/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

  //---------------------------------/
 //- Imported classes and packages -/
//---------------------------------/

import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;

/**
 * Class DataSet.
 * 
 * @version $Revision$ $Date$
 */
public class DataSet 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 _sequenceList.
     */
    private java.util.Vector _sequenceList;

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

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

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

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

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


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

    public DataSet() {
        super();
        this._sequenceList = new java.util.Vector();
        this._sequenceMappingList = new java.util.Vector();
        this._dataSetAnnotationsList = new java.util.Vector();
        this._alignmentList = new java.util.Vector();
        this._treeList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vAlignment
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAlignment(
            final uk.ac.vamsas.objects.core.Alignment vAlignment)
    throws java.lang.IndexOutOfBoundsException {
        this._alignmentList.addElement(vAlignment);
    }

    /**
     * 
     * 
     * @param index
     * @param vAlignment
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAlignment(
            final int index,
            final uk.ac.vamsas.objects.core.Alignment vAlignment)
    throws java.lang.IndexOutOfBoundsException {
        this._alignmentList.add(index, vAlignment);
    }

    /**
     * 
     * 
     * @param vDataSetAnnotations
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDataSetAnnotations(
            final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
    throws java.lang.IndexOutOfBoundsException {
        this._dataSetAnnotationsList.addElement(vDataSetAnnotations);
    }

    /**
     * 
     * 
     * @param index
     * @param vDataSetAnnotations
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDataSetAnnotations(
            final int index,
            final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
    throws java.lang.IndexOutOfBoundsException {
        this._dataSetAnnotationsList.add(index, vDataSetAnnotations);
    }

    /**
     * 
     * 
     * @param vSequence
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSequence(
            final uk.ac.vamsas.objects.core.Sequence vSequence)
    throws java.lang.IndexOutOfBoundsException {
        this._sequenceList.addElement(vSequence);
    }

    /**
     * 
     * 
     * @param index
     * @param vSequence
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSequence(
            final int index,
            final uk.ac.vamsas.objects.core.Sequence vSequence)
    throws java.lang.IndexOutOfBoundsException {
        this._sequenceList.add(index, vSequence);
    }

    /**
     * 
     * 
     * @param vSequenceMapping
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSequenceMapping(
            final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
    throws java.lang.IndexOutOfBoundsException {
        this._sequenceMappingList.addElement(vSequenceMapping);
    }

    /**
     * 
     * 
     * @param index
     * @param vSequenceMapping
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSequenceMapping(
            final int index,
            final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
    throws java.lang.IndexOutOfBoundsException {
        this._sequenceMappingList.add(index, vSequenceMapping);
    }

    /**
     * 
     * 
     * @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 enumerateAlignment.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Alignment elements
     */
    public java.util.Enumeration enumerateAlignment(
    ) {
        return this._alignmentList.elements();
    }

    /**
     * Method enumerateDataSetAnnotations.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.DataSetAnnotations elements
     */
    public java.util.Enumeration enumerateDataSetAnnotations(
    ) {
        return this._dataSetAnnotationsList.elements();
    }

    /**
     * Method enumerateSequence.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Sequence elements
     */
    public java.util.Enumeration enumerateSequence(
    ) {
        return this._sequenceList.elements();
    }

    /**
     * Method enumerateSequenceMapping.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.SequenceMapping elements
     */
    public java.util.Enumeration enumerateSequenceMapping(
    ) {
        return this._sequenceMappingList.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 DataSet) {
        
            DataSet temp = (DataSet)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 (!thcycle) {
                        if (!this._id.equals(temp._id)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
                            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._sequenceList != null) {
                if (temp._sequenceList == null) return false;
                if (this._sequenceList != temp._sequenceList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._sequenceList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._sequenceList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._sequenceList.equals(temp._sequenceList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
                    }
                }
            } else if (temp._sequenceList != null)
                return false;
            if (this._sequenceMappingList != null) {
                if (temp._sequenceMappingList == null) return false;
                if (this._sequenceMappingList != temp._sequenceMappingList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._sequenceMappingList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._sequenceMappingList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceMappingList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceMappingList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceMappingList);
                    }
                }
            } else if (temp._sequenceMappingList != null)
                return false;
            if (this._dataSetAnnotationsList != null) {
                if (temp._dataSetAnnotationsList == null) return false;
                if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dataSetAnnotationsList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dataSetAnnotationsList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetAnnotationsList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetAnnotationsList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetAnnotationsList);
                    }
                }
            } else if (temp._dataSetAnnotationsList != null)
                return false;
            if (this._alignmentList != null) {
                if (temp._alignmentList == null) return false;
                if (this._alignmentList != temp._alignmentList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._alignmentList.equals(temp._alignmentList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentList);
                    }
                }
            } else if (temp._alignmentList != null)
                return false;
            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);
                    }
                }
            } else if (temp._treeList != null)
                return false;
            if (this._provenance != null) {
                if (temp._provenance == null) return false;
                if (this._provenance != temp._provenance) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._provenance.equals(temp._provenance)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
                    }
                }
            } else if (temp._provenance != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Method getAlignment.
     * 
     * @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.Alignment
     * at the given index
     */
    public uk.ac.vamsas.objects.core.Alignment getAlignment(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._alignmentList.size()) {
            throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Alignment) _alignmentList.get(index);
    }

    /**
     * Method getAlignment.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.Alignment[] getAlignment(
    ) {
        uk.ac.vamsas.objects.core.Alignment[] array = new uk.ac.vamsas.objects.core.Alignment[0];
        return (uk.ac.vamsas.objects.core.Alignment[]) this._alignmentList.toArray(array);
    }

    /**
     * Method getAlignmentAsReference.Returns a reference to
     * '_alignmentList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getAlignmentAsReference(
    ) {
        return this._alignmentList;
    }

    /**
     * Method getAlignmentCount.
     * 
     * @return the size of this collection
     */
    public int getAlignmentCount(
    ) {
        return this._alignmentList.size();
    }

    /**
     * Method getDataSetAnnotations.
     * 
     * @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.DataSetAnnotations at the given
     * index
     */
    public uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
            throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '" + index + "' not in range [0.." + (this._dataSetAnnotationsList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.get(index);
    }

    /**
     * Method getDataSetAnnotations.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.DataSetAnnotations[] getDataSetAnnotations(
    ) {
        uk.ac.vamsas.objects.core.DataSetAnnotations[] array = new uk.ac.vamsas.objects.core.DataSetAnnotations[0];
        return (uk.ac.vamsas.objects.core.DataSetAnnotations[]) this._dataSetAnnotationsList.toArray(array);
    }

    /**
     * Method getDataSetAnnotationsAsReference.Returns a reference
     * to '_dataSetAnnotationsList'. No type checking is performed
     * on any modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getDataSetAnnotationsAsReference(
    ) {
        return this._dataSetAnnotationsList;
    }

    /**
     * Method getDataSetAnnotationsCount.
     * 
     * @return the size of this collection
     */
    public int getDataSetAnnotationsCount(
    ) {
        return this._dataSetAnnotationsList.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 'provenance'.
     * 
     * @return the value of field 'Provenance'.
     */
    public uk.ac.vamsas.objects.core.Provenance getProvenance(
    ) {
        return this._provenance;
    }

    /**
     * Method getSequence.
     * 
     * @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.Sequence
     * at the given index
     */
    public uk.ac.vamsas.objects.core.Sequence getSequence(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._sequenceList.size()) {
            throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Sequence) _sequenceList.get(index);
    }

    /**
     * Method getSequence.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.Sequence[] getSequence(
    ) {
        uk.ac.vamsas.objects.core.Sequence[] array = new uk.ac.vamsas.objects.core.Sequence[0];
        return (uk.ac.vamsas.objects.core.Sequence[]) this._sequenceList.toArray(array);
    }

    /**
     * Method getSequenceAsReference.Returns a reference to
     * '_sequenceList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getSequenceAsReference(
    ) {
        return this._sequenceList;
    }

    /**
     * Method getSequenceCount.
     * 
     * @return the size of this collection
     */
    public int getSequenceCount(
    ) {
        return this._sequenceList.size();
    }

    /**
     * Method getSequenceMapping.
     * 
     * @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.SequenceMapping at the given index
     */
    public uk.ac.vamsas.objects.core.SequenceMapping getSequenceMapping(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._sequenceMappingList.size()) {
            throw new IndexOutOfBoundsException("getSequenceMapping: Index value '" + index + "' not in range [0.." + (this._sequenceMappingList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.SequenceMapping) _sequenceMappingList.get(index);
    }

    /**
     * Method getSequenceMapping.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.SequenceMapping[] getSequenceMapping(
    ) {
        uk.ac.vamsas.objects.core.SequenceMapping[] array = new uk.ac.vamsas.objects.core.SequenceMapping[0];
        return (uk.ac.vamsas.objects.core.SequenceMapping[]) this._sequenceMappingList.toArray(array);
    }

    /**
     * Method getSequenceMappingAsReference.Returns a reference to
     * '_sequenceMappingList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getSequenceMappingAsReference(
    ) {
        return this._sequenceMappingList;
    }

    /**
     * Method getSequenceMappingCount.
     * 
     * @return the size of this collection
     */
    public int getSequenceMappingCount(
    ) {
        return this._sequenceMappingList.size();
    }

    /**
     * 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 (_sequenceList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
           result = 37 * result + _sequenceList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
        }
        if (_sequenceMappingList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
           result = 37 * result + _sequenceMappingList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
        }
        if (_dataSetAnnotationsList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_dataSetAnnotationsList)) {
           result = 37 * result + _dataSetAnnotationsList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
        }
        if (_alignmentList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
           result = 37 * result + _alignmentList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
        }
        if (_treeList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
           result = 37 * result + _treeList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
        }
        if (_provenance != null
            && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
           result = 37 * result + _provenance.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
        }
        
        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);
    }

    /**
     * Method removeAlignment.
     * 
     * @param vAlignment
     * @return true if the object was removed from the collection.
     */
    public boolean removeAlignment(
            final uk.ac.vamsas.objects.core.Alignment vAlignment) {
        boolean removed = _alignmentList.remove(vAlignment);
        return removed;
    }

    /**
     * Method removeAlignmentAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Alignment removeAlignmentAt(
            final int index) {
        java.lang.Object obj = this._alignmentList.remove(index);
        return (uk.ac.vamsas.objects.core.Alignment) obj;
    }

    /**
     */
    public void removeAllAlignment(
    ) {
        this._alignmentList.clear();
    }

    /**
     */
    public void removeAllDataSetAnnotations(
    ) {
        this._dataSetAnnotationsList.clear();
    }

    /**
     */
    public void removeAllSequence(
    ) {
        this._sequenceList.clear();
    }

    /**
     */
    public void removeAllSequenceMapping(
    ) {
        this._sequenceMappingList.clear();
    }

    /**
     */
    public void removeAllTree(
    ) {
        this._treeList.clear();
    }

    /**
     * Method removeDataSetAnnotations.
     * 
     * @param vDataSetAnnotations
     * @return true if the object was removed from the collection.
     */
    public boolean removeDataSetAnnotations(
            final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) {
        boolean removed = _dataSetAnnotationsList.remove(vDataSetAnnotations);
        return removed;
    }

    /**
     * Method removeDataSetAnnotationsAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotationsAt(
            final int index) {
        java.lang.Object obj = this._dataSetAnnotationsList.remove(index);
        return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj;
    }

    /**
     * Method removeSequence.
     * 
     * @param vSequence
     * @return true if the object was removed from the collection.
     */
    public boolean removeSequence(
            final uk.ac.vamsas.objects.core.Sequence vSequence) {
        boolean removed = _sequenceList.remove(vSequence);
        return removed;
    }

    /**
     * Method removeSequenceAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Sequence removeSequenceAt(
            final int index) {
        java.lang.Object obj = this._sequenceList.remove(index);
        return (uk.ac.vamsas.objects.core.Sequence) obj;
    }

    /**
     * Method removeSequenceMapping.
     * 
     * @param vSequenceMapping
     * @return true if the object was removed from the collection.
     */
    public boolean removeSequenceMapping(
            final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping) {
        boolean removed = _sequenceMappingList.remove(vSequenceMapping);
        return removed;
    }

    /**
     * Method removeSequenceMappingAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.SequenceMapping removeSequenceMappingAt(
            final int index) {
        java.lang.Object obj = this._sequenceMappingList.remove(index);
        return (uk.ac.vamsas.objects.core.SequenceMapping) 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 vAlignment
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setAlignment(
            final int index,
            final uk.ac.vamsas.objects.core.Alignment vAlignment)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._alignmentList.size()) {
            throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
        }
        
        this._alignmentList.set(index, vAlignment);
    }

    /**
     * 
     * 
     * @param vAlignmentArray
     */
    public void setAlignment(
            final uk.ac.vamsas.objects.core.Alignment[] vAlignmentArray) {
        //-- copy array
        _alignmentList.clear();
        
        for (int i = 0; i < vAlignmentArray.length; i++) {
                this._alignmentList.add(vAlignmentArray[i]);
        }
    }

    /**
     * Sets the value of '_alignmentList' by copying the given
     * Vector. All elements will be checked for type safety.
     * 
     * @param vAlignmentList the Vector to copy.
     */
    public void setAlignment(
            final java.util.Vector vAlignmentList) {
        // copy vector
        this._alignmentList.clear();
        
        this._alignmentList.addAll(vAlignmentList);
    }

    /**
     * Sets the value of '_alignmentList' by setting it to the
     * given Vector. No type checking is performed.
     * @deprecated
     * 
     * @param alignmentVector the Vector to set.
     */
    public void setAlignmentAsReference(
            final java.util.Vector alignmentVector) {
        this._alignmentList = alignmentVector;
    }

    /**
     * 
     * 
     * @param index
     * @param vDataSetAnnotations
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setDataSetAnnotations(
            final int index,
            final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
            throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '" + index + "' not in range [0.." + (this._dataSetAnnotationsList.size() - 1) + "]");
        }
        
        this._dataSetAnnotationsList.set(index, vDataSetAnnotations);
    }

    /**
     * 
     * 
     * @param vDataSetAnnotationsArray
     */
    public void setDataSetAnnotations(
            final uk.ac.vamsas.objects.core.DataSetAnnotations[] vDataSetAnnotationsArray) {
        //-- copy array
        _dataSetAnnotationsList.clear();
        
        for (int i = 0; i < vDataSetAnnotationsArray.length; i++) {
                this._dataSetAnnotationsList.add(vDataSetAnnotationsArray[i]);
        }
    }

    /**
     * Sets the value of '_dataSetAnnotationsList' by copying the
     * given Vector. All elements will be checked for type safety.
     * 
     * @param vDataSetAnnotationsList the Vector to copy.
     */
    public void setDataSetAnnotations(
            final java.util.Vector vDataSetAnnotationsList) {
        // copy vector
        this._dataSetAnnotationsList.clear();
        
        this._dataSetAnnotationsList.addAll(vDataSetAnnotationsList);
    }

    /**
     * Sets the value of '_dataSetAnnotationsList' by setting it to
     * the given Vector. No type checking is performed.
     * @deprecated
     * 
     * @param dataSetAnnotationsVector the Vector to set.
     */
    public void setDataSetAnnotationsAsReference(
            final java.util.Vector dataSetAnnotationsVector) {
        this._dataSetAnnotationsList = dataSetAnnotationsVector;
    }

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

    /**
     * 
     * 
     * @param index
     * @param vSequence
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setSequence(
            final int index,
            final uk.ac.vamsas.objects.core.Sequence vSequence)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._sequenceList.size()) {
            throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
        }
        
        this._sequenceList.set(index, vSequence);
    }

    /**
     * 
     * 
     * @param vSequenceArray
     */
    public void setSequence(
            final uk.ac.vamsas.objects.core.Sequence[] vSequenceArray) {
        //-- copy array
        _sequenceList.clear();
        
        for (int i = 0; i < vSequenceArray.length; i++) {
                this._sequenceList.add(vSequenceArray[i]);
        }
    }

    /**
     * Sets the value of '_sequenceList' by copying the given
     * Vector. All elements will be checked for type safety.
     * 
     * @param vSequenceList the Vector to copy.
     */
    public void setSequence(
            final java.util.Vector vSequenceList) {
        // copy vector
        this._sequenceList.clear();
        
        this._sequenceList.addAll(vSequenceList);
    }

    /**
     * Sets the value of '_sequenceList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param sequenceVector the Vector to set.
     */
    public void setSequenceAsReference(
            final java.util.Vector sequenceVector) {
        this._sequenceList = sequenceVector;
    }

    /**
     * 
     * 
     * @param index
     * @param vSequenceMapping
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setSequenceMapping(
            final int index,
            final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._sequenceMappingList.size()) {
            throw new IndexOutOfBoundsException("setSequenceMapping: Index value '" + index + "' not in range [0.." + (this._sequenceMappingList.size() - 1) + "]");
        }
        
        this._sequenceMappingList.set(index, vSequenceMapping);
    }

    /**
     * 
     * 
     * @param vSequenceMappingArray
     */
    public void setSequenceMapping(
            final uk.ac.vamsas.objects.core.SequenceMapping[] vSequenceMappingArray) {
        //-- copy array
        _sequenceMappingList.clear();
        
        for (int i = 0; i < vSequenceMappingArray.length; i++) {
                this._sequenceMappingList.add(vSequenceMappingArray[i]);
        }
    }

    /**
     * Sets the value of '_sequenceMappingList' by copying the
     * given Vector. All elements will be checked for type safety.
     * 
     * @param vSequenceMappingList the Vector to copy.
     */
    public void setSequenceMapping(
            final java.util.Vector vSequenceMappingList) {
        // copy vector
        this._sequenceMappingList.clear();
        
        this._sequenceMappingList.addAll(vSequenceMappingList);
    }

    /**
     * Sets the value of '_sequenceMappingList' by setting it to
     * the given Vector. No type checking is performed.
     * @deprecated
     * 
     * @param sequenceMappingVector the Vector to set.
     */
    public void setSequenceMappingAsReference(
            final java.util.Vector sequenceMappingVector) {
        this._sequenceMappingList = sequenceMappingVector;
    }

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

}