X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=b4237b85bf82880a9d5374673c94f37bae3243d0;hb=e3cad17c5dba620dafc8459295ecc959cbe52938;hp=037bd3dffee233e7ba9b0dc8af2596ebe2a059c1;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 037bd3d..b4237b8 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with
+ * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,585 +7,570 @@
 
 package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
 
-import org.exolab.castor.xml.*;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
 
 /**
  * Class VAMSAS.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS
-    implements java.io.Serializable
-{
-
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
-
-  /**
-   * Field _alignmentList
-   */
-  private java.util.Vector _alignmentList;
-
-  /**
-   * Field _treeList
-   */
-  private java.util.Vector _treeList;
-
-  /**
-   * Field _sequenceSetList
-   */
-  private java.util.Vector _sequenceSetList;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public VAMSAS()
-  {
-    super();
-    _alignmentList = new Vector();
-    _treeList = new Vector();
-    _sequenceSetList = new Vector();
-  } //-- jalview.binding.VAMSAS()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addAlignment
-   *
-   *
-   *
-   * @param vAlignment
-   */
-  public void addAlignment(jalview.binding.Alignment vAlignment)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _alignmentList.addElement(vAlignment);
-  } //-- void addAlignment(jalview.binding.Alignment)
-
-  /**
-   * Method addAlignment
-   *
-   *
-   *
-   * @param index
-   * @param vAlignment
-   */
-  public void addAlignment(int index, jalview.binding.Alignment vAlignment)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _alignmentList.insertElementAt(vAlignment, index);
-  } //-- void addAlignment(int, jalview.binding.Alignment)
-
-  /**
-   * Method addSequenceSet
-   *
-   *
-   *
-   * @param vSequenceSet
-   */
-  public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _sequenceSetList.addElement(vSequenceSet);
-  } //-- void addSequenceSet(jalview.binding.SequenceSet)
-
-  /**
-   * Method addSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @param vSequenceSet
-   */
-  public void addSequenceSet(int index,
-                             jalview.binding.SequenceSet vSequenceSet)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _sequenceSetList.insertElementAt(vSequenceSet, index);
-  } //-- void addSequenceSet(int, jalview.binding.SequenceSet)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param vTree
-   */
-  public void addTree(java.lang.String vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.addElement(vTree);
-  } //-- void addTree(java.lang.String)
-
-  /**
-   * Method addTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void addTree(int index, java.lang.String vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, java.lang.String)
-
-  /**
-   * Method enumerateAlignment
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateAlignment()
-  {
-    return _alignmentList.elements();
-  } //-- java.util.Enumeration enumerateAlignment()
-
-  /**
-   * Method enumerateSequenceSet
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateSequenceSet()
-  {
-    return _sequenceSetList.elements();
-  } //-- java.util.Enumeration enumerateSequenceSet()
-
-  /**
-   * Method enumerateTree
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateTree()
-  {
-    return _treeList.elements();
-  } //-- java.util.Enumeration enumerateTree()
-
-  /**
-   * Method getAlignment
-   *
-   *
-   *
-   * @param index
-   * @return Alignment
-   */
-  public jalview.binding.Alignment getAlignment(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _alignmentList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.Alignment) _alignmentList.elementAt(index);
-  } //-- jalview.binding.Alignment getAlignment(int)
-
-  /**
-   * Method getAlignment
-   *
-   *
-   *
-   * @return Alignment
-   */
-  public jalview.binding.Alignment[] getAlignment()
-  {
-    int size = _alignmentList.size();
-    jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(
-          index);
-    }
-    return mArray;
-  } //-- jalview.binding.Alignment[] getAlignment()
-
-  /**
-   * Method getAlignmentCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getAlignmentCount()
-  {
-    return _alignmentList.size();
-  } //-- int getAlignmentCount()
-
-  /**
-   * Method getSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @return SequenceSet
-   */
-  public jalview.binding.SequenceSet getSequenceSet(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _sequenceSetList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
-  } //-- jalview.binding.SequenceSet getSequenceSet(int)
-
-  /**
-   * Method getSequenceSet
-   *
-   *
-   *
-   * @return SequenceSet
-   */
-  public jalview.binding.SequenceSet[] getSequenceSet()
-  {
-    int size = _sequenceSetList.size();
-    jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(
-          index);
-    }
-    return mArray;
-  } //-- jalview.binding.SequenceSet[] getSequenceSet()
-
-  /**
-   * Method getSequenceSetCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getSequenceSetCount()
-  {
-    return _sequenceSetList.size();
-  } //-- int getSequenceSetCount()
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @param index
-   * @return String
-   */
-  public java.lang.String getTree(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (String) _treeList.elementAt(index);
-  } //-- java.lang.String getTree(int)
-
-  /**
-   * Method getTree
-   *
-   *
-   *
-   * @return String
-   */
-  public java.lang.String[] getTree()
-  {
-    int size = _treeList.size();
-    java.lang.String[] mArray = new java.lang.String[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (String) _treeList.elementAt(index);
-    }
-    return mArray;
-  } //-- java.lang.String[] getTree()
-
-  /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getTreeCount()
-  {
-    return _treeList.size();
-  } //-- int getTreeCount()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    }
-    catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  } //-- boolean isValid()
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param out
-   */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
-
-  /**
-   * Method marshal
-   *
-   *
-   *
-   * @param handler
-   */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-
-    Marshaller.marshal(this, handler);
-  } //-- void marshal(org.xml.sax.ContentHandler)
-
-  /**
-   * Method removeAlignment
-   *
-   *
-   *
-   * @param index
-   * @return Alignment
-   */
-  public jalview.binding.Alignment removeAlignment(int index)
-  {
-    java.lang.Object obj = _alignmentList.elementAt(index);
-    _alignmentList.removeElementAt(index);
-    return (jalview.binding.Alignment) obj;
-  } //-- jalview.binding.Alignment removeAlignment(int)
-
-  /**
-   * Method removeAllAlignment
-   *
-   */
-  public void removeAllAlignment()
-  {
-    _alignmentList.removeAllElements();
-  } //-- void removeAllAlignment()
-
-  /**
-   * Method removeAllSequenceSet
-   *
-   */
-  public void removeAllSequenceSet()
-  {
-    _sequenceSetList.removeAllElements();
-  } //-- void removeAllSequenceSet()
-
-  /**
-   * Method removeAllTree
-   *
-   */
-  public void removeAllTree()
-  {
-    _treeList.removeAllElements();
-  } //-- void removeAllTree()
-
-  /**
-   * Method removeSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @return SequenceSet
-   */
-  public jalview.binding.SequenceSet removeSequenceSet(int index)
-  {
-    java.lang.Object obj = _sequenceSetList.elementAt(index);
-    _sequenceSetList.removeElementAt(index);
-    return (jalview.binding.SequenceSet) obj;
-  } //-- jalview.binding.SequenceSet removeSequenceSet(int)
-
-  /**
-   * Method removeTree
-   *
-   *
-   *
-   * @param index
-   * @return String
-   */
-  public java.lang.String removeTree(int index)
-  {
-    java.lang.Object obj = _treeList.elementAt(index);
-    _treeList.removeElementAt(index);
-    return (String) obj;
-  } //-- java.lang.String removeTree(int)
-
-  /**
-   * Method setAlignment
-   *
-   *
-   *
-   * @param index
-   * @param vAlignment
-   */
-  public void setAlignment(int index, jalview.binding.Alignment vAlignment)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _alignmentList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _alignmentList.setElementAt(vAlignment, index);
-  } //-- void setAlignment(int, jalview.binding.Alignment)
-
-  /**
-   * Method setAlignment
-   *
-   *
-   *
-   * @param alignmentArray
-   */
-  public void setAlignment(jalview.binding.Alignment[] alignmentArray)
-  {
-    //-- copy array
-    _alignmentList.removeAllElements();
-    for (int i = 0; i < alignmentArray.length; i++)
-    {
-      _alignmentList.addElement(alignmentArray[i]);
-    }
-  } //-- void setAlignment(jalview.binding.Alignment)
-
-  /**
-   * Method setSequenceSet
-   *
-   *
-   *
-   * @param index
-   * @param vSequenceSet
-   */
-  public void setSequenceSet(int index,
-                             jalview.binding.SequenceSet vSequenceSet)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _sequenceSetList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _sequenceSetList.setElementAt(vSequenceSet, index);
-  } //-- void setSequenceSet(int, jalview.binding.SequenceSet)
-
-  /**
-   * Method setSequenceSet
-   *
-   *
-   *
-   * @param sequenceSetArray
-   */
-  public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
-  {
-    //-- copy array
-    _sequenceSetList.removeAllElements();
-    for (int i = 0; i < sequenceSetArray.length; i++)
-    {
-      _sequenceSetList.addElement(sequenceSetArray[i]);
-    }
-  } //-- void setSequenceSet(jalview.binding.SequenceSet)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param index
-   * @param vTree
-   */
-  public void setTree(int index, java.lang.String vTree)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
-    {
-      throw new IndexOutOfBoundsException();
-    }
-    _treeList.setElementAt(vTree, index);
-  } //-- void setTree(int, java.lang.String)
-
-  /**
-   * Method setTree
-   *
-   *
-   *
-   * @param treeArray
-   */
-  public void setTree(java.lang.String[] treeArray)
-  {
-    //-- copy array
-    _treeList.removeAllElements();
-    for (int i = 0; i < treeArray.length; i++)
-    {
-      _treeList.addElement(treeArray[i]);
-    }
-  } //-- void setTree(java.lang.String)
-
-  /**
-   * Method unmarshal
-   *
-   *
-   *
-   * @param reader
-   * @return Object
-   */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.
-        VAMSAS.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
-
-  /**
-   * Method validate
-   *
-   */
-  public void validate()
-      throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
-        Validator();
-    validator.validate(this);
-  } //-- void validate()
+public class VAMSAS implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _alignmentList
+     */
+    private java.util.Vector _alignmentList;
+
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _sequenceSetList
+     */
+    private java.util.Vector _sequenceSetList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VAMSAS() {
+        super();
+        _alignmentList = new Vector();
+        _treeList = new Vector();
+        _sequenceSetList = new Vector();
+    } //-- jalview.binding.VAMSAS()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addAlignment
+     * 
+     * 
+     * 
+     * @param vAlignment
+     */
+    public void addAlignment(jalview.binding.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentList.addElement(vAlignment);
+    } //-- void addAlignment(jalview.binding.Alignment) 
+
+    /**
+     * Method addAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignment
+     */
+    public void addAlignment(int index, jalview.binding.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentList.insertElementAt(vAlignment, index);
+    } //-- void addAlignment(int, jalview.binding.Alignment) 
+
+    /**
+     * Method addSequenceSet
+     * 
+     * 
+     * 
+     * @param vSequenceSet
+     */
+    public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceSetList.addElement(vSequenceSet);
+    } //-- void addSequenceSet(jalview.binding.SequenceSet) 
+
+    /**
+     * Method addSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     */
+    public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceSetList.insertElementAt(vSequenceSet, index);
+    } //-- void addSequenceSet(int, jalview.binding.SequenceSet) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(java.lang.String) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, java.lang.String) 
+
+    /**
+     * Method enumerateAlignment
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAlignment()
+    {
+        return _alignmentList.elements();
+    } //-- java.util.Enumeration enumerateAlignment() 
+
+    /**
+     * Method enumerateSequenceSet
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSequenceSet()
+    {
+        return _sequenceSetList.elements();
+    } //-- java.util.Enumeration enumerateSequenceSet() 
+
+    /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
+     * Method getAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @return Alignment
+     */
+    public jalview.binding.Alignment getAlignment(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Alignment) _alignmentList.elementAt(index);
+    } //-- jalview.binding.Alignment getAlignment(int) 
+
+    /**
+     * Method getAlignment
+     * 
+     * 
+     * 
+     * @return Alignment
+     */
+    public jalview.binding.Alignment[] getAlignment()
+    {
+        int size = _alignmentList.size();
+        jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Alignment[] getAlignment() 
+
+    /**
+     * Method getAlignmentCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAlignmentCount()
+    {
+        return _alignmentList.size();
+    } //-- int getAlignmentCount() 
+
+    /**
+     * Method getSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @return SequenceSet
+     */
+    public jalview.binding.SequenceSet getSequenceSet(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
+    } //-- jalview.binding.SequenceSet getSequenceSet(int) 
+
+    /**
+     * Method getSequenceSet
+     * 
+     * 
+     * 
+     * @return SequenceSet
+     */
+    public jalview.binding.SequenceSet[] getSequenceSet()
+    {
+        int size = _sequenceSetList.size();
+        jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.SequenceSet[] getSequenceSet() 
+
+    /**
+     * Method getSequenceSetCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSequenceSetCount()
+    {
+        return _sequenceSetList.size();
+    } //-- int getSequenceSetCount() 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (String)_treeList.elementAt(index);
+    } //-- java.lang.String getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String[] getTree()
+    {
+        int size = _treeList.size();
+        java.lang.String[] mArray = new java.lang.String[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (String)_treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- java.lang.String[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @return Alignment
+     */
+    public jalview.binding.Alignment removeAlignment(int index)
+    {
+        java.lang.Object obj = _alignmentList.elementAt(index);
+        _alignmentList.removeElementAt(index);
+        return (jalview.binding.Alignment) obj;
+    } //-- jalview.binding.Alignment removeAlignment(int) 
+
+    /**
+     * Method removeAllAlignment
+     * 
+     */
+    public void removeAllAlignment()
+    {
+        _alignmentList.removeAllElements();
+    } //-- void removeAllAlignment() 
+
+    /**
+     * Method removeAllSequenceSet
+     * 
+     */
+    public void removeAllSequenceSet()
+    {
+        _sequenceSetList.removeAllElements();
+    } //-- void removeAllSequenceSet() 
+
+    /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
+     * Method removeSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @return SequenceSet
+     */
+    public jalview.binding.SequenceSet removeSequenceSet(int index)
+    {
+        java.lang.Object obj = _sequenceSetList.elementAt(index);
+        _sequenceSetList.removeElementAt(index);
+        return (jalview.binding.SequenceSet) obj;
+    } //-- jalview.binding.SequenceSet removeSequenceSet(int) 
+
+    /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (String)obj;
+    } //-- java.lang.String removeTree(int) 
+
+    /**
+     * Method setAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignment
+     */
+    public void setAlignment(int index, jalview.binding.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _alignmentList.setElementAt(vAlignment, index);
+    } //-- void setAlignment(int, jalview.binding.Alignment) 
+
+    /**
+     * Method setAlignment
+     * 
+     * 
+     * 
+     * @param alignmentArray
+     */
+    public void setAlignment(jalview.binding.Alignment[] alignmentArray)
+    {
+        //-- copy array
+        _alignmentList.removeAllElements();
+        for (int i = 0; i < alignmentArray.length; i++) {
+            _alignmentList.addElement(alignmentArray[i]);
+        }
+    } //-- void setAlignment(jalview.binding.Alignment) 
+
+    /**
+     * Method setSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     */
+    public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _sequenceSetList.setElementAt(vSequenceSet, index);
+    } //-- void setSequenceSet(int, jalview.binding.SequenceSet) 
+
+    /**
+     * Method setSequenceSet
+     * 
+     * 
+     * 
+     * @param sequenceSetArray
+     */
+    public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
+    {
+        //-- copy array
+        _sequenceSetList.removeAllElements();
+        for (int i = 0; i < sequenceSetArray.length; i++) {
+            _sequenceSetList.addElement(sequenceSetArray[i]);
+        }
+    } //-- void setSequenceSet(jalview.binding.SequenceSet) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, java.lang.String) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(java.lang.String[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
 
 }