /**\r
-   * Field _userColourScheme\r
-   */\r
-  private jalview.schemabinding.version2.UserColourScheme _userColourScheme;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public UserColours()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.UserColours()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'id'.\r
-   */\r
-  public java.lang.String getId()\r
-  {\r
-    return this._id;\r
-  } //-- java.lang.String getId()\r
-\r
-  /**\r
-   * Returns the value of field 'userColourScheme'.\r
-   *\r
-   * @return UserColourScheme\r
-   * @return the value of field 'userColourScheme'.\r
-   */\r
-  public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()\r
-  {\r
-    return this._userColourScheme;\r
-  } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+public class UserColours implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _id\r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
+     * Field _userColourScheme\r
+     */\r
+    private jalview.schemabinding.version2.UserColourScheme _userColourScheme;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColours() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.UserColours()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'id'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'id'.\r
+     */\r
+    public java.lang.String getId()\r
+    {\r
+        return this._id;\r
+    } //-- java.lang.String getId() \r
+\r
+    /**\r
+     * Returns the value of field 'userColourScheme'.\r
+     * \r
+     * @return UserColourScheme\r
+     * @return the value of field 'userColourScheme'.\r
+     */\r
+    public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()\r
+    {\r
+        return this._userColourScheme;\r
+    } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'id'.\r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(java.lang.String id)\r
+    {\r
+        this._id = id;\r
+    } //-- void setId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'userColourScheme'.\r
+     * \r
+     * @param userColourScheme the value of field 'userColourScheme'\r
+     */\r
+    public void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme userColourScheme)\r
+    {\r
+        this._userColourScheme = userColourScheme;\r
+    } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(java.lang.String id)\r
-  {\r
-    this._id = id;\r
-  } //-- void setId(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'userColourScheme'.\r
-   *\r
-   * @param userColourScheme the value of field 'userColourScheme'\r
-   */\r
-  public void setUserColourScheme(jalview.schemabinding.version2.\r
-                                  UserColourScheme userColourScheme)\r
-  {\r
-    this._userColourScheme = userColourScheme;\r
-  } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.UserColours.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
index 29339a2..6c42d0b 100755 (executable)
--- a/src/jalview/schemabinding/version2/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,252 +7,239 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class UserColoursDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class UserColoursDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public UserColoursDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "UserColours";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _id\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        UserColours target = (UserColours) object;\r
-        return target.getId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          UserColours target = (UserColours) object;\r
-          target.setId( (java.lang.String) value);\r
+public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public UserColoursDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "UserColours";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _id\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                UserColours target = (UserColours) object;\r
+                return target.getId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    UserColours target = (UserColours) object;\r
+                    target.setId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _id\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _userColourScheme\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                UserColours target = (UserColours) object;\r
+                return target.getUserColourScheme();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    UserColours target = (UserColours) object;\r
+                    target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.UserColourScheme();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setRequired(true);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _userColourScheme\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(1);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.UserColoursDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _id\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _userColourScheme\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.UserColourScheme.class, "_userColourScheme",\r
-        "UserColourScheme", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        UserColours target = (UserColours) object;\r
-        return target.getUserColourScheme();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          UserColours target = (UserColours) object;\r
-          target.setUserColourScheme( (jalview.schemabinding.version2.\r
-                                       UserColourScheme) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.UserColourScheme();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setRequired(true);\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _userColourScheme\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(1);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.UserColoursDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.UserColours.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.UserColours.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 8a4803c..03633d6 100755 (executable)
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,435 +7,419 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class VAMSAS.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class VAMSAS\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _treeList\r
-   */\r
-  private java.util.Vector _treeList;\r
-\r
-  /**\r
-   * Field _sequenceSetList\r
-   */\r
-  private java.util.Vector _sequenceSetList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public VAMSAS()\r
-  {\r
-    super();\r
-    _treeList = new Vector();\r
-    _sequenceSetList = new Vector();\r
-  } //-- jalview.schemabinding.version2.VAMSAS()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param vSequenceSet\r
-   */\r
-  public void addSequenceSet(jalview.schemabinding.version2.SequenceSet\r
-                             vSequenceSet)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _sequenceSetList.addElement(vSequenceSet);\r
-  } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet)\r
-\r
-  /**\r
-   * Method addSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSequenceSet\r
-   */\r
-  public void addSequenceSet(int index,\r
-                             jalview.schemabinding.version2.SequenceSet\r
-                             vSequenceSet)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _sequenceSetList.insertElementAt(vSequenceSet, index);\r
-  } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet)\r
-\r
-  /**\r
-   * Method addTree\r
-   *\r
-   *\r
-   *\r
-   * @param vTree\r
-   */\r
-  public void addTree(java.lang.String vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _treeList.addElement(vTree);\r
-  } //-- void addTree(java.lang.String)\r
-\r
-  /**\r
-   * Method addTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vTree\r
-   */\r
-  public void addTree(int index, java.lang.String vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _treeList.insertElementAt(vTree, index);\r
-  } //-- void addTree(int, java.lang.String)\r
-\r
-  /**\r
-   * Method enumerateSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateSequenceSet()\r
-  {\r
-    return _sequenceSetList.elements();\r
-  } //-- java.util.Enumeration enumerateSequenceSet()\r
-\r
-  /**\r
-   * Method enumerateTree\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateTree()\r
-  {\r
-    return _treeList.elements();\r
-  } //-- java.util.Enumeration enumerateTree()\r
-\r
-  /**\r
-   * Method getSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return SequenceSet\r
-   */\r
-  public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _sequenceSetList.size()))\r
+public class VAMSAS implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _treeList\r
+     */\r
+    private java.util.Vector _treeList;\r
+\r
+    /**\r
+     * Field _sequenceSetList\r
+     */\r
+    private java.util.Vector _sequenceSetList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public VAMSAS() {\r
+        super();\r
+        _treeList = new Vector();\r
+        _sequenceSetList = new Vector();\r
+    } //-- jalview.schemabinding.version2.VAMSAS()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param vSequenceSet\r
+     */\r
+    public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _sequenceSetList.addElement(vSequenceSet);\r
+    } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
+\r
+    /**\r
+     * Method addSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSequenceSet\r
+     */\r
+    public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _sequenceSetList.insertElementAt(vSequenceSet, index);\r
+    } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
+\r
+    /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param vTree\r
+     */\r
+    public void addTree(java.lang.String vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.addElement(vTree);\r
+    } //-- void addTree(java.lang.String) \r
+\r
+    /**\r
+     * Method addTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void addTree(int index, java.lang.String vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _treeList.insertElementAt(vTree, index);\r
+    } //-- void addTree(int, java.lang.String) \r
+\r
+    /**\r
+     * Method enumerateSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateSequenceSet()\r
+    {\r
+        return _sequenceSetList.elements();\r
+    } //-- java.util.Enumeration enumerateSequenceSet() \r
+\r
+    /**\r
+     * Method enumerateTree\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateTree()\r
+    {\r
+        return _treeList.elements();\r
+    } //-- java.util.Enumeration enumerateTree() \r
+\r
+    /**\r
+     * Method getSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return SequenceSet\r
+     */\r
+    public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceSetList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) \r
+\r
+    /**\r
+     * Method getSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @return SequenceSet\r
+     */\r
+    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
+    {\r
+        int size = _sequenceSetList.size();\r
+        jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() \r
+\r
+    /**\r
+     * Method getSequenceSetCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSequenceSetCount()\r
+    {\r
+        return _sequenceSetList.size();\r
+    } //-- int getSequenceSetCount() \r
+\r
+    /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return String\r
+     */\r
+    public java.lang.String getTree(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (String)_treeList.elementAt(index);\r
+    } //-- java.lang.String getTree(int) \r
+\r
+    /**\r
+     * Method getTree\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String[] getTree()\r
+    {\r
+        int size = _treeList.size();\r
+        java.lang.String[] mArray = new java.lang.String[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (String)_treeList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- java.lang.String[] getTree() \r
+\r
+    /**\r
+     * Method getTreeCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getTreeCount()\r
+    {\r
+        return _treeList.size();\r
+    } //-- int getTreeCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllSequenceSet\r
+     * \r
+     */\r
+    public void removeAllSequenceSet()\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.\r
-        elementAt(index);\r
-  } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int)\r
-\r
-  /**\r
-   * Method getSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @return SequenceSet\r
-   */\r
-  public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
-  {\r
-    int size = _sequenceSetList.size();\r
-    jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.\r
-        schemabinding.version2.SequenceSet[size];\r
-    for (int index = 0; index < size; index++)\r
+        _sequenceSetList.removeAllElements();\r
+    } //-- void removeAllSequenceSet() \r
+\r
+    /**\r
+     * Method removeAllTree\r
+     * \r
+     */\r
+    public void removeAllTree()\r
     {\r
-      mArray[index] = (jalview.schemabinding.version2.SequenceSet)\r
-          _sequenceSetList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet()\r
-\r
-  /**\r
-   * Method getSequenceSetCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getSequenceSetCount()\r
-  {\r
-    return _sequenceSetList.size();\r
-  } //-- int getSequenceSetCount()\r
-\r
-  /**\r
-   * Method getTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return String\r
-   */\r
-  public java.lang.String getTree(int index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _treeList.size()))\r
+        _treeList.removeAllElements();\r
+    } //-- void removeAllTree() \r
+\r
+    /**\r
+     * Method removeSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return SequenceSet\r
+     */\r
+    public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (String) _treeList.elementAt(index);\r
-  } //-- java.lang.String getTree(int)\r
-\r
-  /**\r
-   * Method getTree\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String[] getTree()\r
-  {\r
-    int size = _treeList.size();\r
-    java.lang.String[] mArray = new java.lang.String[size];\r
-    for (int index = 0; index < size; index++)\r
+        java.lang.Object obj = _sequenceSetList.elementAt(index);\r
+        _sequenceSetList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.SequenceSet) obj;\r
+    } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) \r
+\r
+    /**\r
+     * Method removeTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return String\r
+     */\r
+    public java.lang.String removeTree(int index)\r
     {\r
-      mArray[index] = (String) _treeList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- java.lang.String[] getTree()\r
-\r
-  /**\r
-   * Method getTreeCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getTreeCount()\r
-  {\r
-    return _treeList.size();\r
-  } //-- int getTreeCount()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
+        java.lang.Object obj = _treeList.elementAt(index);\r
+        _treeList.removeElementAt(index);\r
+        return (String)obj;\r
+    } //-- java.lang.String removeTree(int) \r
+\r
+    /**\r
+     * Method setSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSequenceSet\r
+     */\r
+    public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _sequenceSetList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _sequenceSetList.setElementAt(vSequenceSet, index);\r
+    } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) \r
+\r
+    /**\r
+     * Method setSequenceSet\r
+     * \r
+     * \r
+     * \r
+     * @param sequenceSetArray\r
+     */\r
+    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)\r
     {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllSequenceSet\r
-   *\r
-   */\r
-  public void removeAllSequenceSet()\r
-  {\r
-    _sequenceSetList.removeAllElements();\r
-  } //-- void removeAllSequenceSet()\r
-\r
-  /**\r
-   * Method removeAllTree\r
-   *\r
-   */\r
-  public void removeAllTree()\r
-  {\r
-    _treeList.removeAllElements();\r
-  } //-- void removeAllTree()\r
-\r
-  /**\r
-   * Method removeSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return SequenceSet\r
-   */\r
-  public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)\r
-  {\r
-    java.lang.Object obj = _sequenceSetList.elementAt(index);\r
-    _sequenceSetList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.SequenceSet) obj;\r
-  } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int)\r
-\r
-  /**\r
-   * Method removeTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return String\r
-   */\r
-  public java.lang.String removeTree(int index)\r
-  {\r
-    java.lang.Object obj = _treeList.elementAt(index);\r
-    _treeList.removeElementAt(index);\r
-    return (String) obj;\r
-  } //-- java.lang.String removeTree(int)\r
-\r
-  /**\r
-   * Method setSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vSequenceSet\r
-   */\r
-  public void setSequenceSet(int index,\r
-                             jalview.schemabinding.version2.SequenceSet\r
-                             vSequenceSet)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _sequenceSetList.size()))\r
+        //-- copy array\r
+        _sequenceSetList.removeAllElements();\r
+        for (int i = 0; i < sequenceSetArray.length; i++) {\r
+            _sequenceSetList.addElement(sequenceSetArray[i]);\r
+        }\r
+    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) \r
+\r
+    /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vTree\r
+     */\r
+    public void setTree(int index, java.lang.String vTree)\r
+        throws java.lang.IndexOutOfBoundsException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _sequenceSetList.setElementAt(vSequenceSet, index);\r
-  } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet)\r
-\r
-  /**\r
-   * Method setSequenceSet\r
-   *\r
-   *\r
-   *\r
-   * @param sequenceSetArray\r
-   */\r
-  public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[]\r
-                             sequenceSetArray)\r
-  {\r
-    //-- copy array\r
-    _sequenceSetList.removeAllElements();\r
-    for (int i = 0; i < sequenceSetArray.length; i++)\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _treeList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _treeList.setElementAt(vTree, index);\r
+    } //-- void setTree(int, java.lang.String) \r
+\r
+    /**\r
+     * Method setTree\r
+     * \r
+     * \r
+     * \r
+     * @param treeArray\r
+     */\r
+    public void setTree(java.lang.String[] treeArray)\r
     {\r
-      _sequenceSetList.addElement(sequenceSetArray[i]);\r
-    }\r
-  } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet)\r
-\r
-  /**\r
-   * Method setTree\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vTree\r
-   */\r
-  public void setTree(int index, java.lang.String vTree)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _treeList.size()))\r
+        //-- copy array\r
+        _treeList.removeAllElements();\r
+        for (int i = 0; i < treeArray.length; i++) {\r
+            _treeList.addElement(treeArray[i]);\r
+        }\r
+    } //-- void setTree(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _treeList.setElementAt(vTree, index);\r
-  } //-- void setTree(int, java.lang.String)\r
-\r
-  /**\r
-   * Method setTree\r
-   *\r
-   *\r
-   *\r
-   * @param treeArray\r
-   */\r
-  public void setTree(java.lang.String[] treeArray)\r
-  {\r
-    //-- copy array\r
-    _treeList.removeAllElements();\r
-    for (int i = 0; i < treeArray.length; i++)\r
+        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
     {\r
-      _treeList.addElement(treeArray[i]);\r
-    }\r
-  } //-- void setTree(java.lang.String)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.VAMSAS.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
index 89d4157..fad185b 100755 (executable)
--- a/src/jalview/schemabinding/version2/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,255 +7,241 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class VAMSASDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class VAMSASDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public VAMSASDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-    xmlName = "VAMSAS";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- initialize element descriptors\r
-\r
-    //-- _treeList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_treeList", "Tree",\r
-        org.exolab.castor.xml.NodeType.Element);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        VAMSAS target = (VAMSAS) object;\r
-        return target.getTree();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          VAMSAS target = (VAMSAS) object;\r
-          target.addTree( (java.lang.String) value);\r
+public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public VAMSASDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "VAMSAS";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _treeList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                VAMSAS target = (VAMSAS) object;\r
+                return target.getTree();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    VAMSAS target = (VAMSAS) object;\r
+                    target.addTree( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _treeList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
+        desc.setValidator(fieldValidator);\r
+        //-- _sequenceSetList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                VAMSAS target = (VAMSAS) object;\r
+                return target.getSequenceSet();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    VAMSAS target = (VAMSAS) object;\r
+                    target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.SequenceSet();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequenceSetList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
         }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.VAMSASDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _treeList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _sequenceSetList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.SequenceSet.class, "_sequenceSetList",\r
-        "SequenceSet", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        VAMSAS target = (VAMSAS) object;\r
-        return target.getSequenceSet();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          VAMSAS target = (VAMSAS) object;\r
-          target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet)\r
-                                value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.SequenceSet();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _sequenceSetList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.VAMSASDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.VAMSAS.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.VAMSAS.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index abd267f..4617903 100755 (executable)
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,110 +7,112 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class VamsasModel.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class VamsasModel\r
-    extends VAMSAS implements java.io.Serializable\r
+public class VamsasModel extends VAMSAS \r
+implements java.io.Serializable\r
 {\r
 \r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
 \r
-  public VamsasModel()\r
-  {\r
-    super();\r
-  } //-- jalview.schemabinding.version2.VamsasModel()\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
 \r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
+    public VamsasModel() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.VamsasModel()\r
 \r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
 \r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
 \r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
 \r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.VamsasModel.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
index 95adf50..e40d9c8 100755 (executable)
--- a/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,159 +7,160 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class VamsasModelDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class VamsasModelDescriptor\r
-    extends VAMSASDescriptor\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public VamsasModelDescriptor()\r
-  {\r
-    super();\r
-    setExtendsWithoutFlatten(new VAMSASDescriptor());\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "vamsasModel";\r
-  } //-- jalview.schemabinding.version2.VamsasModelDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return super.getExtends();\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    if (identity == null)\r
+public class VamsasModelDescriptor extends VAMSASDescriptor {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public VamsasModelDescriptor() {\r
+        super();\r
+        setExtendsWithoutFlatten(new VAMSASDescriptor());\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "vamsasModel";\r
+    } //-- jalview.schemabinding.version2.VamsasModelDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return super.getExtends();\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        if (identity == null)\r
+            return super.getIdentity();\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.VamsasModel.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      return super.getIdentity();\r
-    }\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.VamsasModel.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 978ab5c..6dfb14f 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,1767 +7,1752 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
 \r
-import org.exolab.castor.xml.*;\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
 \r
 /**\r
  * Class Viewport.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Viewport\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _conservationSelected\r
-   */\r
-  private boolean _conservationSelected;\r
-\r
-  /**\r
-   * keeps track of state for field: _conservationSelected\r
-   */\r
-  private boolean _has_conservationSelected;\r
-\r
-  /**\r
-   * Field _pidSelected\r
-   */\r
-  private boolean _pidSelected;\r
-\r
-  /**\r
-   * keeps track of state for field: _pidSelected\r
-   */\r
-  private boolean _has_pidSelected;\r
-\r
-  /**\r
-   * Field _bgColour\r
-   */\r
-  private java.lang.String _bgColour;\r
-\r
-  /**\r
-   * Field _consThreshold\r
-   */\r
-  private int _consThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _consThreshold\r
-   */\r
-  private boolean _has_consThreshold;\r
-\r
-  /**\r
-   * Field _pidThreshold\r
-   */\r
-  private int _pidThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _pidThreshold\r
-   */\r
-  private boolean _has_pidThreshold;\r
-\r
-  /**\r
-   * Field _title\r
-   */\r
-  private java.lang.String _title;\r
-\r
-  /**\r
-   * Field _showFullId\r
-   */\r
-  private boolean _showFullId;\r
-\r
-  /**\r
-   * keeps track of state for field: _showFullId\r
-   */\r
-  private boolean _has_showFullId;\r
-\r
-  /**\r
-   * Field _rightAlignIds\r
-   */\r
-  private boolean _rightAlignIds;\r
-\r
-  /**\r
-   * keeps track of state for field: _rightAlignIds\r
-   */\r
-  private boolean _has_rightAlignIds;\r
-\r
-  /**\r
-   * Field _showText\r
-   */\r
-  private boolean _showText;\r
-\r
-  /**\r
-   * keeps track of state for field: _showText\r
-   */\r
-  private boolean _has_showText;\r
-\r
-  /**\r
-   * Field _showColourText\r
-   */\r
-  private boolean _showColourText;\r
-\r
-  /**\r
-   * keeps track of state for field: _showColourText\r
-   */\r
-  private boolean _has_showColourText;\r
-\r
-  /**\r
-   * Field _showBoxes\r
-   */\r
-  private boolean _showBoxes;\r
-\r
-  /**\r
-   * keeps track of state for field: _showBoxes\r
-   */\r
-  private boolean _has_showBoxes;\r
-\r
-  /**\r
-   * Field _wrapAlignment\r
-   */\r
-  private boolean _wrapAlignment;\r
-\r
-  /**\r
-   * keeps track of state for field: _wrapAlignment\r
-   */\r
-  private boolean _has_wrapAlignment;\r
-\r
-  /**\r
-   * Field _renderGaps\r
-   */\r
-  private boolean _renderGaps;\r
-\r
-  /**\r
-   * keeps track of state for field: _renderGaps\r
-   */\r
-  private boolean _has_renderGaps;\r
-\r
-  /**\r
-   * Field _showSequenceFeatures\r
-   */\r
-  private boolean _showSequenceFeatures;\r
-\r
-  /**\r
-   * keeps track of state for field: _showSequenceFeatures\r
-   */\r
-  private boolean _has_showSequenceFeatures;\r
-\r
-  /**\r
-   * Field _showAnnotation\r
-   */\r
-  private boolean _showAnnotation;\r
-\r
-  /**\r
-   * keeps track of state for field: _showAnnotation\r
-   */\r
-  private boolean _has_showAnnotation;\r
-\r
-  /**\r
-   * Field _xpos\r
-   */\r
-  private int _xpos;\r
-\r
-  /**\r
-   * keeps track of state for field: _xpos\r
-   */\r
-  private boolean _has_xpos;\r
-\r
-  /**\r
-   * Field _ypos\r
-   */\r
-  private int _ypos;\r
-\r
-  /**\r
-   * keeps track of state for field: _ypos\r
-   */\r
-  private boolean _has_ypos;\r
-\r
-  /**\r
-   * Field _width\r
-   */\r
-  private int _width;\r
-\r
-  /**\r
-   * keeps track of state for field: _width\r
-   */\r
-  private boolean _has_width;\r
-\r
-  /**\r
-   * Field _height\r
-   */\r
-  private int _height;\r
-\r
-  /**\r
-   * keeps track of state for field: _height\r
-   */\r
-  private boolean _has_height;\r
-\r
-  /**\r
-   * Field _startRes\r
-   */\r
-  private int _startRes;\r
-\r
-  /**\r
-   * keeps track of state for field: _startRes\r
-   */\r
-  private boolean _has_startRes;\r
-\r
-  /**\r
-   * Field _startSeq\r
-   */\r
-  private int _startSeq;\r
-\r
-  /**\r
-   * keeps track of state for field: _startSeq\r
-   */\r
-  private boolean _has_startSeq;\r
-\r
-  /**\r
-   * Field _fontName\r
-   */\r
-  private java.lang.String _fontName;\r
-\r
-  /**\r
-   * Field _fontSize\r
-   */\r
-  private int _fontSize;\r
-\r
-  /**\r
-   * keeps track of state for field: _fontSize\r
-   */\r
-  private boolean _has_fontSize;\r
-\r
-  /**\r
-   * Field _fontStyle\r
-   */\r
-  private int _fontStyle;\r
-\r
-  /**\r
-   * keeps track of state for field: _fontStyle\r
-   */\r
-  private boolean _has_fontStyle;\r
-\r
-  /**\r
-   * Field _viewName\r
-   */\r
-  private java.lang.String _viewName;\r
-\r
-  /**\r
-   * Field _sequenceSetId\r
-   */\r
-  private java.lang.String _sequenceSetId;\r
-\r
-  /**\r
-   * Field _gatheredViews\r
-   */\r
-  private boolean _gatheredViews;\r
-\r
-  /**\r
-   * keeps track of state for field: _gatheredViews\r
-   */\r
-  private boolean _has_gatheredViews;\r
-\r
-  /**\r
-   * Field _textCol1\r
-   */\r
-  private int _textCol1;\r
-\r
-  /**\r
-   * keeps track of state for field: _textCol1\r
-   */\r
-  private boolean _has_textCol1;\r
-\r
-  /**\r
-   * Field _textCol2\r
-   */\r
-  private int _textCol2;\r
-\r
-  /**\r
-   * keeps track of state for field: _textCol2\r
-   */\r
-  private boolean _has_textCol2;\r
-\r
-  /**\r
-   * Field _textColThreshold\r
-   */\r
-  private int _textColThreshold;\r
-\r
-  /**\r
-   * keeps track of state for field: _textColThreshold\r
-   */\r
-  private boolean _has_textColThreshold;\r
-\r
-  /**\r
-   * Field _annotationColours\r
-   */\r
-  private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
-\r
-  /**\r
-   * Field _hiddenColumnsList\r
-   */\r
-  private java.util.Vector _hiddenColumnsList;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Viewport()\r
-  {\r
-    super();\r
-    _hiddenColumnsList = new Vector();\r
-  } //-- jalview.schemabinding.version2.Viewport()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method addHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param vHiddenColumns\r
-   */\r
-  public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns\r
-                               vHiddenColumns)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _hiddenColumnsList.addElement(vHiddenColumns);\r
-  } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns)\r
-\r
-  /**\r
-   * Method addHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vHiddenColumns\r
-   */\r
-  public void addHiddenColumns(int index,\r
-                               jalview.schemabinding.version2.HiddenColumns\r
-                               vHiddenColumns)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
-  } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)\r
-\r
-  /**\r
-   * Method deleteConsThreshold\r
-   *\r
-   */\r
-  public void deleteConsThreshold()\r
-  {\r
-    this._has_consThreshold = false;\r
-  } //-- void deleteConsThreshold()\r
-\r
-  /**\r
-   * Method deleteConservationSelected\r
-   *\r
-   */\r
-  public void deleteConservationSelected()\r
-  {\r
-    this._has_conservationSelected = false;\r
-  } //-- void deleteConservationSelected()\r
-\r
-  /**\r
-   * Method deleteFontSize\r
-   *\r
-   */\r
-  public void deleteFontSize()\r
-  {\r
-    this._has_fontSize = false;\r
-  } //-- void deleteFontSize()\r
-\r
-  /**\r
-   * Method deleteFontStyle\r
-   *\r
-   */\r
-  public void deleteFontStyle()\r
-  {\r
-    this._has_fontStyle = false;\r
-  } //-- void deleteFontStyle()\r
-\r
-  /**\r
-   * Method deleteGatheredViews\r
-   *\r
-   */\r
-  public void deleteGatheredViews()\r
-  {\r
-    this._has_gatheredViews = false;\r
-  } //-- void deleteGatheredViews()\r
-\r
-  /**\r
-   * Method deleteHeight\r
-   *\r
-   */\r
-  public void deleteHeight()\r
-  {\r
-    this._has_height = false;\r
-  } //-- void deleteHeight()\r
-\r
-  /**\r
-   * Method deletePidSelected\r
-   *\r
-   */\r
-  public void deletePidSelected()\r
-  {\r
-    this._has_pidSelected = false;\r
-  } //-- void deletePidSelected()\r
-\r
-  /**\r
-   * Method deletePidThreshold\r
-   *\r
-   */\r
-  public void deletePidThreshold()\r
-  {\r
-    this._has_pidThreshold = false;\r
-  } //-- void deletePidThreshold()\r
-\r
-  /**\r
-   * Method deleteRenderGaps\r
-   *\r
-   */\r
-  public void deleteRenderGaps()\r
-  {\r
-    this._has_renderGaps = false;\r
-  } //-- void deleteRenderGaps()\r
-\r
-  /**\r
-   * Method deleteRightAlignIds\r
-   *\r
-   */\r
-  public void deleteRightAlignIds()\r
-  {\r
-    this._has_rightAlignIds = false;\r
-  } //-- void deleteRightAlignIds()\r
-\r
-  /**\r
-   * Method deleteShowAnnotation\r
-   *\r
-   */\r
-  public void deleteShowAnnotation()\r
-  {\r
-    this._has_showAnnotation = false;\r
-  } //-- void deleteShowAnnotation()\r
-\r
-  /**\r
-   * Method deleteShowBoxes\r
-   *\r
-   */\r
-  public void deleteShowBoxes()\r
-  {\r
-    this._has_showBoxes = false;\r
-  } //-- void deleteShowBoxes()\r
-\r
-  /**\r
-   * Method deleteShowColourText\r
-   *\r
-   */\r
-  public void deleteShowColourText()\r
-  {\r
-    this._has_showColourText = false;\r
-  } //-- void deleteShowColourText()\r
-\r
-  /**\r
-   * Method deleteShowFullId\r
-   *\r
-   */\r
-  public void deleteShowFullId()\r
-  {\r
-    this._has_showFullId = false;\r
-  } //-- void deleteShowFullId()\r
-\r
-  /**\r
-   * Method deleteShowSequenceFeatures\r
-   *\r
-   */\r
-  public void deleteShowSequenceFeatures()\r
-  {\r
-    this._has_showSequenceFeatures = false;\r
-  } //-- void deleteShowSequenceFeatures()\r
-\r
-  /**\r
-   * Method deleteShowText\r
-   *\r
-   */\r
-  public void deleteShowText()\r
-  {\r
-    this._has_showText = false;\r
-  } //-- void deleteShowText()\r
-\r
-  /**\r
-   * Method deleteStartRes\r
-   *\r
-   */\r
-  public void deleteStartRes()\r
-  {\r
-    this._has_startRes = false;\r
-  } //-- void deleteStartRes()\r
-\r
-  /**\r
-   * Method deleteStartSeq\r
-   *\r
-   */\r
-  public void deleteStartSeq()\r
-  {\r
-    this._has_startSeq = false;\r
-  } //-- void deleteStartSeq()\r
-\r
-  /**\r
-   * Method deleteTextCol1\r
-   *\r
-   */\r
-  public void deleteTextCol1()\r
-  {\r
-    this._has_textCol1 = false;\r
-  } //-- void deleteTextCol1()\r
-\r
-  /**\r
-   * Method deleteTextCol2\r
-   *\r
-   */\r
-  public void deleteTextCol2()\r
-  {\r
-    this._has_textCol2 = false;\r
-  } //-- void deleteTextCol2()\r
-\r
-  /**\r
-   * Method deleteTextColThreshold\r
-   *\r
-   */\r
-  public void deleteTextColThreshold()\r
-  {\r
-    this._has_textColThreshold = false;\r
-  } //-- void deleteTextColThreshold()\r
-\r
-  /**\r
-   * Method deleteWidth\r
-   *\r
-   */\r
-  public void deleteWidth()\r
-  {\r
-    this._has_width = false;\r
-  } //-- void deleteWidth()\r
-\r
-  /**\r
-   * Method deleteWrapAlignment\r
-   *\r
-   */\r
-  public void deleteWrapAlignment()\r
-  {\r
-    this._has_wrapAlignment = false;\r
-  } //-- void deleteWrapAlignment()\r
-\r
-  /**\r
-   * Method deleteXpos\r
-   *\r
-   */\r
-  public void deleteXpos()\r
-  {\r
-    this._has_xpos = false;\r
-  } //-- void deleteXpos()\r
-\r
-  /**\r
-   * Method deleteYpos\r
-   *\r
-   */\r
-  public void deleteYpos()\r
-  {\r
-    this._has_ypos = false;\r
-  } //-- void deleteYpos()\r
-\r
-  /**\r
-   * Method enumerateHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @return Enumeration\r
-   */\r
-  public java.util.Enumeration enumerateHiddenColumns()\r
-  {\r
-    return _hiddenColumnsList.elements();\r
-  } //-- java.util.Enumeration enumerateHiddenColumns()\r
-\r
-  /**\r
-   * Returns the value of field 'annotationColours'.\r
-   *\r
-   * @return AnnotationColours\r
-   * @return the value of field 'annotationColours'.\r
-   */\r
-  public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
-  {\r
-    return this._annotationColours;\r
-  } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
-\r
-  /**\r
-   * Returns the value of field 'bgColour'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'bgColour'.\r
-   */\r
-  public java.lang.String getBgColour()\r
-  {\r
-    return this._bgColour;\r
-  } //-- java.lang.String getBgColour()\r
-\r
-  /**\r
-   * Returns the value of field 'consThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'consThreshold'.\r
-   */\r
-  public int getConsThreshold()\r
-  {\r
-    return this._consThreshold;\r
-  } //-- int getConsThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'conservationSelected'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'conservationSelected'.\r
-   */\r
-  public boolean getConservationSelected()\r
-  {\r
-    return this._conservationSelected;\r
-  } //-- boolean getConservationSelected()\r
-\r
-  /**\r
-   * Returns the value of field 'fontName'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'fontName'.\r
-   */\r
-  public java.lang.String getFontName()\r
-  {\r
-    return this._fontName;\r
-  } //-- java.lang.String getFontName()\r
-\r
-  /**\r
-   * Returns the value of field 'fontSize'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'fontSize'.\r
-   */\r
-  public int getFontSize()\r
-  {\r
-    return this._fontSize;\r
-  } //-- int getFontSize()\r
-\r
-  /**\r
-   * Returns the value of field 'fontStyle'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'fontStyle'.\r
-   */\r
-  public int getFontStyle()\r
-  {\r
-    return this._fontStyle;\r
-  } //-- int getFontStyle()\r
-\r
-  /**\r
-   * Returns the value of field 'gatheredViews'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'gatheredViews'.\r
-   */\r
-  public boolean getGatheredViews()\r
-  {\r
-    return this._gatheredViews;\r
-  } //-- boolean getGatheredViews()\r
-\r
-  /**\r
-   * Returns the value of field 'height'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'height'.\r
-   */\r
-  public int getHeight()\r
-  {\r
-    return this._height;\r
-  } //-- int getHeight()\r
-\r
-  /**\r
-   * Method getHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return HiddenColumns\r
-   */\r
-  public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int\r
-      index)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _hiddenColumnsList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-\r
-    return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.\r
-        elementAt(index);\r
-  } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int)\r
-\r
-  /**\r
-   * Method getHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @return HiddenColumns\r
-   */\r
-  public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
-  {\r
-    int size = _hiddenColumnsList.size();\r
-    jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.\r
-        schemabinding.version2.HiddenColumns[size];\r
-    for (int index = 0; index < size; index++)\r
-    {\r
-      mArray[index] = (jalview.schemabinding.version2.HiddenColumns)\r
-          _hiddenColumnsList.elementAt(index);\r
-    }\r
-    return mArray;\r
-  } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
-\r
-  /**\r
-   * Method getHiddenColumnsCount\r
-   *\r
-   *\r
-   *\r
-   * @return int\r
-   */\r
-  public int getHiddenColumnsCount()\r
-  {\r
-    return _hiddenColumnsList.size();\r
-  } //-- int getHiddenColumnsCount()\r
-\r
-  /**\r
-   * Returns the value of field 'pidSelected'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'pidSelected'.\r
-   */\r
-  public boolean getPidSelected()\r
-  {\r
-    return this._pidSelected;\r
-  } //-- boolean getPidSelected()\r
-\r
-  /**\r
-   * Returns the value of field 'pidThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'pidThreshold'.\r
-   */\r
-  public int getPidThreshold()\r
-  {\r
-    return this._pidThreshold;\r
-  } //-- int getPidThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'renderGaps'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'renderGaps'.\r
-   */\r
-  public boolean getRenderGaps()\r
-  {\r
-    return this._renderGaps;\r
-  } //-- boolean getRenderGaps()\r
-\r
-  /**\r
-   * Returns the value of field 'rightAlignIds'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'rightAlignIds'.\r
-   */\r
-  public boolean getRightAlignIds()\r
-  {\r
-    return this._rightAlignIds;\r
-  } //-- boolean getRightAlignIds()\r
-\r
-  /**\r
-   * Returns the value of field 'sequenceSetId'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'sequenceSetId'.\r
-   */\r
-  public java.lang.String getSequenceSetId()\r
-  {\r
-    return this._sequenceSetId;\r
-  } //-- java.lang.String getSequenceSetId()\r
-\r
-  /**\r
-   * Returns the value of field 'showAnnotation'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showAnnotation'.\r
-   */\r
-  public boolean getShowAnnotation()\r
-  {\r
-    return this._showAnnotation;\r
-  } //-- boolean getShowAnnotation()\r
-\r
-  /**\r
-   * Returns the value of field 'showBoxes'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showBoxes'.\r
-   */\r
-  public boolean getShowBoxes()\r
-  {\r
-    return this._showBoxes;\r
-  } //-- boolean getShowBoxes()\r
-\r
-  /**\r
-   * Returns the value of field 'showColourText'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showColourText'.\r
-   */\r
-  public boolean getShowColourText()\r
-  {\r
-    return this._showColourText;\r
-  } //-- boolean getShowColourText()\r
-\r
-  /**\r
-   * Returns the value of field 'showFullId'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showFullId'.\r
-   */\r
-  public boolean getShowFullId()\r
-  {\r
-    return this._showFullId;\r
-  } //-- boolean getShowFullId()\r
-\r
-  /**\r
-   * Returns the value of field 'showSequenceFeatures'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showSequenceFeatures'.\r
-   */\r
-  public boolean getShowSequenceFeatures()\r
-  {\r
-    return this._showSequenceFeatures;\r
-  } //-- boolean getShowSequenceFeatures()\r
-\r
-  /**\r
-   * Returns the value of field 'showText'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'showText'.\r
-   */\r
-  public boolean getShowText()\r
-  {\r
-    return this._showText;\r
-  } //-- boolean getShowText()\r
-\r
-  /**\r
-   * Returns the value of field 'startRes'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'startRes'.\r
-   */\r
-  public int getStartRes()\r
-  {\r
-    return this._startRes;\r
-  } //-- int getStartRes()\r
-\r
-  /**\r
-   * Returns the value of field 'startSeq'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'startSeq'.\r
-   */\r
-  public int getStartSeq()\r
-  {\r
-    return this._startSeq;\r
-  } //-- int getStartSeq()\r
-\r
-  /**\r
-   * Returns the value of field 'textCol1'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textCol1'.\r
-   */\r
-  public int getTextCol1()\r
-  {\r
-    return this._textCol1;\r
-  } //-- int getTextCol1()\r
-\r
-  /**\r
-   * Returns the value of field 'textCol2'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textCol2'.\r
-   */\r
-  public int getTextCol2()\r
-  {\r
-    return this._textCol2;\r
-  } //-- int getTextCol2()\r
-\r
-  /**\r
-   * Returns the value of field 'textColThreshold'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'textColThreshold'.\r
-   */\r
-  public int getTextColThreshold()\r
-  {\r
-    return this._textColThreshold;\r
-  } //-- int getTextColThreshold()\r
-\r
-  /**\r
-   * Returns the value of field 'title'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'title'.\r
-   */\r
-  public java.lang.String getTitle()\r
-  {\r
-    return this._title;\r
-  } //-- java.lang.String getTitle()\r
-\r
-  /**\r
-   * Returns the value of field 'viewName'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'viewName'.\r
-   */\r
-  public java.lang.String getViewName()\r
-  {\r
-    return this._viewName;\r
-  } //-- java.lang.String getViewName()\r
-\r
-  /**\r
-   * Returns the value of field 'width'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'width'.\r
-   */\r
-  public int getWidth()\r
-  {\r
-    return this._width;\r
-  } //-- int getWidth()\r
-\r
-  /**\r
-   * Returns the value of field 'wrapAlignment'.\r
-   *\r
-   * @return boolean\r
-   * @return the value of field 'wrapAlignment'.\r
-   */\r
-  public boolean getWrapAlignment()\r
-  {\r
-    return this._wrapAlignment;\r
-  } //-- boolean getWrapAlignment()\r
-\r
-  /**\r
-   * Returns the value of field 'xpos'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'xpos'.\r
-   */\r
-  public int getXpos()\r
-  {\r
-    return this._xpos;\r
-  } //-- int getXpos()\r
-\r
-  /**\r
-   * Returns the value of field 'ypos'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'ypos'.\r
-   */\r
-  public int getYpos()\r
-  {\r
-    return this._ypos;\r
-  } //-- int getYpos()\r
-\r
-  /**\r
-   * Method hasConsThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasConsThreshold()\r
-  {\r
-    return this._has_consThreshold;\r
-  } //-- boolean hasConsThreshold()\r
-\r
-  /**\r
-   * Method hasConservationSelected\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasConservationSelected()\r
-  {\r
-    return this._has_conservationSelected;\r
-  } //-- boolean hasConservationSelected()\r
-\r
-  /**\r
-   * Method hasFontSize\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasFontSize()\r
-  {\r
-    return this._has_fontSize;\r
-  } //-- boolean hasFontSize()\r
-\r
-  /**\r
-   * Method hasFontStyle\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasFontStyle()\r
-  {\r
-    return this._has_fontStyle;\r
-  } //-- boolean hasFontStyle()\r
-\r
-  /**\r
-   * Method hasGatheredViews\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasGatheredViews()\r
-  {\r
-    return this._has_gatheredViews;\r
-  } //-- boolean hasGatheredViews()\r
-\r
-  /**\r
-   * Method hasHeight\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasHeight()\r
-  {\r
-    return this._has_height;\r
-  } //-- boolean hasHeight()\r
-\r
-  /**\r
-   * Method hasPidSelected\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasPidSelected()\r
-  {\r
-    return this._has_pidSelected;\r
-  } //-- boolean hasPidSelected()\r
-\r
-  /**\r
-   * Method hasPidThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasPidThreshold()\r
-  {\r
-    return this._has_pidThreshold;\r
-  } //-- boolean hasPidThreshold()\r
-\r
-  /**\r
-   * Method hasRenderGaps\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasRenderGaps()\r
-  {\r
-    return this._has_renderGaps;\r
-  } //-- boolean hasRenderGaps()\r
-\r
-  /**\r
-   * Method hasRightAlignIds\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasRightAlignIds()\r
-  {\r
-    return this._has_rightAlignIds;\r
-  } //-- boolean hasRightAlignIds()\r
-\r
-  /**\r
-   * Method hasShowAnnotation\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowAnnotation()\r
-  {\r
-    return this._has_showAnnotation;\r
-  } //-- boolean hasShowAnnotation()\r
-\r
-  /**\r
-   * Method hasShowBoxes\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowBoxes()\r
-  {\r
-    return this._has_showBoxes;\r
-  } //-- boolean hasShowBoxes()\r
-\r
-  /**\r
-   * Method hasShowColourText\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowColourText()\r
-  {\r
-    return this._has_showColourText;\r
-  } //-- boolean hasShowColourText()\r
-\r
-  /**\r
-   * Method hasShowFullId\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowFullId()\r
-  {\r
-    return this._has_showFullId;\r
-  } //-- boolean hasShowFullId()\r
-\r
-  /**\r
-   * Method hasShowSequenceFeatures\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowSequenceFeatures()\r
-  {\r
-    return this._has_showSequenceFeatures;\r
-  } //-- boolean hasShowSequenceFeatures()\r
-\r
-  /**\r
-   * Method hasShowText\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasShowText()\r
-  {\r
-    return this._has_showText;\r
-  } //-- boolean hasShowText()\r
-\r
-  /**\r
-   * Method hasStartRes\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasStartRes()\r
-  {\r
-    return this._has_startRes;\r
-  } //-- boolean hasStartRes()\r
-\r
-  /**\r
-   * Method hasStartSeq\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasStartSeq()\r
-  {\r
-    return this._has_startSeq;\r
-  } //-- boolean hasStartSeq()\r
-\r
-  /**\r
-   * Method hasTextCol1\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextCol1()\r
-  {\r
-    return this._has_textCol1;\r
-  } //-- boolean hasTextCol1()\r
-\r
-  /**\r
-   * Method hasTextCol2\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextCol2()\r
-  {\r
-    return this._has_textCol2;\r
-  } //-- boolean hasTextCol2()\r
-\r
-  /**\r
-   * Method hasTextColThreshold\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasTextColThreshold()\r
-  {\r
-    return this._has_textColThreshold;\r
-  } //-- boolean hasTextColThreshold()\r
-\r
-  /**\r
-   * Method hasWidth\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasWidth()\r
-  {\r
-    return this._has_width;\r
-  } //-- boolean hasWidth()\r
-\r
-  /**\r
-   * Method hasWrapAlignment\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasWrapAlignment()\r
-  {\r
-    return this._has_wrapAlignment;\r
-  } //-- boolean hasWrapAlignment()\r
-\r
-  /**\r
-   * Method hasXpos\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasXpos()\r
-  {\r
-    return this._has_xpos;\r
-  } //-- boolean hasXpos()\r
-\r
-  /**\r
-   * Method hasYpos\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasYpos()\r
-  {\r
-    return this._has_ypos;\r
-  } //-- boolean hasYpos()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Method removeAllHiddenColumns\r
-   *\r
-   */\r
-  public void removeAllHiddenColumns()\r
-  {\r
-    _hiddenColumnsList.removeAllElements();\r
-  } //-- void removeAllHiddenColumns()\r
-\r
-  /**\r
-   * Method removeHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @return HiddenColumns\r
-   */\r
-  public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int\r
-      index)\r
-  {\r
-    java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
-    _hiddenColumnsList.removeElementAt(index);\r
-    return (jalview.schemabinding.version2.HiddenColumns) obj;\r
-  } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int)\r
-\r
-  /**\r
-   * Sets the value of field 'annotationColours'.\r
-   *\r
-   * @param annotationColours the value of field\r
-   * 'annotationColours'.\r
-   */\r
-  public void setAnnotationColours(jalview.schemabinding.version2.\r
-                                   AnnotationColours annotationColours)\r
-  {\r
-    this._annotationColours = annotationColours;\r
-  } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours)\r
-\r
-  /**\r
-   * Sets the value of field 'bgColour'.\r
-   *\r
-   * @param bgColour the value of field 'bgColour'.\r
-   */\r
-  public void setBgColour(java.lang.String bgColour)\r
-  {\r
-    this._bgColour = bgColour;\r
-  } //-- void setBgColour(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'consThreshold'.\r
-   *\r
-   * @param consThreshold the value of field 'consThreshold'.\r
-   */\r
-  public void setConsThreshold(int consThreshold)\r
-  {\r
-    this._consThreshold = consThreshold;\r
-    this._has_consThreshold = true;\r
-  } //-- void setConsThreshold(int)\r
-\r
-  /**\r
-   * Sets the value of field 'conservationSelected'.\r
-   *\r
-   * @param conservationSelected the value of field\r
-   * 'conservationSelected'.\r
-   */\r
-  public void setConservationSelected(boolean conservationSelected)\r
-  {\r
-    this._conservationSelected = conservationSelected;\r
-    this._has_conservationSelected = true;\r
-  } //-- void setConservationSelected(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'fontName'.\r
-   *\r
-   * @param fontName the value of field 'fontName'.\r
-   */\r
-  public void setFontName(java.lang.String fontName)\r
-  {\r
-    this._fontName = fontName;\r
-  } //-- void setFontName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'fontSize'.\r
-   *\r
-   * @param fontSize the value of field 'fontSize'.\r
-   */\r
-  public void setFontSize(int fontSize)\r
-  {\r
-    this._fontSize = fontSize;\r
-    this._has_fontSize = true;\r
-  } //-- void setFontSize(int)\r
-\r
-  /**\r
-   * Sets the value of field 'fontStyle'.\r
-   *\r
-   * @param fontStyle the value of field 'fontStyle'.\r
-   */\r
-  public void setFontStyle(int fontStyle)\r
-  {\r
-    this._fontStyle = fontStyle;\r
-    this._has_fontStyle = true;\r
-  } //-- void setFontStyle(int)\r
-\r
-  /**\r
-   * Sets the value of field 'gatheredViews'.\r
-   *\r
-   * @param gatheredViews the value of field 'gatheredViews'.\r
-   */\r
-  public void setGatheredViews(boolean gatheredViews)\r
-  {\r
-    this._gatheredViews = gatheredViews;\r
-    this._has_gatheredViews = true;\r
-  } //-- void setGatheredViews(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'height'.\r
-   *\r
-   * @param height the value of field 'height'.\r
-   */\r
-  public void setHeight(int height)\r
-  {\r
-    this._height = height;\r
-    this._has_height = true;\r
-  } //-- void setHeight(int)\r
-\r
-  /**\r
-   * Method setHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param index\r
-   * @param vHiddenColumns\r
-   */\r
-  public void setHiddenColumns(int index,\r
-                               jalview.schemabinding.version2.HiddenColumns\r
-                               vHiddenColumns)\r
-      throws java.lang.IndexOutOfBoundsException\r
-  {\r
-    //-- check bounds for index\r
-    if ( (index < 0) || (index > _hiddenColumnsList.size()))\r
-    {\r
-      throw new IndexOutOfBoundsException();\r
-    }\r
-    _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
-  } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)\r
-\r
-  /**\r
-   * Method setHiddenColumns\r
-   *\r
-   *\r
-   *\r
-   * @param hiddenColumnsArray\r
-   */\r
-  public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[]\r
-                               hiddenColumnsArray)\r
-  {\r
-    //-- copy array\r
-    _hiddenColumnsList.removeAllElements();\r
-    for (int i = 0; i < hiddenColumnsArray.length; i++)\r
-    {\r
-      _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
-    }\r
-  } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns)\r
-\r
-  /**\r
-   * Sets the value of field 'pidSelected'.\r
-   *\r
-   * @param pidSelected the value of field 'pidSelected'.\r
-   */\r
-  public void setPidSelected(boolean pidSelected)\r
-  {\r
-    this._pidSelected = pidSelected;\r
-    this._has_pidSelected = true;\r
-  } //-- void setPidSelected(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'pidThreshold'.\r
-   *\r
-   * @param pidThreshold the value of field 'pidThreshold'.\r
-   */\r
-  public void setPidThreshold(int pidThreshold)\r
-  {\r
-    this._pidThreshold = pidThreshold;\r
-    this._has_pidThreshold = true;\r
-  } //-- void setPidThreshold(int)\r
-\r
-  /**\r
-   * Sets the value of field 'renderGaps'.\r
-   *\r
-   * @param renderGaps the value of field 'renderGaps'.\r
-   */\r
-  public void setRenderGaps(boolean renderGaps)\r
-  {\r
-    this._renderGaps = renderGaps;\r
-    this._has_renderGaps = true;\r
-  } //-- void setRenderGaps(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'rightAlignIds'.\r
-   *\r
-   * @param rightAlignIds the value of field 'rightAlignIds'.\r
-   */\r
-  public void setRightAlignIds(boolean rightAlignIds)\r
-  {\r
-    this._rightAlignIds = rightAlignIds;\r
-    this._has_rightAlignIds = true;\r
-  } //-- void setRightAlignIds(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'sequenceSetId'.\r
-   *\r
-   * @param sequenceSetId the value of field 'sequenceSetId'.\r
-   */\r
-  public void setSequenceSetId(java.lang.String sequenceSetId)\r
-  {\r
-    this._sequenceSetId = sequenceSetId;\r
-  } //-- void setSequenceSetId(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'showAnnotation'.\r
-   *\r
-   * @param showAnnotation the value of field 'showAnnotation'.\r
-   */\r
-  public void setShowAnnotation(boolean showAnnotation)\r
-  {\r
-    this._showAnnotation = showAnnotation;\r
-    this._has_showAnnotation = true;\r
-  } //-- void setShowAnnotation(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showBoxes'.\r
-   *\r
-   * @param showBoxes the value of field 'showBoxes'.\r
-   */\r
-  public void setShowBoxes(boolean showBoxes)\r
-  {\r
-    this._showBoxes = showBoxes;\r
-    this._has_showBoxes = true;\r
-  } //-- void setShowBoxes(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showColourText'.\r
-   *\r
-   * @param showColourText the value of field 'showColourText'.\r
-   */\r
-  public void setShowColourText(boolean showColourText)\r
-  {\r
-    this._showColourText = showColourText;\r
-    this._has_showColourText = true;\r
-  } //-- void setShowColourText(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showFullId'.\r
-   *\r
-   * @param showFullId the value of field 'showFullId'.\r
-   */\r
-  public void setShowFullId(boolean showFullId)\r
-  {\r
-    this._showFullId = showFullId;\r
-    this._has_showFullId = true;\r
-  } //-- void setShowFullId(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showSequenceFeatures'.\r
-   *\r
-   * @param showSequenceFeatures the value of field\r
-   * 'showSequenceFeatures'.\r
-   */\r
-  public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
-  {\r
-    this._showSequenceFeatures = showSequenceFeatures;\r
-    this._has_showSequenceFeatures = true;\r
-  } //-- void setShowSequenceFeatures(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'showText'.\r
-   *\r
-   * @param showText the value of field 'showText'.\r
-   */\r
-  public void setShowText(boolean showText)\r
-  {\r
-    this._showText = showText;\r
-    this._has_showText = true;\r
-  } //-- void setShowText(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'startRes'.\r
-   *\r
-   * @param startRes the value of field 'startRes'.\r
-   */\r
-  public void setStartRes(int startRes)\r
-  {\r
-    this._startRes = startRes;\r
-    this._has_startRes = true;\r
-  } //-- void setStartRes(int)\r
-\r
-  /**\r
-   * Sets the value of field 'startSeq'.\r
-   *\r
-   * @param startSeq the value of field 'startSeq'.\r
-   */\r
-  public void setStartSeq(int startSeq)\r
-  {\r
-    this._startSeq = startSeq;\r
-    this._has_startSeq = true;\r
-  } //-- void setStartSeq(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textCol1'.\r
-   *\r
-   * @param textCol1 the value of field 'textCol1'.\r
-   */\r
-  public void setTextCol1(int textCol1)\r
-  {\r
-    this._textCol1 = textCol1;\r
-    this._has_textCol1 = true;\r
-  } //-- void setTextCol1(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textCol2'.\r
-   *\r
-   * @param textCol2 the value of field 'textCol2'.\r
-   */\r
-  public void setTextCol2(int textCol2)\r
-  {\r
-    this._textCol2 = textCol2;\r
-    this._has_textCol2 = true;\r
-  } //-- void setTextCol2(int)\r
-\r
-  /**\r
-   * Sets the value of field 'textColThreshold'.\r
-   *\r
-   * @param textColThreshold the value of field 'textColThreshold'\r
-   */\r
-  public void setTextColThreshold(int textColThreshold)\r
-  {\r
-    this._textColThreshold = textColThreshold;\r
-    this._has_textColThreshold = true;\r
-  } //-- void setTextColThreshold(int)\r
-\r
-  /**\r
-   * Sets the value of field 'title'.\r
-   *\r
-   * @param title the value of field 'title'.\r
-   */\r
-  public void setTitle(java.lang.String title)\r
-  {\r
-    this._title = title;\r
-  } //-- void setTitle(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'viewName'.\r
-   *\r
-   * @param viewName the value of field 'viewName'.\r
-   */\r
-  public void setViewName(java.lang.String viewName)\r
-  {\r
-    this._viewName = viewName;\r
-  } //-- void setViewName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'width'.\r
-   *\r
-   * @param width the value of field 'width'.\r
-   */\r
-  public void setWidth(int width)\r
-  {\r
-    this._width = width;\r
-    this._has_width = true;\r
-  } //-- void setWidth(int)\r
-\r
-  /**\r
-   * Sets the value of field 'wrapAlignment'.\r
-   *\r
-   * @param wrapAlignment the value of field 'wrapAlignment'.\r
-   */\r
-  public void setWrapAlignment(boolean wrapAlignment)\r
-  {\r
-    this._wrapAlignment = wrapAlignment;\r
-    this._has_wrapAlignment = true;\r
-  } //-- void setWrapAlignment(boolean)\r
-\r
-  /**\r
-   * Sets the value of field 'xpos'.\r
-   *\r
-   * @param xpos the value of field 'xpos'.\r
-   */\r
-  public void setXpos(int xpos)\r
-  {\r
-    this._xpos = xpos;\r
-    this._has_xpos = true;\r
-  } //-- void setXpos(int)\r
-\r
-  /**\r
-   * Sets the value of field 'ypos'.\r
-   *\r
-   * @param ypos the value of field 'ypos'.\r
-   */\r
-  public void setYpos(int ypos)\r
-  {\r
-    this._ypos = ypos;\r
-    this._has_ypos = true;\r
-  } //-- void setYpos(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(\r
-        jalview.schemabinding.version2.Viewport.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
+public class Viewport implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _conservationSelected\r
+     */\r
+    private boolean _conservationSelected;\r
+\r
+    /**\r
+     * keeps track of state for field: _conservationSelected\r
+     */\r
+    private boolean _has_conservationSelected;\r
+\r
+    /**\r
+     * Field _pidSelected\r
+     */\r
+    private boolean _pidSelected;\r
+\r
+    /**\r
+     * keeps track of state for field: _pidSelected\r
+     */\r
+    private boolean _has_pidSelected;\r
+\r
+    /**\r
+     * Field _bgColour\r
+     */\r
+    private java.lang.String _bgColour;\r
+\r
+    /**\r
+     * Field _consThreshold\r
+     */\r
+    private int _consThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _consThreshold\r
+     */\r
+    private boolean _has_consThreshold;\r
+\r
+    /**\r
+     * Field _pidThreshold\r
+     */\r
+    private int _pidThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _pidThreshold\r
+     */\r
+    private boolean _has_pidThreshold;\r
+\r
+    /**\r
+     * Field _title\r
+     */\r
+    private java.lang.String _title;\r
+\r
+    /**\r
+     * Field _showFullId\r
+     */\r
+    private boolean _showFullId;\r
+\r
+    /**\r
+     * keeps track of state for field: _showFullId\r
+     */\r
+    private boolean _has_showFullId;\r
+\r
+    /**\r
+     * Field _rightAlignIds\r
+     */\r
+    private boolean _rightAlignIds;\r
+\r
+    /**\r
+     * keeps track of state for field: _rightAlignIds\r
+     */\r
+    private boolean _has_rightAlignIds;\r
+\r
+    /**\r
+     * Field _showText\r
+     */\r
+    private boolean _showText;\r
+\r
+    /**\r
+     * keeps track of state for field: _showText\r
+     */\r
+    private boolean _has_showText;\r
+\r
+    /**\r
+     * Field _showColourText\r
+     */\r
+    private boolean _showColourText;\r
+\r
+    /**\r
+     * keeps track of state for field: _showColourText\r
+     */\r
+    private boolean _has_showColourText;\r
+\r
+    /**\r
+     * Field _showBoxes\r
+     */\r
+    private boolean _showBoxes;\r
+\r
+    /**\r
+     * keeps track of state for field: _showBoxes\r
+     */\r
+    private boolean _has_showBoxes;\r
+\r
+    /**\r
+     * Field _wrapAlignment\r
+     */\r
+    private boolean _wrapAlignment;\r
+\r
+    /**\r
+     * keeps track of state for field: _wrapAlignment\r
+     */\r
+    private boolean _has_wrapAlignment;\r
+\r
+    /**\r
+     * Field _renderGaps\r
+     */\r
+    private boolean _renderGaps;\r
+\r
+    /**\r
+     * keeps track of state for field: _renderGaps\r
+     */\r
+    private boolean _has_renderGaps;\r
+\r
+    /**\r
+     * Field _showSequenceFeatures\r
+     */\r
+    private boolean _showSequenceFeatures;\r
+\r
+    /**\r
+     * keeps track of state for field: _showSequenceFeatures\r
+     */\r
+    private boolean _has_showSequenceFeatures;\r
+\r
+    /**\r
+     * Field _showAnnotation\r
+     */\r
+    private boolean _showAnnotation;\r
+\r
+    /**\r
+     * keeps track of state for field: _showAnnotation\r
+     */\r
+    private boolean _has_showAnnotation;\r
+\r
+    /**\r
+     * Field _xpos\r
+     */\r
+    private int _xpos;\r
+\r
+    /**\r
+     * keeps track of state for field: _xpos\r
+     */\r
+    private boolean _has_xpos;\r
+\r
+    /**\r
+     * Field _ypos\r
+     */\r
+    private int _ypos;\r
+\r
+    /**\r
+     * keeps track of state for field: _ypos\r
+     */\r
+    private boolean _has_ypos;\r
+\r
+    /**\r
+     * Field _width\r
+     */\r
+    private int _width;\r
+\r
+    /**\r
+     * keeps track of state for field: _width\r
+     */\r
+    private boolean _has_width;\r
+\r
+    /**\r
+     * Field _height\r
+     */\r
+    private int _height;\r
+\r
+    /**\r
+     * keeps track of state for field: _height\r
+     */\r
+    private boolean _has_height;\r
+\r
+    /**\r
+     * Field _startRes\r
+     */\r
+    private int _startRes;\r
+\r
+    /**\r
+     * keeps track of state for field: _startRes\r
+     */\r
+    private boolean _has_startRes;\r
+\r
+    /**\r
+     * Field _startSeq\r
+     */\r
+    private int _startSeq;\r
+\r
+    /**\r
+     * keeps track of state for field: _startSeq\r
+     */\r
+    private boolean _has_startSeq;\r
+\r
+    /**\r
+     * Field _fontName\r
+     */\r
+    private java.lang.String _fontName;\r
+\r
+    /**\r
+     * Field _fontSize\r
+     */\r
+    private int _fontSize;\r
+\r
+    /**\r
+     * keeps track of state for field: _fontSize\r
+     */\r
+    private boolean _has_fontSize;\r
+\r
+    /**\r
+     * Field _fontStyle\r
+     */\r
+    private int _fontStyle;\r
+\r
+    /**\r
+     * keeps track of state for field: _fontStyle\r
+     */\r
+    private boolean _has_fontStyle;\r
+\r
+    /**\r
+     * Field _viewName\r
+     */\r
+    private java.lang.String _viewName;\r
+\r
+    /**\r
+     * Field _sequenceSetId\r
+     */\r
+    private java.lang.String _sequenceSetId;\r
+\r
+    /**\r
+     * Field _gatheredViews\r
+     */\r
+    private boolean _gatheredViews;\r
+\r
+    /**\r
+     * keeps track of state for field: _gatheredViews\r
+     */\r
+    private boolean _has_gatheredViews;\r
+\r
+    /**\r
+     * Field _textCol1\r
+     */\r
+    private int _textCol1;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol1\r
+     */\r
+    private boolean _has_textCol1;\r
+\r
+    /**\r
+     * Field _textCol2\r
+     */\r
+    private int _textCol2;\r
+\r
+    /**\r
+     * keeps track of state for field: _textCol2\r
+     */\r
+    private boolean _has_textCol2;\r
+\r
+    /**\r
+     * Field _textColThreshold\r
+     */\r
+    private int _textColThreshold;\r
+\r
+    /**\r
+     * keeps track of state for field: _textColThreshold\r
+     */\r
+    private boolean _has_textColThreshold;\r
+\r
+    /**\r
+     * Field _annotationColours\r
+     */\r
+    private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
+\r
+    /**\r
+     * Field _hiddenColumnsList\r
+     */\r
+    private java.util.Vector _hiddenColumnsList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Viewport() {\r
+        super();\r
+        _hiddenColumnsList = new Vector();\r
+    } //-- jalview.schemabinding.version2.Viewport()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param vHiddenColumns\r
+     */\r
+    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenColumnsList.addElement(vHiddenColumns);\r
+    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Method addHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenColumns\r
+     */\r
+    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
+    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Method deleteConsThreshold\r
+     * \r
+     */\r
+    public void deleteConsThreshold()\r
+    {\r
+        this._has_consThreshold= false;\r
+    } //-- void deleteConsThreshold() \r
+\r
+    /**\r
+     * Method deleteConservationSelected\r
+     * \r
+     */\r
+    public void deleteConservationSelected()\r
+    {\r
+        this._has_conservationSelected= false;\r
+    } //-- void deleteConservationSelected() \r
+\r
+    /**\r
+     * Method deleteFontSize\r
+     * \r
+     */\r
+    public void deleteFontSize()\r
+    {\r
+        this._has_fontSize= false;\r
+    } //-- void deleteFontSize() \r
+\r
+    /**\r
+     * Method deleteFontStyle\r
+     * \r
+     */\r
+    public void deleteFontStyle()\r
+    {\r
+        this._has_fontStyle= false;\r
+    } //-- void deleteFontStyle() \r
+\r
+    /**\r
+     * Method deleteGatheredViews\r
+     * \r
+     */\r
+    public void deleteGatheredViews()\r
+    {\r
+        this._has_gatheredViews= false;\r
+    } //-- void deleteGatheredViews() \r
+\r
+    /**\r
+     * Method deleteHeight\r
+     * \r
+     */\r
+    public void deleteHeight()\r
+    {\r
+        this._has_height= false;\r
+    } //-- void deleteHeight() \r
+\r
+    /**\r
+     * Method deletePidSelected\r
+     * \r
+     */\r
+    public void deletePidSelected()\r
+    {\r
+        this._has_pidSelected= false;\r
+    } //-- void deletePidSelected() \r
+\r
+    /**\r
+     * Method deletePidThreshold\r
+     * \r
+     */\r
+    public void deletePidThreshold()\r
+    {\r
+        this._has_pidThreshold= false;\r
+    } //-- void deletePidThreshold() \r
+\r
+    /**\r
+     * Method deleteRenderGaps\r
+     * \r
+     */\r
+    public void deleteRenderGaps()\r
+    {\r
+        this._has_renderGaps= false;\r
+    } //-- void deleteRenderGaps() \r
+\r
+    /**\r
+     * Method deleteRightAlignIds\r
+     * \r
+     */\r
+    public void deleteRightAlignIds()\r
+    {\r
+        this._has_rightAlignIds= false;\r
+    } //-- void deleteRightAlignIds() \r
+\r
+    /**\r
+     * Method deleteShowAnnotation\r
+     * \r
+     */\r
+    public void deleteShowAnnotation()\r
+    {\r
+        this._has_showAnnotation= false;\r
+    } //-- void deleteShowAnnotation() \r
+\r
+    /**\r
+     * Method deleteShowBoxes\r
+     * \r
+     */\r
+    public void deleteShowBoxes()\r
+    {\r
+        this._has_showBoxes= false;\r
+    } //-- void deleteShowBoxes() \r
+\r
+    /**\r
+     * Method deleteShowColourText\r
+     * \r
+     */\r
+    public void deleteShowColourText()\r
+    {\r
+        this._has_showColourText= false;\r
+    } //-- void deleteShowColourText() \r
+\r
+    /**\r
+     * Method deleteShowFullId\r
+     * \r
+     */\r
+    public void deleteShowFullId()\r
+    {\r
+        this._has_showFullId= false;\r
+    } //-- void deleteShowFullId() \r
+\r
+    /**\r
+     * Method deleteShowSequenceFeatures\r
+     * \r
+     */\r
+    public void deleteShowSequenceFeatures()\r
+    {\r
+        this._has_showSequenceFeatures= false;\r
+    } //-- void deleteShowSequenceFeatures() \r
+\r
+    /**\r
+     * Method deleteShowText\r
+     * \r
+     */\r
+    public void deleteShowText()\r
+    {\r
+        this._has_showText= false;\r
+    } //-- void deleteShowText() \r
+\r
+    /**\r
+     * Method deleteStartRes\r
+     * \r
+     */\r
+    public void deleteStartRes()\r
+    {\r
+        this._has_startRes= false;\r
+    } //-- void deleteStartRes() \r
+\r
+    /**\r
+     * Method deleteStartSeq\r
+     * \r
+     */\r
+    public void deleteStartSeq()\r
+    {\r
+        this._has_startSeq= false;\r
+    } //-- void deleteStartSeq() \r
+\r
+    /**\r
+     * Method deleteTextCol1\r
+     * \r
+     */\r
+    public void deleteTextCol1()\r
+    {\r
+        this._has_textCol1= false;\r
+    } //-- void deleteTextCol1() \r
+\r
+    /**\r
+     * Method deleteTextCol2\r
+     * \r
+     */\r
+    public void deleteTextCol2()\r
+    {\r
+        this._has_textCol2= false;\r
+    } //-- void deleteTextCol2() \r
+\r
+    /**\r
+     * Method deleteTextColThreshold\r
+     * \r
+     */\r
+    public void deleteTextColThreshold()\r
+    {\r
+        this._has_textColThreshold= false;\r
+    } //-- void deleteTextColThreshold() \r
+\r
+    /**\r
+     * Method deleteWidth\r
+     * \r
+     */\r
+    public void deleteWidth()\r
+    {\r
+        this._has_width= false;\r
+    } //-- void deleteWidth() \r
+\r
+    /**\r
+     * Method deleteWrapAlignment\r
+     * \r
+     */\r
+    public void deleteWrapAlignment()\r
+    {\r
+        this._has_wrapAlignment= false;\r
+    } //-- void deleteWrapAlignment() \r
+\r
+    /**\r
+     * Method deleteXpos\r
+     * \r
+     */\r
+    public void deleteXpos()\r
+    {\r
+        this._has_xpos= false;\r
+    } //-- void deleteXpos() \r
+\r
+    /**\r
+     * Method deleteYpos\r
+     * \r
+     */\r
+    public void deleteYpos()\r
+    {\r
+        this._has_ypos= false;\r
+    } //-- void deleteYpos() \r
+\r
+    /**\r
+     * Method enumerateHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateHiddenColumns()\r
+    {\r
+        return _hiddenColumnsList.elements();\r
+    } //-- java.util.Enumeration enumerateHiddenColumns() \r
+\r
+    /**\r
+     * Returns the value of field 'annotationColours'.\r
+     * \r
+     * @return AnnotationColours\r
+     * @return the value of field 'annotationColours'.\r
+     */\r
+    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()\r
+    {\r
+        return this._annotationColours;\r
+    } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() \r
+\r
+    /**\r
+     * Returns the value of field 'bgColour'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'bgColour'.\r
+     */\r
+    public java.lang.String getBgColour()\r
+    {\r
+        return this._bgColour;\r
+    } //-- java.lang.String getBgColour() \r
+\r
+    /**\r
+     * Returns the value of field 'consThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'consThreshold'.\r
+     */\r
+    public int getConsThreshold()\r
+    {\r
+        return this._consThreshold;\r
+    } //-- int getConsThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'conservationSelected'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'conservationSelected'.\r
+     */\r
+    public boolean getConservationSelected()\r
+    {\r
+        return this._conservationSelected;\r
+    } //-- boolean getConservationSelected() \r
+\r
+    /**\r
+     * Returns the value of field 'fontName'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'fontName'.\r
+     */\r
+    public java.lang.String getFontName()\r
+    {\r
+        return this._fontName;\r
+    } //-- java.lang.String getFontName() \r
+\r
+    /**\r
+     * Returns the value of field 'fontSize'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'fontSize'.\r
+     */\r
+    public int getFontSize()\r
+    {\r
+        return this._fontSize;\r
+    } //-- int getFontSize() \r
+\r
+    /**\r
+     * Returns the value of field 'fontStyle'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'fontStyle'.\r
+     */\r
+    public int getFontStyle()\r
+    {\r
+        return this._fontStyle;\r
+    } //-- int getFontStyle() \r
+\r
+    /**\r
+     * Returns the value of field 'gatheredViews'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'gatheredViews'.\r
+     */\r
+    public boolean getGatheredViews()\r
+    {\r
+        return this._gatheredViews;\r
+    } //-- boolean getGatheredViews() \r
+\r
+    /**\r
+     * Returns the value of field 'height'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'height'.\r
+     */\r
+    public int getHeight()\r
+    {\r
+        return this._height;\r
+    } //-- int getHeight() \r
+\r
+    /**\r
+     * Method getHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+\r
+    /**\r
+     * Method getHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
+    {\r
+        int size = _hiddenColumnsList.size();\r
+        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+\r
+    /**\r
+     * Method getHiddenColumnsCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getHiddenColumnsCount()\r
+    {\r
+        return _hiddenColumnsList.size();\r
+    } //-- int getHiddenColumnsCount() \r
+\r
+    /**\r
+     * Returns the value of field 'pidSelected'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'pidSelected'.\r
+     */\r
+    public boolean getPidSelected()\r
+    {\r
+        return this._pidSelected;\r
+    } //-- boolean getPidSelected() \r
+\r
+    /**\r
+     * Returns the value of field 'pidThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'pidThreshold'.\r
+     */\r
+    public int getPidThreshold()\r
+    {\r
+        return this._pidThreshold;\r
+    } //-- int getPidThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'renderGaps'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'renderGaps'.\r
+     */\r
+    public boolean getRenderGaps()\r
+    {\r
+        return this._renderGaps;\r
+    } //-- boolean getRenderGaps() \r
+\r
+    /**\r
+     * Returns the value of field 'rightAlignIds'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'rightAlignIds'.\r
+     */\r
+    public boolean getRightAlignIds()\r
+    {\r
+        return this._rightAlignIds;\r
+    } //-- boolean getRightAlignIds() \r
+\r
+    /**\r
+     * Returns the value of field 'sequenceSetId'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'sequenceSetId'.\r
+     */\r
+    public java.lang.String getSequenceSetId()\r
+    {\r
+        return this._sequenceSetId;\r
+    } //-- java.lang.String getSequenceSetId() \r
+\r
+    /**\r
+     * Returns the value of field 'showAnnotation'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showAnnotation'.\r
+     */\r
+    public boolean getShowAnnotation()\r
+    {\r
+        return this._showAnnotation;\r
+    } //-- boolean getShowAnnotation() \r
+\r
+    /**\r
+     * Returns the value of field 'showBoxes'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showBoxes'.\r
+     */\r
+    public boolean getShowBoxes()\r
+    {\r
+        return this._showBoxes;\r
+    } //-- boolean getShowBoxes() \r
+\r
+    /**\r
+     * Returns the value of field 'showColourText'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showColourText'.\r
+     */\r
+    public boolean getShowColourText()\r
+    {\r
+        return this._showColourText;\r
+    } //-- boolean getShowColourText() \r
+\r
+    /**\r
+     * Returns the value of field 'showFullId'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showFullId'.\r
+     */\r
+    public boolean getShowFullId()\r
+    {\r
+        return this._showFullId;\r
+    } //-- boolean getShowFullId() \r
+\r
+    /**\r
+     * Returns the value of field 'showSequenceFeatures'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showSequenceFeatures'.\r
+     */\r
+    public boolean getShowSequenceFeatures()\r
+    {\r
+        return this._showSequenceFeatures;\r
+    } //-- boolean getShowSequenceFeatures() \r
+\r
+    /**\r
+     * Returns the value of field 'showText'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'showText'.\r
+     */\r
+    public boolean getShowText()\r
+    {\r
+        return this._showText;\r
+    } //-- boolean getShowText() \r
+\r
+    /**\r
+     * Returns the value of field 'startRes'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'startRes'.\r
+     */\r
+    public int getStartRes()\r
+    {\r
+        return this._startRes;\r
+    } //-- int getStartRes() \r
+\r
+    /**\r
+     * Returns the value of field 'startSeq'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'startSeq'.\r
+     */\r
+    public int getStartSeq()\r
+    {\r
+        return this._startSeq;\r
+    } //-- int getStartSeq() \r
+\r
+    /**\r
+     * Returns the value of field 'textCol1'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textCol1'.\r
+     */\r
+    public int getTextCol1()\r
+    {\r
+        return this._textCol1;\r
+    } //-- int getTextCol1() \r
+\r
+    /**\r
+     * Returns the value of field 'textCol2'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textCol2'.\r
+     */\r
+    public int getTextCol2()\r
+    {\r
+        return this._textCol2;\r
+    } //-- int getTextCol2() \r
+\r
+    /**\r
+     * Returns the value of field 'textColThreshold'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'textColThreshold'.\r
+     */\r
+    public int getTextColThreshold()\r
+    {\r
+        return this._textColThreshold;\r
+    } //-- int getTextColThreshold() \r
+\r
+    /**\r
+     * Returns the value of field 'title'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'title'.\r
+     */\r
+    public java.lang.String getTitle()\r
+    {\r
+        return this._title;\r
+    } //-- java.lang.String getTitle() \r
+\r
+    /**\r
+     * Returns the value of field 'viewName'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'viewName'.\r
+     */\r
+    public java.lang.String getViewName()\r
+    {\r
+        return this._viewName;\r
+    } //-- java.lang.String getViewName() \r
+\r
+    /**\r
+     * Returns the value of field 'width'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'width'.\r
+     */\r
+    public int getWidth()\r
+    {\r
+        return this._width;\r
+    } //-- int getWidth() \r
+\r
+    /**\r
+     * Returns the value of field 'wrapAlignment'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'wrapAlignment'.\r
+     */\r
+    public boolean getWrapAlignment()\r
+    {\r
+        return this._wrapAlignment;\r
+    } //-- boolean getWrapAlignment() \r
+\r
+    /**\r
+     * Returns the value of field 'xpos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'xpos'.\r
+     */\r
+    public int getXpos()\r
+    {\r
+        return this._xpos;\r
+    } //-- int getXpos() \r
+\r
+    /**\r
+     * Returns the value of field 'ypos'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'ypos'.\r
+     */\r
+    public int getYpos()\r
+    {\r
+        return this._ypos;\r
+    } //-- int getYpos() \r
+\r
+    /**\r
+     * Method hasConsThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasConsThreshold()\r
+    {\r
+        return this._has_consThreshold;\r
+    } //-- boolean hasConsThreshold() \r
+\r
+    /**\r
+     * Method hasConservationSelected\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasConservationSelected()\r
+    {\r
+        return this._has_conservationSelected;\r
+    } //-- boolean hasConservationSelected() \r
+\r
+    /**\r
+     * Method hasFontSize\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasFontSize()\r
+    {\r
+        return this._has_fontSize;\r
+    } //-- boolean hasFontSize() \r
+\r
+    /**\r
+     * Method hasFontStyle\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasFontStyle()\r
+    {\r
+        return this._has_fontStyle;\r
+    } //-- boolean hasFontStyle() \r
+\r
+    /**\r
+     * Method hasGatheredViews\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGatheredViews()\r
+    {\r
+        return this._has_gatheredViews;\r
+    } //-- boolean hasGatheredViews() \r
+\r
+    /**\r
+     * Method hasHeight\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHeight()\r
+    {\r
+        return this._has_height;\r
+    } //-- boolean hasHeight() \r
+\r
+    /**\r
+     * Method hasPidSelected\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasPidSelected()\r
+    {\r
+        return this._has_pidSelected;\r
+    } //-- boolean hasPidSelected() \r
+\r
+    /**\r
+     * Method hasPidThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasPidThreshold()\r
+    {\r
+        return this._has_pidThreshold;\r
+    } //-- boolean hasPidThreshold() \r
+\r
+    /**\r
+     * Method hasRenderGaps\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasRenderGaps()\r
+    {\r
+        return this._has_renderGaps;\r
+    } //-- boolean hasRenderGaps() \r
+\r
+    /**\r
+     * Method hasRightAlignIds\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasRightAlignIds()\r
+    {\r
+        return this._has_rightAlignIds;\r
+    } //-- boolean hasRightAlignIds() \r
+\r
+    /**\r
+     * Method hasShowAnnotation\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowAnnotation()\r
+    {\r
+        return this._has_showAnnotation;\r
+    } //-- boolean hasShowAnnotation() \r
+\r
+    /**\r
+     * Method hasShowBoxes\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowBoxes()\r
+    {\r
+        return this._has_showBoxes;\r
+    } //-- boolean hasShowBoxes() \r
+\r
+    /**\r
+     * Method hasShowColourText\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowColourText()\r
+    {\r
+        return this._has_showColourText;\r
+    } //-- boolean hasShowColourText() \r
+\r
+    /**\r
+     * Method hasShowFullId\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowFullId()\r
+    {\r
+        return this._has_showFullId;\r
+    } //-- boolean hasShowFullId() \r
+\r
+    /**\r
+     * Method hasShowSequenceFeatures\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowSequenceFeatures()\r
+    {\r
+        return this._has_showSequenceFeatures;\r
+    } //-- boolean hasShowSequenceFeatures() \r
+\r
+    /**\r
+     * Method hasShowText\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasShowText()\r
+    {\r
+        return this._has_showText;\r
+    } //-- boolean hasShowText() \r
+\r
+    /**\r
+     * Method hasStartRes\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStartRes()\r
+    {\r
+        return this._has_startRes;\r
+    } //-- boolean hasStartRes() \r
+\r
+    /**\r
+     * Method hasStartSeq\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStartSeq()\r
+    {\r
+        return this._has_startSeq;\r
+    } //-- boolean hasStartSeq() \r
+\r
+    /**\r
+     * Method hasTextCol1\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextCol1()\r
+    {\r
+        return this._has_textCol1;\r
+    } //-- boolean hasTextCol1() \r
+\r
+    /**\r
+     * Method hasTextCol2\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextCol2()\r
+    {\r
+        return this._has_textCol2;\r
+    } //-- boolean hasTextCol2() \r
+\r
+    /**\r
+     * Method hasTextColThreshold\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasTextColThreshold()\r
+    {\r
+        return this._has_textColThreshold;\r
+    } //-- boolean hasTextColThreshold() \r
+\r
+    /**\r
+     * Method hasWidth\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasWidth()\r
+    {\r
+        return this._has_width;\r
+    } //-- boolean hasWidth() \r
+\r
+    /**\r
+     * Method hasWrapAlignment\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasWrapAlignment()\r
+    {\r
+        return this._has_wrapAlignment;\r
+    } //-- boolean hasWrapAlignment() \r
+\r
+    /**\r
+     * Method hasXpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasXpos()\r
+    {\r
+        return this._has_xpos;\r
+    } //-- boolean hasXpos() \r
+\r
+    /**\r
+     * Method hasYpos\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasYpos()\r
+    {\r
+        return this._has_ypos;\r
+    } //-- boolean hasYpos() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllHiddenColumns\r
+     * \r
+     */\r
+    public void removeAllHiddenColumns()\r
+    {\r
+        _hiddenColumnsList.removeAllElements();\r
+    } //-- void removeAllHiddenColumns() \r
+\r
+    /**\r
+     * Method removeHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
+    {\r
+        java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
+        _hiddenColumnsList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.HiddenColumns) obj;\r
+    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+\r
+    /**\r
+     * Sets the value of field 'annotationColours'.\r
+     * \r
+     * @param annotationColours the value of field\r
+     * 'annotationColours'.\r
+     */\r
+    public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)\r
+    {\r
+        this._annotationColours = annotationColours;\r
+    } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) \r
+\r
+    /**\r
+     * Sets the value of field 'bgColour'.\r
+     * \r
+     * @param bgColour the value of field 'bgColour'.\r
+     */\r
+    public void setBgColour(java.lang.String bgColour)\r
+    {\r
+        this._bgColour = bgColour;\r
+    } //-- void setBgColour(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'consThreshold'.\r
+     * \r
+     * @param consThreshold the value of field 'consThreshold'.\r
+     */\r
+    public void setConsThreshold(int consThreshold)\r
+    {\r
+        this._consThreshold = consThreshold;\r
+        this._has_consThreshold = true;\r
+    } //-- void setConsThreshold(int) \r
+\r
+    /**\r
+     * Sets the value of field 'conservationSelected'.\r
+     * \r
+     * @param conservationSelected the value of field\r
+     * 'conservationSelected'.\r
+     */\r
+    public void setConservationSelected(boolean conservationSelected)\r
+    {\r
+        this._conservationSelected = conservationSelected;\r
+        this._has_conservationSelected = true;\r
+    } //-- void setConservationSelected(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'fontName'.\r
+     * \r
+     * @param fontName the value of field 'fontName'.\r
+     */\r
+    public void setFontName(java.lang.String fontName)\r
+    {\r
+        this._fontName = fontName;\r
+    } //-- void setFontName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'fontSize'.\r
+     * \r
+     * @param fontSize the value of field 'fontSize'.\r
+     */\r
+    public void setFontSize(int fontSize)\r
+    {\r
+        this._fontSize = fontSize;\r
+        this._has_fontSize = true;\r
+    } //-- void setFontSize(int) \r
+\r
+    /**\r
+     * Sets the value of field 'fontStyle'.\r
+     * \r
+     * @param fontStyle the value of field 'fontStyle'.\r
+     */\r
+    public void setFontStyle(int fontStyle)\r
+    {\r
+        this._fontStyle = fontStyle;\r
+        this._has_fontStyle = true;\r
+    } //-- void setFontStyle(int) \r
+\r
+    /**\r
+     * Sets the value of field 'gatheredViews'.\r
+     * \r
+     * @param gatheredViews the value of field 'gatheredViews'.\r
+     */\r
+    public void setGatheredViews(boolean gatheredViews)\r
+    {\r
+        this._gatheredViews = gatheredViews;\r
+        this._has_gatheredViews = true;\r
+    } //-- void setGatheredViews(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'height'.\r
+     * \r
+     * @param height the value of field 'height'.\r
+     */\r
+    public void setHeight(int height)\r
+    {\r
+        this._height = height;\r
+        this._has_height = true;\r
+    } //-- void setHeight(int) \r
+\r
+    /**\r
+     * Method setHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenColumns\r
+     */\r
+    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
+    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Method setHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param hiddenColumnsArray\r
+     */\r
+    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
+    {\r
+        //-- copy array\r
+        _hiddenColumnsList.removeAllElements();\r
+        for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
+            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+        }\r
+    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Sets the value of field 'pidSelected'.\r
+     * \r
+     * @param pidSelected the value of field 'pidSelected'.\r
+     */\r
+    public void setPidSelected(boolean pidSelected)\r
+    {\r
+        this._pidSelected = pidSelected;\r
+        this._has_pidSelected = true;\r
+    } //-- void setPidSelected(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'pidThreshold'.\r
+     * \r
+     * @param pidThreshold the value of field 'pidThreshold'.\r
+     */\r
+    public void setPidThreshold(int pidThreshold)\r
+    {\r
+        this._pidThreshold = pidThreshold;\r
+        this._has_pidThreshold = true;\r
+    } //-- void setPidThreshold(int) \r
+\r
+    /**\r
+     * Sets the value of field 'renderGaps'.\r
+     * \r
+     * @param renderGaps the value of field 'renderGaps'.\r
+     */\r
+    public void setRenderGaps(boolean renderGaps)\r
+    {\r
+        this._renderGaps = renderGaps;\r
+        this._has_renderGaps = true;\r
+    } //-- void setRenderGaps(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'rightAlignIds'.\r
+     * \r
+     * @param rightAlignIds the value of field 'rightAlignIds'.\r
+     */\r
+    public void setRightAlignIds(boolean rightAlignIds)\r
+    {\r
+        this._rightAlignIds = rightAlignIds;\r
+        this._has_rightAlignIds = true;\r
+    } //-- void setRightAlignIds(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'sequenceSetId'.\r
+     * \r
+     * @param sequenceSetId the value of field 'sequenceSetId'.\r
+     */\r
+    public void setSequenceSetId(java.lang.String sequenceSetId)\r
+    {\r
+        this._sequenceSetId = sequenceSetId;\r
+    } //-- void setSequenceSetId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'showAnnotation'.\r
+     * \r
+     * @param showAnnotation the value of field 'showAnnotation'.\r
+     */\r
+    public void setShowAnnotation(boolean showAnnotation)\r
+    {\r
+        this._showAnnotation = showAnnotation;\r
+        this._has_showAnnotation = true;\r
+    } //-- void setShowAnnotation(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showBoxes'.\r
+     * \r
+     * @param showBoxes the value of field 'showBoxes'.\r
+     */\r
+    public void setShowBoxes(boolean showBoxes)\r
+    {\r
+        this._showBoxes = showBoxes;\r
+        this._has_showBoxes = true;\r
+    } //-- void setShowBoxes(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showColourText'.\r
+     * \r
+     * @param showColourText the value of field 'showColourText'.\r
+     */\r
+    public void setShowColourText(boolean showColourText)\r
+    {\r
+        this._showColourText = showColourText;\r
+        this._has_showColourText = true;\r
+    } //-- void setShowColourText(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showFullId'.\r
+     * \r
+     * @param showFullId the value of field 'showFullId'.\r
+     */\r
+    public void setShowFullId(boolean showFullId)\r
+    {\r
+        this._showFullId = showFullId;\r
+        this._has_showFullId = true;\r
+    } //-- void setShowFullId(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showSequenceFeatures'.\r
+     * \r
+     * @param showSequenceFeatures the value of field\r
+     * 'showSequenceFeatures'.\r
+     */\r
+    public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
+    {\r
+        this._showSequenceFeatures = showSequenceFeatures;\r
+        this._has_showSequenceFeatures = true;\r
+    } //-- void setShowSequenceFeatures(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'showText'.\r
+     * \r
+     * @param showText the value of field 'showText'.\r
+     */\r
+    public void setShowText(boolean showText)\r
+    {\r
+        this._showText = showText;\r
+        this._has_showText = true;\r
+    } //-- void setShowText(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'startRes'.\r
+     * \r
+     * @param startRes the value of field 'startRes'.\r
+     */\r
+    public void setStartRes(int startRes)\r
+    {\r
+        this._startRes = startRes;\r
+        this._has_startRes = true;\r
+    } //-- void setStartRes(int) \r
+\r
+    /**\r
+     * Sets the value of field 'startSeq'.\r
+     * \r
+     * @param startSeq the value of field 'startSeq'.\r
+     */\r
+    public void setStartSeq(int startSeq)\r
+    {\r
+        this._startSeq = startSeq;\r
+        this._has_startSeq = true;\r
+    } //-- void setStartSeq(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textCol1'.\r
+     * \r
+     * @param textCol1 the value of field 'textCol1'.\r
+     */\r
+    public void setTextCol1(int textCol1)\r
+    {\r
+        this._textCol1 = textCol1;\r
+        this._has_textCol1 = true;\r
+    } //-- void setTextCol1(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textCol2'.\r
+     * \r
+     * @param textCol2 the value of field 'textCol2'.\r
+     */\r
+    public void setTextCol2(int textCol2)\r
+    {\r
+        this._textCol2 = textCol2;\r
+        this._has_textCol2 = true;\r
+    } //-- void setTextCol2(int) \r
+\r
+    /**\r
+     * Sets the value of field 'textColThreshold'.\r
+     * \r
+     * @param textColThreshold the value of field 'textColThreshold'\r
+     */\r
+    public void setTextColThreshold(int textColThreshold)\r
+    {\r
+        this._textColThreshold = textColThreshold;\r
+        this._has_textColThreshold = true;\r
+    } //-- void setTextColThreshold(int) \r
+\r
+    /**\r
+     * Sets the value of field 'title'.\r
+     * \r
+     * @param title the value of field 'title'.\r
+     */\r
+    public void setTitle(java.lang.String title)\r
+    {\r
+        this._title = title;\r
+    } //-- void setTitle(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'viewName'.\r
+     * \r
+     * @param viewName the value of field 'viewName'.\r
+     */\r
+    public void setViewName(java.lang.String viewName)\r
+    {\r
+        this._viewName = viewName;\r
+    } //-- void setViewName(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'width'.\r
+     * \r
+     * @param width the value of field 'width'.\r
+     */\r
+    public void setWidth(int width)\r
+    {\r
+        this._width = width;\r
+        this._has_width = true;\r
+    } //-- void setWidth(int) \r
+\r
+    /**\r
+     * Sets the value of field 'wrapAlignment'.\r
+     * \r
+     * @param wrapAlignment the value of field 'wrapAlignment'.\r
+     */\r
+    public void setWrapAlignment(boolean wrapAlignment)\r
+    {\r
+        this._wrapAlignment = wrapAlignment;\r
+        this._has_wrapAlignment = true;\r
+    } //-- void setWrapAlignment(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'xpos'.\r
+     * \r
+     * @param xpos the value of field 'xpos'.\r
+     */\r
+    public void setXpos(int xpos)\r
+    {\r
+        this._xpos = xpos;\r
+        this._has_xpos = true;\r
+    } //-- void setXpos(int) \r
+\r
+    /**\r
+     * Sets the value of field 'ypos'.\r
+     * \r
+     * @param ypos the value of field 'ypos'.\r
+     */\r
+    public void setYpos(int ypos)\r
+    {\r
+        this._ypos = ypos;\r
+        this._has_ypos = true;\r
+    } //-- void setYpos(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
 \r
 }\r

diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index 5b2e45c..09544ef 100755 (executable)
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -1,5 +1,5 @@
 /*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
@@ -7,1783 +7,1441 @@
 \r
 package jalview.schemabinding.version2;\r
 \r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
 import org.exolab.castor.xml.validators.*;\r
 \r
 /**\r
  * Class ViewportDescriptor.\r
- *\r
+ * \r
  * @version $Revision$ $Date$\r
  */\r
-public class ViewportDescriptor\r
-    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field nsPrefix\r
-   */\r
-  private java.lang.String nsPrefix;\r
-\r
-  /**\r
-   * Field nsURI\r
-   */\r
-  private java.lang.String nsURI;\r
-\r
-  /**\r
-   * Field xmlName\r
-   */\r
-  private java.lang.String xmlName;\r
-\r
-  /**\r
-   * Field identity\r
-   */\r
-  private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public ViewportDescriptor()\r
-  {\r
-    super();\r
-    nsURI = "www.jalview.org";\r
-    xmlName = "Viewport";\r
-\r
-    //-- set grouping compositor\r
-    setCompositorAsSequence();\r
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
-    org.exolab.castor.xml.XMLFieldHandler handler = null;\r
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
-    //-- initialize attribute descriptors\r
-\r
-    //-- _conservationSelected\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_conservationSelected", "conservationSelected",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public ViewportDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "Viewport";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _conservationSelected\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasConservationSelected())\r
+                    return null;\r
+                return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteConservationSelected();\r
+                        return;\r
+                    }\r
+                    target.setConservationSelected( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _conservationSelected\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _pidSelected\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasPidSelected())\r
+                    return null;\r
+                return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deletePidSelected();\r
+                        return;\r
+                    }\r
+                    target.setPidSelected( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _pidSelected\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _bgColour\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getBgColour();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setBgColour( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _bgColour\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _consThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasConsThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getConsThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteConsThreshold();\r
+                        return;\r
+                    }\r
+                    target.setConsThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _consThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _pidThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasPidThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getPidThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deletePidThreshold();\r
+                        return;\r
+                    }\r
+                    target.setPidThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _pidThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _title\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getTitle();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setTitle( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _title\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showFullId\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowFullId())\r
+                    return null;\r
+                return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowFullId();\r
+                        return;\r
+                    }\r
+                    target.setShowFullId( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showFullId\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _rightAlignIds\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasRightAlignIds())\r
+                    return null;\r
+                return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteRightAlignIds();\r
+                        return;\r
+                    }\r
+                    target.setRightAlignIds( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _rightAlignIds\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showText\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowText())\r
+                    return null;\r
+                return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowText();\r
+                        return;\r
+                    }\r
+                    target.setShowText( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showText\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showColourText\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowColourText())\r
+                    return null;\r
+                return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowColourText();\r
+                        return;\r
+                    }\r
+                    target.setShowColourText( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showColourText\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showBoxes\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowBoxes())\r
+                    return null;\r
+                return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowBoxes();\r
+                        return;\r
+                    }\r
+                    target.setShowBoxes( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showBoxes\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _wrapAlignment\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasWrapAlignment())\r
+                    return null;\r
+                return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteWrapAlignment();\r
+                        return;\r
+                    }\r
+                    target.setWrapAlignment( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _wrapAlignment\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _renderGaps\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasRenderGaps())\r
+                    return null;\r
+                return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteRenderGaps();\r
+                        return;\r
+                    }\r
+                    target.setRenderGaps( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _renderGaps\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showSequenceFeatures\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowSequenceFeatures())\r
+                    return null;\r
+                return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowSequenceFeatures();\r
+                        return;\r
+                    }\r
+                    target.setShowSequenceFeatures( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showSequenceFeatures\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showAnnotation\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasShowAnnotation())\r
+                    return null;\r
+                return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowAnnotation();\r
+                        return;\r
+                    }\r
+                    target.setShowAnnotation( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showAnnotation\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _xpos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasXpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getXpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteXpos();\r
+                        return;\r
+                    }\r
+                    target.setXpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _xpos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _ypos\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasYpos())\r
+                    return null;\r
+                return new java.lang.Integer(target.getYpos());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteYpos();\r
+                        return;\r
+                    }\r
+                    target.setYpos( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _ypos\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _width\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasWidth())\r
+                    return null;\r
+                return new java.lang.Integer(target.getWidth());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteWidth();\r
+                        return;\r
+                    }\r
+                    target.setWidth( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _width\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _height\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasHeight())\r
+                    return null;\r
+                return new java.lang.Integer(target.getHeight());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteHeight();\r
+                        return;\r
+                    }\r
+                    target.setHeight( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _height\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _startRes\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasStartRes())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStartRes());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteStartRes();\r
+                        return;\r
+                    }\r
+                    target.setStartRes( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _startRes\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _startSeq\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasStartSeq())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStartSeq());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteStartSeq();\r
+                        return;\r
+                    }\r
+                    target.setStartSeq( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _startSeq\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontName\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getFontName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setFontName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontName\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontSize\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasFontSize())\r
+                    return null;\r
+                return new java.lang.Integer(target.getFontSize());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteFontSize();\r
+                        return;\r
+                    }\r
+                    target.setFontSize( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontSize\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _fontStyle\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasFontStyle())\r
+                    return null;\r
+                return new java.lang.Integer(target.getFontStyle());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteFontStyle();\r
+                        return;\r
+                    }\r
+                    target.setFontStyle( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _fontStyle\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _viewName\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getViewName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setViewName( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _viewName\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _sequenceSetId\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getSequenceSetId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setSequenceSetId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequenceSetId\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _gatheredViews\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasGatheredViews())\r
+                    return null;\r
+                return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteGatheredViews();\r
+                        return;\r
+                    }\r
+                    target.setGatheredViews( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _gatheredViews\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textCol1\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasTextCol1())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextCol1());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextCol1();\r
+                        return;\r
+                    }\r
+                    target.setTextCol1( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textCol1\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textCol2\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasTextCol2())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextCol2());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextCol2();\r
+                        return;\r
+                    }\r
+                    target.setTextCol2( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textCol2\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _textColThreshold\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                if(!target.hasTextColThreshold())\r
+                    return null;\r
+                return new java.lang.Integer(target.getTextColThreshold());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteTextColThreshold();\r
+                        return;\r
+                    }\r
+                    target.setTextColThreshold( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _textColThreshold\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _annotationColours\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getAnnotationColours();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.AnnotationColours();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _annotationColours\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _hiddenColumnsList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getHiddenColumns();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.HiddenColumns();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hiddenColumnsList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+    } //-- jalview.schemabinding.version2.ViewportDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasConservationSelected())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getConservationSelected() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteConservationSelected();\r
-            return;\r
-          }\r
-          target.setConservationSelected( ( (java.lang.Boolean) value).\r
-                                         booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _conservationSelected\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _pidSelected\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_pidSelected", "pidSelected",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasPidSelected())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getPidSelected() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deletePidSelected();\r
-            return;\r
-          }\r
-          target.setPidSelected( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
         return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _pidSelected\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _bgColour\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_bgColour", "bgColour",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getBgColour();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setBgColour( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _bgColour\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _consThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_consThreshold", "consThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasConsThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getConsThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteConsThreshold();\r
-            return;\r
-          }\r
-          target.setConsThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _consThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _pidThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_pidThreshold", "pidThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasPidThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getPidThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deletePidThreshold();\r
-            return;\r
-          }\r
-          target.setPidThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _pidThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _title\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_title", "title",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return jalview.schemabinding.version2.Viewport.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getTitle();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setTitle( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _title\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showFullId\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showFullId", "showFullId",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowFullId())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowFullId() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowFullId();\r
-            return;\r
-          }\r
-          target.setShowFullId( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showFullId\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _rightAlignIds\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_rightAlignIds", "rightAlignIds",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasRightAlignIds())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getRightAlignIds() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteRightAlignIds();\r
-            return;\r
-          }\r
-          target.setRightAlignIds( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _rightAlignIds\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showText\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showText", "showText",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
     {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowText())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowText() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowText();\r
-            return;\r
-          }\r
-          target.setShowText( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showText\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showColourText\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showColourText", "showColourText",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowColourText())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowColourText() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowColourText();\r
-            return;\r
-          }\r
-          target.setShowColourText( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showColourText\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showBoxes\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showBoxes", "showBoxes",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowBoxes())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowBoxes() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowBoxes();\r
-            return;\r
-          }\r
-          target.setShowBoxes( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showBoxes\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _wrapAlignment\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_wrapAlignment", "wrapAlignment",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasWrapAlignment())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getWrapAlignment() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteWrapAlignment();\r
-            return;\r
-          }\r
-          target.setWrapAlignment( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _wrapAlignment\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _renderGaps\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_renderGaps", "renderGaps",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasRenderGaps())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getRenderGaps() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteRenderGaps();\r
-            return;\r
-          }\r
-          target.setRenderGaps( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _renderGaps\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showSequenceFeatures\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowSequenceFeatures())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowSequenceFeatures();\r
-            return;\r
-          }\r
-          target.setShowSequenceFeatures( ( (java.lang.Boolean) value).\r
-                                         booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showSequenceFeatures\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _showAnnotation\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_showAnnotation", "showAnnotation",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasShowAnnotation())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getShowAnnotation() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteShowAnnotation();\r
-            return;\r
-          }\r
-          target.setShowAnnotation( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _showAnnotation\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _xpos\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasXpos())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getXpos());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteXpos();\r
-            return;\r
-          }\r
-          target.setXpos( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _xpos\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _ypos\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasYpos())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getYpos());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteYpos();\r
-            return;\r
-          }\r
-          target.setYpos( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _ypos\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _width\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_width", "width",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasWidth())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getWidth());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteWidth();\r
-            return;\r
-          }\r
-          target.setWidth( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _width\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _height\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_height", "height",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasHeight())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getHeight());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteHeight();\r
-            return;\r
-          }\r
-          target.setHeight( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _height\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _startRes\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_startRes", "startRes",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasStartRes())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getStartRes());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteStartRes();\r
-            return;\r
-          }\r
-          target.setStartRes( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _startRes\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _startSeq\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_startSeq", "startSeq",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasStartSeq())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getStartSeq());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteStartSeq();\r
-            return;\r
-          }\r
-          target.setStartSeq( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _startSeq\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontName\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_fontName", "fontName",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getFontName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setFontName( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontName\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontSize\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_fontSize", "fontSize",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasFontSize())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getFontSize());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteFontSize();\r
-            return;\r
-          }\r
-          target.setFontSize( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontSize\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _fontStyle\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_fontStyle", "fontStyle",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasFontStyle())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getFontStyle());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteFontStyle();\r
-            return;\r
-          }\r
-          target.setFontStyle( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _fontStyle\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _viewName\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_viewName", "viewName",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getViewName();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setViewName( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _viewName\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _sequenceSetId\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        String.class, "_sequenceSetId", "sequenceSetId",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    desc.setImmutable(true);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getSequenceSetId();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setSequenceSetId( (java.lang.String) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _sequenceSetId\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      StringValidator typeValidator = new StringValidator();\r
-      typeValidator.setWhiteSpace("preserve");\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _gatheredViews\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Boolean.TYPE, "_gatheredViews", "gatheredViews",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasGatheredViews())\r
-        {\r
-          return null;\r
-        }\r
-        return (target.getGatheredViews() ? java.lang.Boolean.TRUE :\r
-                java.lang.Boolean.FALSE);\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteGatheredViews();\r
-            return;\r
-          }\r
-          target.setGatheredViews( ( (java.lang.Boolean) value).booleanValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _gatheredViews\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      BooleanValidator typeValidator = new BooleanValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textCol1\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textCol1", "textCol1",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasTextCol1())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextCol1());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextCol1();\r
-            return;\r
-          }\r
-          target.setTextCol1( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textCol1\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textCol2\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textCol2", "textCol2",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasTextCol2())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextCol2());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextCol2();\r
-            return;\r
-          }\r
-          target.setTextCol2( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textCol2\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _textColThreshold\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.\r
-        Integer.TYPE, "_textColThreshold", "textColThreshold",\r
-        org.exolab.castor.xml.NodeType.Attribute);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        if (!target.hasTextColThreshold())\r
-        {\r
-          return null;\r
-        }\r
-        return new java.lang.Integer(target.getTextColThreshold());\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          // if null, use delete method for optional primitives\r
-          if (value == null)\r
-          {\r
-            target.deleteTextColThreshold();\r
-            return;\r
-          }\r
-          target.setTextColThreshold( ( (java.lang.Integer) value).intValue());\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return null;\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _textColThreshold\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-      IntegerValidator typeValidator = new IntegerValidator();\r
-      fieldValidator.setValidator(typeValidator);\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- initialize element descriptors\r
-\r
-    //-- _annotationColours\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.AnnotationColours.class, "_annotationColours",\r
-        "AnnotationColours", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getAnnotationColours();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.setAnnotationColours( (jalview.schemabinding.version2.\r
-                                        AnnotationColours) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.AnnotationColours();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(false);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _annotationColours\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-    //-- _hiddenColumnsList\r
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.\r
-        schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList",\r
-        "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
-    handler = (new org.exolab.castor.xml.XMLFieldHandler()\r
-    {\r
-      public java.lang.Object getValue(java.lang.Object object)\r
-          throws IllegalStateException\r
-      {\r
-        Viewport target = (Viewport) object;\r
-        return target.getHiddenColumns();\r
-      }\r
-\r
-      public void setValue(java.lang.Object object, java.lang.Object value)\r
-          throws IllegalStateException, IllegalArgumentException\r
-      {\r
-        try\r
-        {\r
-          Viewport target = (Viewport) object;\r
-          target.addHiddenColumns( (jalview.schemabinding.version2.\r
-                                    HiddenColumns) value);\r
-        }\r
-        catch (java.lang.Exception ex)\r
-        {\r
-          throw new IllegalStateException(ex.toString());\r
-        }\r
-      }\r
-\r
-      public java.lang.Object newInstance(java.lang.Object parent)\r
-      {\r
-        return new jalview.schemabinding.version2.HiddenColumns();\r
-      }\r
-    });\r
-    desc.setHandler(handler);\r
-    desc.setNameSpaceURI("www.jalview.org");\r
-    desc.setMultivalued(true);\r
-    addFieldDescriptor(desc);\r
-\r
-    //-- validation code for: _hiddenColumnsList\r
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-    fieldValidator.setMinOccurs(0);\r
-    { //-- local scope\r
-    }\r
-    desc.setValidator(fieldValidator);\r
-  } //-- jalview.schemabinding.version2.ViewportDescriptor()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method getAccessMode\r
-   *\r
-   *\r
-   *\r
-   * @return AccessMode\r
-   */\r
-  public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()\r
-\r
-  /**\r
-   * Method getExtends\r
-   *\r
-   *\r
-   *\r
-   * @return ClassDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-  {\r
-    return null;\r
-  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-\r
-  /**\r
-   * Method getIdentity\r
-   *\r
-   *\r
-   *\r
-   * @return FieldDescriptor\r
-   */\r
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-  {\r
-    return identity;\r
-  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-\r
-  /**\r
-   * Method getJavaClass\r
-   *\r
-   *\r
-   *\r
-   * @return Class\r
-   */\r
-  public java.lang.Class getJavaClass()\r
-  {\r
-    return jalview.schemabinding.version2.Viewport.class;\r
-  } //-- java.lang.Class getJavaClass()\r
-\r
-  /**\r
-   * Method getNameSpacePrefix\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpacePrefix()\r
-  {\r
-    return nsPrefix;\r
-  } //-- java.lang.String getNameSpacePrefix()\r
-\r
-  /**\r
-   * Method getNameSpaceURI\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getNameSpaceURI()\r
-  {\r
-    return nsURI;\r
-  } //-- java.lang.String getNameSpaceURI()\r
-\r
-  /**\r
-   * Method getValidator\r
-   *\r
-   *\r
-   *\r
-   * @return TypeValidator\r
-   */\r
-  public org.exolab.castor.xml.TypeValidator getValidator()\r
-  {\r
-    return this;\r
-  } //-- org.exolab.castor.xml.TypeValidator getValidator()\r
-\r
-  /**\r
-   * Method getXMLName\r
-   *\r
-   *\r
-   *\r
-   * @return String\r
-   */\r
-  public java.lang.String getXMLName()\r
-  {\r
-    return xmlName;\r
-  } //-- java.lang.String getXMLName()\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
 \r
 }\r