X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FVAMSAS.java;h=320dcb56a80d3bbc14bc560c9ab8bbaaefc15dd5;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=2c8edc64378ce4a2062b332753019b44aa3bf6c9;hpb=a06295cc0912455e0bc53b26cb4e0134e6759d0f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/VAMSAS.java b/src/uk/ac/vamsas/objects/core/VAMSAS.java
index 2c8edc6..320dcb5 100644
--- a/src/uk/ac/vamsas/objects/core/VAMSAS.java
+++ b/src/uk/ac/vamsas/objects/core/VAMSAS.java
@@ -1,535 +1,735 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:VAMSAS.java 264 2006-12-14 17:42:54Z JimP $
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package uk.ac.vamsas.objects.core;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-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;
 
 /**
  * contains unassociated trees and a number of analysis sets
- *  
  * 
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * 
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ *          $
  */
-public class VAMSAS extends uk.ac.vamsas.client.Vobject 
-implements java.io.Serializable
-{
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Primary Key for vamsas object referencing 
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _modifiable
-     */
-    private java.lang.String _modifiable;
-
-    /**
-     * Field _treeList
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _dataSetList
-     */
-    private java.util.Vector _dataSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() 
-     {
-        super();
-        _treeList = new Vector();
-        _dataSetList = new Vector();
-    } //-- uk.ac.vamsas.objects.core.VAMSAS()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addDataSet
-     * 
-     * 
-     * 
-     * @param vDataSet
-     */
-    public void addDataSet(uk.ac.vamsas.objects.core.DataSet vDataSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dataSetList.addElement(vDataSet);
-    } //-- void addDataSet(uk.ac.vamsas.objects.core.DataSet) 
-
-    /**
-     * Method addDataSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDataSet
-     */
-    public void addDataSet(int index, uk.ac.vamsas.objects.core.DataSet vDataSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dataSetList.insertElementAt(vDataSet, index);
-    } //-- void addDataSet(int, uk.ac.vamsas.objects.core.DataSet) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param vTree
-     */
-    public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(uk.ac.vamsas.objects.core.Tree) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, uk.ac.vamsas.objects.core.Tree) 
-
-    /**
-     * Method enumerateDataSet
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateDataSet()
-    {
-        return _dataSetList.elements();
-    } //-- java.util.Enumeration enumerateDataSet() 
-
-    /**
-     * Method enumerateTree
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
-
-    /**
-     * Note: hashCode() has not been overriden
-     * 
-     * @param obj
-     * @return boolean
-     */
-    public boolean equals(java.lang.Object obj)
-    {
-        if ( this == obj )
-            return true;
-        
-        if (super.equals(obj)==false)
+public class VAMSAS extends uk.ac.vamsas.client.Vobject implements
+    java.io.Serializable {
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Primary Key for vamsas object referencing
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _modifiable.
+   */
+  private java.lang.String _modifiable;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _dataSetList.
+   */
+  private java.util.Vector _dataSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSAS() {
+    super();
+    this._treeList = new java.util.Vector();
+    this._dataSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vDataSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet)
+      throws java.lang.IndexOutOfBoundsException {
+    this._dataSetList.addElement(vDataSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDataSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDataSet(final int index,
+      final uk.ac.vamsas.objects.core.DataSet vDataSet)
+      throws java.lang.IndexOutOfBoundsException {
+    this._dataSetList.add(index, vDataSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final uk.ac.vamsas.objects.core.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index,
+      final uk.ac.vamsas.objects.core.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * Method enumerateDataSet.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.DataSet elements
+   */
+  public java.util.Enumeration enumerateDataSet() {
+    return this._dataSetList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Tree elements
+   */
+  public java.util.Enumeration enumerateTree() {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Overrides the java.lang.Object.equals method.
+   * 
+   * @param obj
+   * @return true if the objects are equal.
+   */
+  public boolean equals(final java.lang.Object obj) {
+    if (this == obj)
+      return true;
+
+    if (super.equals(obj) == false)
+      return false;
+
+    if (obj instanceof VAMSAS) {
+
+      VAMSAS temp = (VAMSAS) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._id != null) {
+        if (temp._id == null)
+          return false;
+        if (this._id != temp._id) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+            }
+            ;
             return false;
-        
-        if (obj instanceof VAMSAS) {
-        
-            VAMSAS temp = (VAMSAS)obj;
-            if (this._id != null) {
-                if (temp._id == null) return false;
-                else if (!(this._id.equals(temp._id))) 
-                    return false;
+          }
+          if (!thcycle) {
+            if (!this._id.equals(temp._id)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+              return false;
             }
-            else if (temp._id != null)
-                return false;
-            if (this._modifiable != null) {
-                if (temp._modifiable == null) return false;
-                else if (!(this._modifiable.equals(temp._modifiable))) 
-                    return false;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+          }
+        }
+      } else if (temp._id != null)
+        return false;
+      if (this._modifiable != null) {
+        if (temp._modifiable == null)
+          return false;
+        if (this._modifiable != temp._modifiable) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._modifiable);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._modifiable);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
             }
-            else if (temp._modifiable != null)
-                return false;
-            if (this._treeList != null) {
-                if (temp._treeList == null) return false;
-                else if (!(this._treeList.equals(temp._treeList))) 
-                    return false;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
             }
-            else if (temp._treeList != null)
-                return false;
-            if (this._dataSetList != null) {
-                if (temp._dataSetList == null) return false;
-                else if (!(this._dataSetList.equals(temp._dataSetList))) 
-                    return false;
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._modifiable.equals(temp._modifiable)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+              return false;
             }
-            else if (temp._dataSetList != null)
-                return false;
-            return true;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+          }
         }
+      } else if (temp._modifiable != null)
         return false;
-    } //-- boolean equals(java.lang.Object) 
-
-    /**
-     * Method getDataSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return DataSet
-     */
-    public uk.ac.vamsas.objects.core.DataSet getDataSet(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dataSetList.size())) {
-            throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
-        }
-        
-        return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.DataSet getDataSet(int) 
-
-    /**
-     * Method getDataSet
-     * 
-     * 
-     * 
-     * @return DataSet
-     */
-    public uk.ac.vamsas.objects.core.DataSet[] getDataSet()
-    {
-        int size = _dataSetList.size();
-        uk.ac.vamsas.objects.core.DataSet[] mArray = new uk.ac.vamsas.objects.core.DataSet[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.vamsas.objects.core.DataSet[] getDataSet() 
-
-    /**
-     * Method getDataSetCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getDataSetCount()
-    {
-        return _dataSetList.size();
-    } //-- int getDataSetCount() 
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     * referencing 
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'modifiable'.
-     * 
-     * @return String
-     * @return the value of field 'modifiable'.
-     */
-    public java.lang.String getModifiable()
-    {
-        return this._modifiable;
-    } //-- java.lang.String getModifiable() 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public uk.ac.vamsas.objects.core.Tree getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
-        }
-        
-        return (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.Tree getTree(int) 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @return Tree
-     */
-    public uk.ac.vamsas.objects.core.Tree[] getTree()
-    {
-        int size = _treeList.size();
-        uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.vamsas.objects.core.Tree[] 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) {
+      if (this._treeList != null) {
+        if (temp._treeList == null)
+          return false;
+        if (this._treeList != temp._treeList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._treeList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._treeList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+            }
+            ;
             return false;
+          }
+          if (!thcycle) {
+            if (!this._treeList.equals(temp._treeList)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+          }
         }
-        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 removeAllDataSet
-     * 
-     */
-    public void removeAllDataSet()
-    {
-        _dataSetList.removeAllElements();
-    } //-- void removeAllDataSet() 
-
-    /**
-     * Method removeAllTree
-     * 
-     */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
-
-    /**
-     * Method removeDataSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return DataSet
-     */
-    public uk.ac.vamsas.objects.core.DataSet removeDataSet(int index)
-    {
-        java.lang.Object obj = _dataSetList.elementAt(index);
-        _dataSetList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.DataSet) obj;
-    } //-- uk.ac.vamsas.objects.core.DataSet removeDataSet(int) 
-
-    /**
-     * Method removeTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public uk.ac.vamsas.objects.core.Tree removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.Tree) obj;
-    } //-- uk.ac.vamsas.objects.core.Tree removeTree(int) 
-
-    /**
-     * Method setDataSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDataSet
-     */
-    public void setDataSet(int index, uk.ac.vamsas.objects.core.DataSet vDataSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dataSetList.size())) {
-            throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
-        }
-        _dataSetList.setElementAt(vDataSet, index);
-    } //-- void setDataSet(int, uk.ac.vamsas.objects.core.DataSet) 
-
-    /**
-     * Method setDataSet
-     * 
-     * 
-     * 
-     * @param dataSetArray
-     */
-    public void setDataSet(uk.ac.vamsas.objects.core.DataSet[] dataSetArray)
-    {
-        //-- copy array
-        _dataSetList.removeAllElements();
-        for (int i = 0; i < dataSetArray.length; i++) {
-            _dataSetList.addElement(dataSetArray[i]);
-        }
-    } //-- void setDataSet(uk.ac.vamsas.objects.core.DataSet) 
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     * referencing 
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'modifiable'.
-     * 
-     * @param modifiable the value of field 'modifiable'.
-     */
-    public void setModifiable(java.lang.String modifiable)
-    {
-        this._modifiable = modifiable;
-    } //-- void setModifiable(java.lang.String) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void setTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
-        }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, uk.ac.vamsas.objects.core.Tree) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param treeArray
-     */
-    public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
-    {
-        //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
+      } else if (temp._treeList != null)
+        return false;
+      if (this._dataSetList != null) {
+        if (temp._dataSetList == null)
+          return false;
+        if (this._dataSetList != temp._dataSetList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._dataSetList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._dataSetList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._dataSetList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._dataSetList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._dataSetList.equals(temp._dataSetList)) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._dataSetList);
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._dataSetList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
+          }
         }
-    } //-- void setTree(uk.ac.vamsas.objects.core.Tree) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return VAMSAS
-     */
-    public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VAMSAS.class, reader);
-    } //-- uk.ac.vamsas.objects.core.VAMSAS 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() 
+      } else if (temp._dataSetList != null)
+        return false;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Method getDataSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the uk.ac.vamsas.objects.core.DataSet at the given
+   *         index
+   */
+  public uk.ac.vamsas.objects.core.DataSet getDataSet(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._dataSetList.size()) {
+      throw new IndexOutOfBoundsException("getDataSet: Index value '" + index
+          + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.get(index);
+  }
+
+  /**
+   * Method getDataSet.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.DataSet[] getDataSet() {
+    uk.ac.vamsas.objects.core.DataSet[] array = new uk.ac.vamsas.objects.core.DataSet[0];
+    return (uk.ac.vamsas.objects.core.DataSet[]) this._dataSetList
+        .toArray(array);
+  }
+
+  /**
+   * Method getDataSetAsReference.Returns a reference to '_dataSetList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getDataSetAsReference() {
+    return this._dataSetList;
+  }
+
+  /**
+   * Method getDataSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getDataSetCount() {
+    return this._dataSetList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Primary Key for vamsas object referencing
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId() {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'modifiable'.
+   * 
+   * @return the value of field 'Modifiable'.
+   */
+  public java.lang.String getModifiable() {
+    return this._modifiable;
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the uk.ac.vamsas.objects.core.Tree at the given index
+   */
+  public uk.ac.vamsas.objects.core.Tree getTree(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size()) {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+          + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.Tree[] getTree() {
+    uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
+    return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeAsReference.Returns a reference to '_treeList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getTreeAsReference() {
+    return this._treeList;
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount() {
+    return this._treeList.size();
+  }
+
+  /**
+   * Overrides the java.lang.Object.hashCode method.
+   * <p>
+   * The following steps came from <b>Effective Java Programming Language
+   * Guide</b> by Joshua Bloch, Chapter 3
+   * 
+   * @return a hash code value for the object.
+   */
+  public int hashCode() {
+    int result = super.hashCode();
+
+    long tmp;
+    if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+      result = 37 * result + _id.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+    }
+    if (_modifiable != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
+      result = 37 * result + _modifiable.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
+    }
+    if (_treeList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
+      result = 37 * result + _treeList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
+    }
+    if (_dataSetList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
+      result = 37 * result + _dataSetList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
+    }
+
+    return result;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid() {
+    try {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex) {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllDataSet() {
+    this._dataSetList.clear();
+  }
+
+  /**
+     */
+  public void removeAllTree() {
+    this._treeList.clear();
+  }
+
+  /**
+   * Method removeDataSet.
+   * 
+   * @param vDataSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet) {
+    boolean removed = _dataSetList.remove(vDataSet);
+    return removed;
+  }
+
+  /**
+   * Method removeDataSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.DataSet removeDataSetAt(final int index) {
+    java.lang.Object obj = this._dataSetList.remove(index);
+    return (uk.ac.vamsas.objects.core.DataSet) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (uk.ac.vamsas.objects.core.Tree) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDataSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setDataSet(final int index,
+      final uk.ac.vamsas.objects.core.DataSet vDataSet)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._dataSetList.size()) {
+      throw new IndexOutOfBoundsException("setDataSet: Index value '" + index
+          + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
+    }
+
+    this._dataSetList.set(index, vDataSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vDataSetArray
+   */
+  public void setDataSet(final uk.ac.vamsas.objects.core.DataSet[] vDataSetArray) {
+    // -- copy array
+    _dataSetList.clear();
+
+    for (int i = 0; i < vDataSetArray.length; i++) {
+      this._dataSetList.add(vDataSetArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_dataSetList' by copying the given Vector. All elements
+   * will be checked for type safety.
+   * 
+   * @param vDataSetList
+   *          the Vector to copy.
+   */
+  public void setDataSet(final java.util.Vector vDataSetList) {
+    // copy vector
+    this._dataSetList.clear();
+
+    this._dataSetList.addAll(vDataSetList);
+  }
+
+  /**
+   * Sets the value of '_dataSetList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param dataSetVector
+   *          the Vector to set.
+   */
+  public void setDataSetAsReference(final java.util.Vector dataSetVector) {
+    this._dataSetList = dataSetVector;
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * Primary Key for vamsas object referencing
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id) {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'modifiable'.
+   * 
+   * @param modifiable
+   *          the value of field 'modifiable'.
+   */
+  public void setModifiable(final java.lang.String modifiable) {
+    this._modifiable = modifiable;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index,
+      final uk.ac.vamsas.objects.core.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size()) {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+          + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++) {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_treeList' by copying the given Vector. All elements
+   * will be checked for type safety.
+   * 
+   * @param vTreeList
+   *          the Vector to copy.
+   */
+  public void setTree(final java.util.Vector vTreeList) {
+    // copy vector
+    this._treeList.clear();
+
+    this._treeList.addAll(vTreeList);
+  }
+
+  /**
+   * Sets the value of '_treeList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param treeVector
+   *          the Vector to set.
+   */
+  public void setTreeAsReference(final java.util.Vector treeVector) {
+    this._treeList = treeVector;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled uk.ac.vamsas.objects.core.VAMSAS
+   */
+  public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(
+      final java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(
+        uk.ac.vamsas.objects.core.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }