/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

  //---------------------------------/
 //- 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;

/**
 * Class Alignment.
 * 
 * @version $Revision$ $Date$
 */
public class Alignment extends uk.ac.vamsas.client.Vobject 
implements java.io.Serializable
{


      //--------------------------/
     //- Class/Member Variables -/
    //--------------------------/

    /**
     * Field _gapChar
     */
    private java.lang.String _gapChar;

    /**
     * Field _aligned
     */
    private boolean _aligned;

    /**
     * keeps track of state for field: _aligned
     */
    private boolean _has_aligned;

    /**
     * Primary Key for vamsas object referencing
     *  
     */
    private java.lang.String _id;

    /**
     * Field _modifiable
     */
    private java.lang.String _modifiable;

    /**
     * This is annotation over the coordinate frame
     *  defined by all the columns in the alignment.
     *  
     */
    private java.util.Vector _alignmentAnnotationList;

    /**
     * Field _treeList
     */
    private java.util.Vector _treeList;

    /**
     * Field _alignmentSequenceList
     */
    private java.util.Vector _alignmentSequenceList;

    /**
     * typical properties may be additional
     *  alignment score objects 
     */
    private java.util.Vector _propertyList;

    /**
     * Field _provenance
     */
    private uk.ac.vamsas.objects.core.Provenance _provenance;


      //----------------/
     //- Constructors -/
    //----------------/

    public Alignment() 
     {
        super();
        _alignmentAnnotationList = new Vector();
        _treeList = new Vector();
        _alignmentSequenceList = new Vector();
        _propertyList = new Vector();
    } //-- uk.ac.vamsas.objects.core.Alignment()


      //-----------/
     //- Methods -/
    //-----------/

    /**
     * Method addAlignmentAnnotation
     * 
     * 
     * 
     * @param vAlignmentAnnotation
     */
    public void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentAnnotationList.addElement(vAlignmentAnnotation);
    } //-- void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation) 

    /**
     * Method addAlignmentAnnotation
     * 
     * 
     * 
     * @param index
     * @param vAlignmentAnnotation
     */
    public void addAlignmentAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
    } //-- void addAlignmentAnnotation(int, uk.ac.vamsas.objects.core.AlignmentAnnotation) 

    /**
     * Method addAlignmentSequence
     * 
     * 
     * 
     * @param vAlignmentSequence
     */
    public void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentSequenceList.addElement(vAlignmentSequence);
    } //-- void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence) 

    /**
     * Method addAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @param vAlignmentSequence
     */
    public void addAlignmentSequence(int index, uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
    } //-- void addAlignmentSequence(int, uk.ac.vamsas.objects.core.AlignmentSequence) 

    /**
     * Method addProperty
     * 
     * 
     * 
     * @param vProperty
     */
    public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        _propertyList.addElement(vProperty);
    } //-- void addProperty(uk.ac.vamsas.objects.core.Property) 

    /**
     * Method addProperty
     * 
     * 
     * 
     * @param index
     * @param vProperty
     */
    public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        _propertyList.insertElementAt(vProperty, index);
    } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property) 

    /**
     * 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 deleteAligned
     * 
     */
    public void deleteAligned()
    {
        this._has_aligned= false;
    } //-- void deleteAligned() 

    /**
     * Method enumerateAlignmentAnnotation
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateAlignmentAnnotation()
    {
        return _alignmentAnnotationList.elements();
    } //-- java.util.Enumeration enumerateAlignmentAnnotation() 

    /**
     * Method enumerateAlignmentSequence
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateAlignmentSequence()
    {
        return _alignmentSequenceList.elements();
    } //-- java.util.Enumeration enumerateAlignmentSequence() 

    /**
     * Method enumerateProperty
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateProperty()
    {
        return _propertyList.elements();
    } //-- java.util.Enumeration enumerateProperty() 

    /**
     * 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)
            return false;
        
        if (obj instanceof Alignment) {
        
            Alignment temp = (Alignment)obj;
            if (this._gapChar != null) {
                if (temp._gapChar == null) return false;
                else if (!(this._gapChar.equals(temp._gapChar))) 
                    return false;
            }
            else if (temp._gapChar != null)
                return false;
            if (this._aligned != temp._aligned)
                return false;
            if (this._has_aligned != temp._has_aligned)
                return false;
            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._modifiable != null) {
                if (temp._modifiable == null) return false;
                else if (!(this._modifiable.equals(temp._modifiable))) 
                    return false;
            }
            else if (temp._modifiable != null)
                return false;
            if (this._alignmentAnnotationList != null) {
                if (temp._alignmentAnnotationList == null) return false;
                else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList))) 
                    return false;
            }
            else if (temp._alignmentAnnotationList != null)
                return false;
            if (this._treeList != null) {
                if (temp._treeList == null) return false;
                else if (!(this._treeList.equals(temp._treeList))) 
                    return false;
            }
            else if (temp._treeList != null)
                return false;
            if (this._alignmentSequenceList != null) {
                if (temp._alignmentSequenceList == null) return false;
                else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList))) 
                    return false;
            }
            else if (temp._alignmentSequenceList != null)
                return false;
            if (this._propertyList != null) {
                if (temp._propertyList == null) return false;
                else if (!(this._propertyList.equals(temp._propertyList))) 
                    return false;
            }
            else if (temp._propertyList != 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 'aligned'.
     * 
     * @return boolean
     * @return the value of field 'aligned'.
     */
    public boolean getAligned()
    {
        return this._aligned;
    } //-- boolean getAligned() 

    /**
     * Method getAlignmentAnnotation
     * 
     * 
     * 
     * @param index
     * @return AlignmentAnnotation
     */
    public uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _alignmentAnnotationList.size())) {
            throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int) 

    /**
     * Method getAlignmentAnnotation
     * 
     * 
     * 
     * @return AlignmentAnnotation
     */
    public uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
    {
        int size = _alignmentAnnotationList.size();
        uk.ac.vamsas.objects.core.AlignmentAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentAnnotation[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() 

    /**
     * Method getAlignmentAnnotationCount
     * 
     * 
     * 
     * @return int
     */
    public int getAlignmentAnnotationCount()
    {
        return _alignmentAnnotationList.size();
    } //-- int getAlignmentAnnotationCount() 

    /**
     * Method getAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @return AlignmentSequence
     */
    public uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _alignmentSequenceList.size())) {
            throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int) 

    /**
     * Method getAlignmentSequence
     * 
     * 
     * 
     * @return AlignmentSequence
     */
    public uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
    {
        int size = _alignmentSequenceList.size();
        uk.ac.vamsas.objects.core.AlignmentSequence[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequence[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() 

    /**
     * Method getAlignmentSequenceCount
     * 
     * 
     * 
     * @return int
     */
    public int getAlignmentSequenceCount()
    {
        return _alignmentSequenceList.size();
    } //-- int getAlignmentSequenceCount() 

    /**
     * Returns the value of field 'gapChar'.
     * 
     * @return String
     * @return the value of field 'gapChar'.
     */
    public java.lang.String getGapChar()
    {
        return this._gapChar;
    } //-- java.lang.String getGapChar() 

    /**
     * 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 getProperty
     * 
     * 
     * 
     * @param index
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property getProperty(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _propertyList.size())) {
            throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.Property getProperty(int) 

    /**
     * Method getProperty
     * 
     * 
     * 
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property[] getProperty()
    {
        int size = _propertyList.size();
        uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.Property[] getProperty() 

    /**
     * Method getPropertyCount
     * 
     * 
     * 
     * @return int
     */
    public int getPropertyCount()
    {
        return _propertyList.size();
    } //-- int getPropertyCount() 

    /**
     * Returns the value of field 'provenance'.
     * 
     * @return Provenance
     * @return the value of field 'provenance'.
     */
    public uk.ac.vamsas.objects.core.Provenance getProvenance()
    {
        return this._provenance;
    } //-- uk.ac.vamsas.objects.core.Provenance getProvenance() 

    /**
     * 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 hasAligned
     * 
     * 
     * 
     * @return boolean
     */
    public boolean hasAligned()
    {
        return this._has_aligned;
    } //-- boolean hasAligned() 

    /**
     * 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 removeAlignmentAnnotation
     * 
     * 
     * 
     * @param index
     * @return AlignmentAnnotation
     */
    public uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
    {
        java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
        _alignmentAnnotationList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.AlignmentAnnotation) obj;
    } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int) 

    /**
     * Method removeAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @return AlignmentSequence
     */
    public uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
    {
        java.lang.Object obj = _alignmentSequenceList.elementAt(index);
        _alignmentSequenceList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.AlignmentSequence) obj;
    } //-- uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int) 

    /**
     * Method removeAllAlignmentAnnotation
     * 
     */
    public void removeAllAlignmentAnnotation()
    {
        _alignmentAnnotationList.removeAllElements();
    } //-- void removeAllAlignmentAnnotation() 

    /**
     * Method removeAllAlignmentSequence
     * 
     */
    public void removeAllAlignmentSequence()
    {
        _alignmentSequenceList.removeAllElements();
    } //-- void removeAllAlignmentSequence() 

    /**
     * Method removeAllProperty
     * 
     */
    public void removeAllProperty()
    {
        _propertyList.removeAllElements();
    } //-- void removeAllProperty() 

    /**
     * Method removeAllTree
     * 
     */
    public void removeAllTree()
    {
        _treeList.removeAllElements();
    } //-- void removeAllTree() 

    /**
     * Method removeProperty
     * 
     * 
     * 
     * @param index
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property removeProperty(int index)
    {
        java.lang.Object obj = _propertyList.elementAt(index);
        _propertyList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.Property) obj;
    } //-- uk.ac.vamsas.objects.core.Property removeProperty(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) 

    /**
     * Sets the value of field 'aligned'.
     * 
     * @param aligned the value of field 'aligned'.
     */
    public void setAligned(boolean aligned)
    {
        this._aligned = aligned;
        this._has_aligned = true;
    } //-- void setAligned(boolean) 

    /**
     * Method setAlignmentAnnotation
     * 
     * 
     * 
     * @param index
     * @param vAlignmentAnnotation
     */
    public void setAlignmentAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _alignmentAnnotationList.size())) {
            throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
        }
        _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
    } //-- void setAlignmentAnnotation(int, uk.ac.vamsas.objects.core.AlignmentAnnotation) 

    /**
     * Method setAlignmentAnnotation
     * 
     * 
     * 
     * @param alignmentAnnotationArray
     */
    public void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
    {
        //-- copy array
        _alignmentAnnotationList.removeAllElements();
        for (int i = 0; i < alignmentAnnotationArray.length; i++) {
            _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
        }
    } //-- void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation) 

    /**
     * Method setAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @param vAlignmentSequence
     */
    public void setAlignmentSequence(int index, uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _alignmentSequenceList.size())) {
            throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
        }
        _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
    } //-- void setAlignmentSequence(int, uk.ac.vamsas.objects.core.AlignmentSequence) 

    /**
     * Method setAlignmentSequence
     * 
     * 
     * 
     * @param alignmentSequenceArray
     */
    public void setAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
    {
        //-- copy array
        _alignmentSequenceList.removeAllElements();
        for (int i = 0; i < alignmentSequenceArray.length; i++) {
            _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
        }
    } //-- void setAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence) 

    /**
     * Sets the value of field 'gapChar'.
     * 
     * @param gapChar the value of field 'gapChar'.
     */
    public void setGapChar(java.lang.String gapChar)
    {
        this._gapChar = gapChar;
    } //-- void setGapChar(java.lang.String) 

    /**
     * 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 setProperty
     * 
     * 
     * 
     * @param index
     * @param vProperty
     */
    public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _propertyList.size())) {
            throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
        }
        _propertyList.setElementAt(vProperty, index);
    } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property) 

    /**
     * Method setProperty
     * 
     * 
     * 
     * @param propertyArray
     */
    public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
    {
        //-- copy array
        _propertyList.removeAllElements();
        for (int i = 0; i < propertyArray.length; i++) {
            _propertyList.addElement(propertyArray[i]);
        }
    } //-- void setProperty(uk.ac.vamsas.objects.core.Property) 

    /**
     * Sets the value of field 'provenance'.
     * 
     * @param provenance the value of field 'provenance'.
     */
    public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
    {
        this._provenance = provenance;
    } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance) 

    /**
     * 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]);
        }
    } //-- void setTree(uk.ac.vamsas.objects.core.Tree) 

    /**
     * Method unmarshal
     * 
     * 
     * 
     * @param reader
     * @return Alignment
     */
    public static uk.ac.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        return (uk.ac.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Alignment.class, reader);
    } //-- uk.ac.vamsas.objects.core.Alignment 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() 

}