From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 20 Sep 2005 10:13:56 +0000 (+0000)
Subject: objects from refactored schema.
X-Git-Tag: Release_0.2~483
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c062fe4c183d567877484f0229631dc555ddc9f5;p=vamsas.git

objects from refactored schema.


git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@37 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr
index 415b24d..ce4c376 100644
--- a/src/org/vamsas/objects/core/.castor.cdr
+++ b/src/org/vamsas/objects/core/.castor.cdr
@@ -1,20 +1,18 @@
 -- listing properties --
-org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor
-org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes...
-org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
 org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte...
-org.vamsas.objects.core.TreeType=org.vamsas.objects.core.TreeTypeDescr...
-org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
-org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
-org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
-org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
-org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
-org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
-org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
+org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
+org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor
 org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr...
+org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
 org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr...
 org.vamsas.objects.core.Entry=org.vamsas.objects.core.EntryDescriptor
+org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
+org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
 org.vamsas.objects.core.SequenceSet=org.vamsas.objects.core.SequenceSetDe...
+org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
 org.vamsas.objects.core.ApplicationData=org.vamsas.objects.core.ApplicationDa...
-org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
-org.vamsas.objects.core.Dendro=org.vamsas.objects.core.DendroDescriptor
+org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
+org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes...
+org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
+org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
+org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java
index 8e20b93..684f619 100644
--- a/src/org/vamsas/objects/core/AlignmentDescriptor.java
+++ b/src/org/vamsas/objects/core/AlignmentDescriptor.java
@@ -103,7 +103,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         }
         desc.setValidator(fieldValidator);
         //-- _treeList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
diff --git a/src/org/vamsas/objects/core/Dendro.java b/src/org/vamsas/objects/core/Dendro.java
deleted file mode 100644
index eb04f13..0000000
--- a/src/org/vamsas/objects/core/Dendro.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-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 Dendro.
- * 
- * @version $Revision$ $Date$
- */
-public class Dendro extends TreeType 
-implements java.io.Serializable
-{
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Dendro() 
-     {
-        super();
-    } //-- org.vamsas.objects.core.Dendro()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 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)
-            return false;
-        
-        if (obj instanceof Dendro) {
-        
-            Dendro temp = (Dendro)obj;
-            return true;
-        }
-        return false;
-    } //-- boolean equals(java.lang.Object) 
-
-    /**
-     * 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 unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Dendro
-     */
-    public static org.vamsas.objects.core.Dendro unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (org.vamsas.objects.core.Dendro) Unmarshaller.unmarshal(org.vamsas.objects.core.Dendro.class, reader);
-    } //-- org.vamsas.objects.core.Dendro 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() 
-
-}
diff --git a/src/org/vamsas/objects/core/DendroDescriptor.java b/src/org/vamsas/objects/core/DendroDescriptor.java
deleted file mode 100644
index 1b3cc2f..0000000
--- a/src/org/vamsas/objects/core/DendroDescriptor.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
-
-/**
- * Class DendroDescriptor.
- * 
- * @version $Revision$ $Date$
- */
-public class DendroDescriptor extends TreeTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DendroDescriptor() 
-     {
-        super();
-        setExtendsWithoutFlatten(new TreeTypeDescriptor());
-        nsURI = "http://www.vamsas.org";
-        xmlName = "Dendro";
-    } //-- org.vamsas.objects.core.DendroDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return org.vamsas.objects.core.Dendro.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
-
-}
diff --git a/src/org/vamsas/objects/core/SequenceSet.java b/src/org/vamsas/objects/core/SequenceSet.java
index f41fdc0..816da66 100644
--- a/src/org/vamsas/objects/core/SequenceSet.java
+++ b/src/org/vamsas/objects/core/SequenceSet.java
@@ -73,9 +73,9 @@ implements java.io.Serializable
     private java.util.Vector _alignmentList;
 
     /**
-     * Field _tree
+     * Field _treeList
      */
-    private org.vamsas.objects.core.Tree _tree;
+    private java.util.Vector _treeList;
 
     /**
      * Field _provenance
@@ -93,6 +93,7 @@ implements java.io.Serializable
         _sequenceList = new Vector();
         _sequenceSetAnnotationsList = new Vector();
         _alignmentList = new Vector();
+        _treeList = new Vector();
     } //-- org.vamsas.objects.core.SequenceSet()
 
 
@@ -182,6 +183,33 @@ implements java.io.Serializable
     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations) 
 
     /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(org.vamsas.objects.core.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(org.vamsas.objects.core.Tree) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, org.vamsas.objects.core.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, org.vamsas.objects.core.Tree) 
+
+    /**
      * Method deleteAligned
      * 
      */
@@ -227,6 +255,18 @@ implements java.io.Serializable
     } //-- java.util.Enumeration enumerateSequenceSetAnnotations() 
 
     /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -282,12 +322,12 @@ implements java.io.Serializable
             }
             else if (temp._alignmentList != null)
                 return false;
-            if (this._tree != null) {
-                if (temp._tree == null) return false;
-                else if (!(this._tree.equals(temp._tree))) 
+            if (this._treeList != null) {
+                if (temp._treeList == null) return false;
+                else if (!(this._treeList.equals(temp._treeList))) 
                     return false;
             }
-            else if (temp._tree != null)
+            else if (temp._treeList != null)
                 return false;
             if (this._provenance != null) {
                 if (temp._provenance == null) return false;
@@ -490,15 +530,52 @@ implements java.io.Serializable
     } //-- int getSequenceSetAnnotationsCount() 
 
     /**
-     * Returns the value of field 'tree'.
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public org.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 (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+    } //-- org.vamsas.objects.core.Tree getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
      * 
      * @return Tree
-     * @return the value of field 'tree'.
      */
-    public org.vamsas.objects.core.Tree getTree()
+    public org.vamsas.objects.core.Tree[] getTree()
     {
-        return this._tree;
-    } //-- org.vamsas.objects.core.Tree getTree() 
+        int size = _treeList.size();
+        org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.Tree[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
 
     /**
      * Method hasAligned
@@ -601,6 +678,15 @@ implements java.io.Serializable
     } //-- void removeAllSequenceSetAnnotations() 
 
     /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
      * Method removeSequence
      * 
      * 
@@ -631,6 +717,21 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int) 
 
     /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public org.vamsas.objects.core.Tree removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (org.vamsas.objects.core.Tree) obj;
+    } //-- org.vamsas.objects.core.Tree removeTree(int) 
+
+    /**
      * Sets the value of field 'aligned'.
      * 
      * @param aligned the value of field 'aligned'.
@@ -774,13 +875,37 @@ implements java.io.Serializable
     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations) 
 
     /**
-     * Sets the value of field 'tree'.
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, org.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, org.vamsas.objects.core.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
      * 
-     * @param tree the value of field 'tree'.
+     * @param treeArray
      */
-    public void setTree(org.vamsas.objects.core.Tree tree)
+    public void setTree(org.vamsas.objects.core.Tree[] treeArray)
     {
-        this._tree = tree;
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
     } //-- void setTree(org.vamsas.objects.core.Tree) 
 
     /**
diff --git a/src/org/vamsas/objects/core/SequenceSetDescriptor.java b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
index 0f05d2a..5c4242a 100644
--- a/src/org/vamsas/objects/core/SequenceSetDescriptor.java
+++ b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
@@ -289,8 +289,8 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
-        //-- _tree
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_tree", "tree", org.exolab.castor.xml.NodeType.Element);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
@@ -303,7 +303,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             {
                 try {
                     SequenceSet target = (SequenceSet) object;
-                    target.setTree( (org.vamsas.objects.core.Tree) value);
+                    target.addTree( (org.vamsas.objects.core.Tree) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -315,13 +315,12 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         };
         desc.setHandler(handler);
         desc.setNameSpaceURI("http://www.vamsas.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
+        desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _tree
+        //-- validation code for: _treeList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
+        fieldValidator.setMinOccurs(0);
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java
index 8290635..ddb22b8 100644
--- a/src/org/vamsas/objects/core/Tree.java
+++ b/src/org/vamsas/objects/core/Tree.java
@@ -15,6 +15,8 @@ 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;
@@ -26,11 +28,31 @@ import org.xml.sax.ContentHandler;
  * 
  * @version $Revision$ $Date$
  */
-public class Tree extends TreeType 
+public class Tree extends org.vamsas.client.object 
 implements java.io.Serializable
 {
 
 
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _newickFormatList
+     */
+    private java.util.Vector _newickFormatList;
+
+    /**
+     * Field _provenance
+     */
+    private org.vamsas.objects.core.Provenance _provenance;
+
+
       //----------------/
      //- Constructors -/
     //----------------/
@@ -38,6 +60,7 @@ implements java.io.Serializable
     public Tree() 
      {
         super();
+        _newickFormatList = new Vector();
     } //-- org.vamsas.objects.core.Tree()
 
 
@@ -46,6 +69,45 @@ implements java.io.Serializable
     //-----------/
 
     /**
+     * Method addNewickFormat
+     * 
+     * 
+     * 
+     * @param vNewickFormat
+     */
+    public void addNewickFormat(java.lang.String vNewickFormat)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _newickFormatList.addElement(vNewickFormat);
+    } //-- void addNewickFormat(java.lang.String) 
+
+    /**
+     * Method addNewickFormat
+     * 
+     * 
+     * 
+     * @param index
+     * @param vNewickFormat
+     */
+    public void addNewickFormat(int index, java.lang.String vNewickFormat)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _newickFormatList.insertElementAt(vNewickFormat, index);
+    } //-- void addNewickFormat(int, java.lang.String) 
+
+    /**
+     * Method enumerateNewickFormat
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateNewickFormat()
+    {
+        return _newickFormatList.elements();
+    } //-- java.util.Enumeration enumerateNewickFormat() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -62,12 +124,103 @@ implements java.io.Serializable
         if (obj instanceof Tree) {
         
             Tree temp = (Tree)obj;
+            if (this._id != null) {
+                if (temp._id == null) return false;
+                else if (!(this._id.equals(temp._id))) 
+                    return false;
+            }
+            else if (temp._id != null)
+                return false;
+            if (this._newickFormatList != null) {
+                if (temp._newickFormatList == null) return false;
+                else if (!(this._newickFormatList.equals(temp._newickFormatList))) 
+                    return false;
+            }
+            else if (temp._newickFormatList != null)
+                return false;
+            if (this._provenance != null) {
+                if (temp._provenance == null) return false;
+                else if (!(this._provenance.equals(temp._provenance))) 
+                    return false;
+            }
+            else if (temp._provenance != null)
+                return false;
             return true;
         }
         return false;
     } //-- boolean equals(java.lang.Object) 
 
     /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Method getNewickFormat
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String getNewickFormat(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _newickFormatList.size())) {
+            throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        }
+        
+        return (String)_newickFormatList.elementAt(index);
+    } //-- java.lang.String getNewickFormat(int) 
+
+    /**
+     * Method getNewickFormat
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String[] getNewickFormat()
+    {
+        int size = _newickFormatList.size();
+        java.lang.String[] mArray = new java.lang.String[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (String)_newickFormatList.elementAt(index);
+        }
+        return mArray;
+    } //-- java.lang.String[] getNewickFormat() 
+
+    /**
+     * Method getNewickFormatCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getNewickFormatCount()
+    {
+        return _newickFormatList.size();
+    } //-- int getNewickFormatCount() 
+
+    /**
+     * Returns the value of field 'provenance'.
+     * 
+     * @return Provenance
+     * @return the value of field 'provenance'.
+     */
+    public org.vamsas.objects.core.Provenance getProvenance()
+    {
+        return this._provenance;
+    } //-- org.vamsas.objects.core.Provenance getProvenance() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -114,6 +267,84 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Method removeAllNewickFormat
+     * 
+     */
+    public void removeAllNewickFormat()
+    {
+        _newickFormatList.removeAllElements();
+    } //-- void removeAllNewickFormat() 
+
+    /**
+     * Method removeNewickFormat
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String removeNewickFormat(int index)
+    {
+        java.lang.Object obj = _newickFormatList.elementAt(index);
+        _newickFormatList.removeElementAt(index);
+        return (String)obj;
+    } //-- java.lang.String removeNewickFormat(int) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Method setNewickFormat
+     * 
+     * 
+     * 
+     * @param index
+     * @param vNewickFormat
+     */
+    public void setNewickFormat(int index, java.lang.String vNewickFormat)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _newickFormatList.size())) {
+            throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        }
+        _newickFormatList.setElementAt(vNewickFormat, index);
+    } //-- void setNewickFormat(int, java.lang.String) 
+
+    /**
+     * Method setNewickFormat
+     * 
+     * 
+     * 
+     * @param newickFormatArray
+     */
+    public void setNewickFormat(java.lang.String[] newickFormatArray)
+    {
+        //-- copy array
+        _newickFormatList.removeAllElements();
+        for (int i = 0; i < newickFormatArray.length; i++) {
+            _newickFormatList.addElement(newickFormatArray[i]);
+        }
+    } //-- void setNewickFormat(java.lang.String) 
+
+    /**
+     * Sets the value of field 'provenance'.
+     * 
+     * @param provenance the value of field 'provenance'.
+     */
+    public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+    {
+        this._provenance = provenance;
+    } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
+
+    /**
      * Method unmarshal
      * 
      * 
diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java
index b0012ef..af3b115 100644
--- a/src/org/vamsas/objects/core/TreeDescriptor.java
+++ b/src/org/vamsas/objects/core/TreeDescriptor.java
@@ -21,7 +21,7 @@ import org.exolab.castor.xml.validators.*;
  * 
  * @version $Revision$ $Date$
  */
-public class TreeDescriptor extends TreeTypeDescriptor {
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
 
 
       //--------------------------/
@@ -56,9 +56,128 @@ public class TreeDescriptor extends TreeTypeDescriptor {
     public TreeDescriptor() 
      {
         super();
-        setExtendsWithoutFlatten(new TreeTypeDescriptor());
         nsURI = "http://www.vamsas.org";
-        xmlName = "tree";
+        xmlName = "Tree";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        this.identity = desc;
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.String();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _newickFormatList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getNewickFormat();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.addNewickFormat( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _newickFormatList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
     } //-- org.vamsas.objects.core.TreeDescriptor()
 
 
@@ -87,7 +206,7 @@ public class TreeDescriptor extends TreeTypeDescriptor {
      */
     public org.exolab.castor.mapping.ClassDescriptor getExtends()
     {
-        return super.getExtends();
+        return null;
     } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
 
     /**
@@ -99,8 +218,6 @@ public class TreeDescriptor extends TreeTypeDescriptor {
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity()
     {
-        if (identity == null)
-            return super.getIdentity();
         return identity;
     } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
 
diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java
index 12a81f2..0cd3f56 100644
--- a/src/org/vamsas/objects/core/VAMSAS.java
+++ b/src/org/vamsas/objects/core/VAMSAS.java
@@ -43,9 +43,9 @@ implements java.io.Serializable
     private java.lang.String _id;
 
     /**
-     * Field _dendroList
+     * Field _treeList
      */
-    private java.util.Vector _dendroList;
+    private java.util.Vector _treeList;
 
     /**
      * Field _sequenceSetList
@@ -60,7 +60,7 @@ implements java.io.Serializable
     public VAMSAS() 
      {
         super();
-        _dendroList = new Vector();
+        _treeList = new Vector();
         _sequenceSetList = new Vector();
     } //-- org.vamsas.objects.core.VAMSAS()
 
@@ -70,82 +70,82 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addDendro
+     * Method addSequenceSet
      * 
      * 
      * 
-     * @param vDendro
+     * @param vSequenceSet
      */
-    public void addDendro(org.vamsas.objects.core.Dendro vDendro)
+    public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _dendroList.addElement(vDendro);
-    } //-- void addDendro(org.vamsas.objects.core.Dendro) 
+        _sequenceSetList.addElement(vSequenceSet);
+    } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) 
 
     /**
-     * Method addDendro
+     * Method addSequenceSet
      * 
      * 
      * 
      * @param index
-     * @param vDendro
+     * @param vSequenceSet
      */
-    public void addDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+    public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
         throws java.lang.IndexOutOfBoundsException
     {
-        _dendroList.insertElementAt(vDendro, index);
-    } //-- void addDendro(int, org.vamsas.objects.core.Dendro) 
+        _sequenceSetList.insertElementAt(vSequenceSet, index);
+    } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
 
     /**
-     * Method addSequenceSet
+     * Method addTree
      * 
      * 
      * 
-     * @param vSequenceSet
+     * @param vTree
      */
-    public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addTree(org.vamsas.objects.core.Tree vTree)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet) 
+        _treeList.addElement(vTree);
+    } //-- void addTree(org.vamsas.objects.core.Tree) 
 
     /**
-     * Method addSequenceSet
+     * Method addTree
      * 
      * 
      * 
      * @param index
-     * @param vSequenceSet
+     * @param vTree
      */
-    public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+    public void addTree(int index, org.vamsas.objects.core.Tree vTree)
         throws java.lang.IndexOutOfBoundsException
     {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet) 
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, org.vamsas.objects.core.Tree) 
 
     /**
-     * Method enumerateDendro
+     * Method enumerateSequenceSet
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateDendro()
+    public java.util.Enumeration enumerateSequenceSet()
     {
-        return _dendroList.elements();
-    } //-- java.util.Enumeration enumerateDendro() 
+        return _sequenceSetList.elements();
+    } //-- java.util.Enumeration enumerateSequenceSet() 
 
     /**
-     * Method enumerateSequenceSet
+     * Method enumerateTree
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequenceSet()
+    public java.util.Enumeration enumerateTree()
     {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -171,12 +171,12 @@ implements java.io.Serializable
             }
             else if (temp._id != null)
                 return false;
-            if (this._dendroList != null) {
-                if (temp._dendroList == null) return false;
-                else if (!(this._dendroList.equals(temp._dendroList))) 
+            if (this._treeList != null) {
+                if (temp._treeList == null) return false;
+                else if (!(this._treeList.equals(temp._treeList))) 
                     return false;
             }
-            else if (temp._dendroList != null)
+            else if (temp._treeList != null)
                 return false;
             if (this._sequenceSetList != null) {
                 if (temp._sequenceSetList == null) return false;
@@ -191,111 +191,111 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getDendro
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Method getSequenceSet
      * 
      * 
      * 
      * @param index
-     * @return Dendro
+     * @return SequenceSet
      */
-    public org.vamsas.objects.core.Dendro getDendro(int index)
+    public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _dendroList.size())) {
-            throw new IndexOutOfBoundsException("getDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+        if ((index < 0) || (index > _sequenceSetList.size())) {
+            throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
-    } //-- org.vamsas.objects.core.Dendro getDendro(int) 
+        return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+    } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) 
 
     /**
-     * Method getDendro
+     * Method getSequenceSet
      * 
      * 
      * 
-     * @return Dendro
+     * @return SequenceSet
      */
-    public org.vamsas.objects.core.Dendro[] getDendro()
+    public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
     {
-        int size = _dendroList.size();
-        org.vamsas.objects.core.Dendro[] mArray = new org.vamsas.objects.core.Dendro[size];
+        int size = _sequenceSetList.size();
+        org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.Dendro[] getDendro() 
+    } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() 
 
     /**
-     * Method getDendroCount
+     * Method getSequenceSetCount
      * 
      * 
      * 
      * @return int
      */
-    public int getDendroCount()
-    {
-        return _dendroList.size();
-    } //-- int getDendroCount() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
+    public int getSequenceSetCount()
     {
-        return this._id;
-    } //-- java.lang.String getId() 
+        return _sequenceSetList.size();
+    } //-- int getSequenceSetCount() 
 
     /**
-     * Method getSequenceSet
+     * Method getTree
      * 
      * 
      * 
      * @param index
-     * @return SequenceSet
+     * @return Tree
      */
-    public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+    public org.vamsas.objects.core.Tree getTree(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int) 
+        return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+    } //-- org.vamsas.objects.core.Tree getTree(int) 
 
     /**
-     * Method getSequenceSet
+     * Method getTree
      * 
      * 
      * 
-     * @return SequenceSet
+     * @return Tree
      */
-    public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+    public org.vamsas.objects.core.Tree[] getTree()
     {
-        int size = _sequenceSetList.size();
-        org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+        int size = _treeList.size();
+        org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet() 
+    } //-- org.vamsas.objects.core.Tree[] getTree() 
 
     /**
-     * Method getSequenceSetCount
+     * Method getTreeCount
      * 
      * 
      * 
      * @return int
      */
-    public int getSequenceSetCount()
+    public int getTreeCount()
     {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
+        return _treeList.size();
+    } //-- int getTreeCount() 
 
     /**
      * Method isValid
@@ -344,15 +344,6 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllDendro
-     * 
-     */
-    public void removeAllDendro()
-    {
-        _dendroList.removeAllElements();
-    } //-- void removeAllDendro() 
-
-    /**
      * Method removeAllSequenceSet
      * 
      */
@@ -362,19 +353,13 @@ implements java.io.Serializable
     } //-- void removeAllSequenceSet() 
 
     /**
-     * Method removeDendro
+     * Method removeAllTree
      * 
-     * 
-     * 
-     * @param index
-     * @return Dendro
      */
-    public org.vamsas.objects.core.Dendro removeDendro(int index)
+    public void removeAllTree()
     {
-        java.lang.Object obj = _dendroList.elementAt(index);
-        _dendroList.removeElementAt(index);
-        return (org.vamsas.objects.core.Dendro) obj;
-    } //-- org.vamsas.objects.core.Dendro removeDendro(int) 
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
 
     /**
      * Method removeSequenceSet
@@ -392,38 +377,19 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int) 
 
     /**
-     * Method setDendro
+     * Method removeTree
      * 
      * 
      * 
      * @param index
-     * @param vDendro
+     * @return Tree
      */
-    public void setDendro(int index, org.vamsas.objects.core.Dendro vDendro)
-        throws java.lang.IndexOutOfBoundsException
+    public org.vamsas.objects.core.Tree removeTree(int index)
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dendroList.size())) {
-            throw new IndexOutOfBoundsException("setDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
-        }
-        _dendroList.setElementAt(vDendro, index);
-    } //-- void setDendro(int, org.vamsas.objects.core.Dendro) 
-
-    /**
-     * Method setDendro
-     * 
-     * 
-     * 
-     * @param dendroArray
-     */
-    public void setDendro(org.vamsas.objects.core.Dendro[] dendroArray)
-    {
-        //-- copy array
-        _dendroList.removeAllElements();
-        for (int i = 0; i < dendroArray.length; i++) {
-            _dendroList.addElement(dendroArray[i]);
-        }
-    } //-- void setDendro(org.vamsas.objects.core.Dendro) 
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (org.vamsas.objects.core.Tree) obj;
+    } //-- org.vamsas.objects.core.Tree removeTree(int) 
 
     /**
      * Sets the value of field 'id'.
@@ -470,6 +436,40 @@ implements java.io.Serializable
     } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet) 
 
     /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, org.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, org.vamsas.objects.core.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(org.vamsas.objects.core.Tree[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(org.vamsas.objects.core.Tree) 
+
+    /**
      * Method unmarshal
      * 
      * 
diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java
index e46ddd0..a691eda 100644
--- a/src/org/vamsas/objects/core/VAMSASDescriptor.java
+++ b/src/org/vamsas/objects/core/VAMSASDescriptor.java
@@ -102,28 +102,28 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
-        //-- _dendroList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Dendro.class, "_dendroList", "Dendro", org.exolab.castor.xml.NodeType.Element);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 VAMSAS target = (VAMSAS) object;
-                return target.getDendro();
+                return target.getTree();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     VAMSAS target = (VAMSAS) object;
-                    target.addDendro( (org.vamsas.objects.core.Dendro) value);
+                    target.addTree( (org.vamsas.objects.core.Tree) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
                 }
             }
             public java.lang.Object newInstance( java.lang.Object parent ) {
-                return new org.vamsas.objects.core.Dendro();
+                return new org.vamsas.objects.core.Tree();
             }
         };
         desc.setHandler(handler);
@@ -131,7 +131,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _dendroList
+        //-- validation code for: _treeList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(0);
         { //-- local scope