/*
 * 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 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 SequenceSet.
 * 
 * @version $Revision$ $Date$
 */
public class SequenceSet extends org.vamsas.client.object 
implements java.io.Serializable
{


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

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

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

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

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

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

    /**
     * Field _provenance
     */
    private org.vamsas.objects.core.Provenance _provenance;


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

    public SequenceSet() 
     {
        super();
        _sequenceList = new Vector();
        _sequenceSetAnnotationsList = new Vector();
        _alignmentList = new Vector();
        _treeList = new Vector();
    } //-- org.vamsas.objects.core.SequenceSet()


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

    /**
     * Method addAlignment
     * 
     * 
     * 
     * @param vAlignment
     */
    public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentList.addElement(vAlignment);
    } //-- void addAlignment(org.vamsas.objects.core.Alignment) 

    /**
     * Method addAlignment
     * 
     * 
     * 
     * @param index
     * @param vAlignment
     */
    public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentList.insertElementAt(vAlignment, index);
    } //-- void addAlignment(int, org.vamsas.objects.core.Alignment) 

    /**
     * Method addSequence
     * 
     * 
     * 
     * @param vSequence
     */
    public void addSequence(org.vamsas.objects.core.Sequence vSequence)
        throws java.lang.IndexOutOfBoundsException
    {
        _sequenceList.addElement(vSequence);
    } //-- void addSequence(org.vamsas.objects.core.Sequence) 

    /**
     * Method addSequence
     * 
     * 
     * 
     * @param index
     * @param vSequence
     */
    public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
        throws java.lang.IndexOutOfBoundsException
    {
        _sequenceList.insertElementAt(vSequence, index);
    } //-- void addSequence(int, org.vamsas.objects.core.Sequence) 

    /**
     * Method addSequenceSetAnnotations
     * 
     * 
     * 
     * @param vSequenceSetAnnotations
     */
    public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
        throws java.lang.IndexOutOfBoundsException
    {
        _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
    } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations) 

    /**
     * Method addSequenceSetAnnotations
     * 
     * 
     * 
     * @param index
     * @param vSequenceSetAnnotations
     */
    public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
        throws java.lang.IndexOutOfBoundsException
    {
        _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
    } //-- 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 enumerateAlignment
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateAlignment()
    {
        return _alignmentList.elements();
    } //-- java.util.Enumeration enumerateAlignment() 

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

    /**
     * Method enumerateSequenceSetAnnotations
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateSequenceSetAnnotations()
    {
        return _sequenceSetAnnotationsList.elements();
    } //-- 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
     * @return boolean
     */
    public boolean equals(java.lang.Object obj)
    {
        if ( this == obj )
            return true;
        
        if (super.equals(obj)==false)
            return false;
        
        if (obj instanceof SequenceSet) {
        
            SequenceSet temp = (SequenceSet)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._sequenceList != null) {
                if (temp._sequenceList == null) return false;
                else if (!(this._sequenceList.equals(temp._sequenceList))) 
                    return false;
            }
            else if (temp._sequenceList != null)
                return false;
            if (this._sequenceSetAnnotationsList != null) {
                if (temp._sequenceSetAnnotationsList == null) return false;
                else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList))) 
                    return false;
            }
            else if (temp._sequenceSetAnnotationsList != null)
                return false;
            if (this._alignmentList != null) {
                if (temp._alignmentList == null) return false;
                else if (!(this._alignmentList.equals(temp._alignmentList))) 
                    return false;
            }
            else if (temp._alignmentList != 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._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) 

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

    /**
     * Method getAlignment
     * 
     * 
     * 
     * @return Alignment
     */
    public org.vamsas.objects.core.Alignment[] getAlignment()
    {
        int size = _alignmentList.size();
        org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
        }
        return mArray;
    } //-- org.vamsas.objects.core.Alignment[] getAlignment() 

    /**
     * Method getAlignmentCount
     * 
     * 
     * 
     * @return int
     */
    public int getAlignmentCount()
    {
        return _alignmentList.size();
    } //-- int getAlignmentCount() 

    /**
     * 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() 

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

    /**
     * Method getSequence
     * 
     * 
     * 
     * @return Sequence
     */
    public org.vamsas.objects.core.Sequence[] getSequence()
    {
        int size = _sequenceList.size();
        org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
        }
        return mArray;
    } //-- org.vamsas.objects.core.Sequence[] getSequence() 

    /**
     * Method getSequenceCount
     * 
     * 
     * 
     * @return int
     */
    public int getSequenceCount()
    {
        return _sequenceList.size();
    } //-- int getSequenceCount() 

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

    /**
     * Method getSequenceSetAnnotations
     * 
     * 
     * 
     * @return SequenceSetAnnotations
     */
    public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
    {
        int size = _sequenceSetAnnotationsList.size();
        org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
        }
        return mArray;
    } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations() 

    /**
     * Method getSequenceSetAnnotationsCount
     * 
     * 
     * 
     * @return int
     */
    public int getSequenceSetAnnotationsCount()
    {
        return _sequenceSetAnnotationsList.size();
    } //-- int getSequenceSetAnnotationsCount() 

    /**
     * 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
     */
    public 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 isValid
     * 
     * 
     * 
     * @return boolean
     */
    public boolean isValid()
    {
        try {
            validate();
        }
        catch (org.exolab.castor.xml.ValidationException vex) {
            return false;
        }
        return true;
    } //-- boolean isValid() 

    /**
     * Method marshal
     * 
     * 
     * 
     * @param out
     */
    public void marshal(java.io.Writer out)
        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        
        Marshaller.marshal(this, out);
    } //-- void marshal(java.io.Writer) 

    /**
     * Method marshal
     * 
     * 
     * 
     * @param handler
     */
    public void marshal(org.xml.sax.ContentHandler handler)
        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        
        Marshaller.marshal(this, handler);
    } //-- void marshal(org.xml.sax.ContentHandler) 

    /**
     * Method removeAlignment
     * 
     * 
     * 
     * @param index
     * @return Alignment
     */
    public org.vamsas.objects.core.Alignment removeAlignment(int index)
    {
        java.lang.Object obj = _alignmentList.elementAt(index);
        _alignmentList.removeElementAt(index);
        return (org.vamsas.objects.core.Alignment) obj;
    } //-- org.vamsas.objects.core.Alignment removeAlignment(int) 

    /**
     * Method removeAllAlignment
     * 
     */
    public void removeAllAlignment()
    {
        _alignmentList.removeAllElements();
    } //-- void removeAllAlignment() 

    /**
     * Method removeAllSequence
     * 
     */
    public void removeAllSequence()
    {
        _sequenceList.removeAllElements();
    } //-- void removeAllSequence() 

    /**
     * Method removeAllSequenceSetAnnotations
     * 
     */
    public void removeAllSequenceSetAnnotations()
    {
        _sequenceSetAnnotationsList.removeAllElements();
    } //-- void removeAllSequenceSetAnnotations() 

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

    /**
     * Method removeSequence
     * 
     * 
     * 
     * @param index
     * @return Sequence
     */
    public org.vamsas.objects.core.Sequence removeSequence(int index)
    {
        java.lang.Object obj = _sequenceList.elementAt(index);
        _sequenceList.removeElementAt(index);
        return (org.vamsas.objects.core.Sequence) obj;
    } //-- org.vamsas.objects.core.Sequence removeSequence(int) 

    /**
     * Method removeSequenceSetAnnotations
     * 
     * 
     * 
     * @param index
     * @return SequenceSetAnnotations
     */
    public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
    {
        java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
        _sequenceSetAnnotationsList.removeElementAt(index);
        return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
    } //-- 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) 

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

    /**
     * Method setAlignment
     * 
     * 
     * 
     * @param alignmentArray
     */
    public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
    {
        //-- copy array
        _alignmentList.removeAllElements();
        for (int i = 0; i < alignmentArray.length; i++) {
            _alignmentList.addElement(alignmentArray[i]);
        }
    } //-- void setAlignment(org.vamsas.objects.core.Alignment) 

    /**
     * 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) 

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

    /**
     * Method setSequence
     * 
     * 
     * 
     * @param sequenceArray
     */
    public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
    {
        //-- copy array
        _sequenceList.removeAllElements();
        for (int i = 0; i < sequenceArray.length; i++) {
            _sequenceList.addElement(sequenceArray[i]);
        }
    } //-- void setSequence(org.vamsas.objects.core.Sequence) 

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

    /**
     * Method setSequenceSetAnnotations
     * 
     * 
     * 
     * @param sequenceSetAnnotationsArray
     */
    public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
    {
        //-- copy array
        _sequenceSetAnnotationsList.removeAllElements();
        for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
            _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
        }
    } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations) 

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

}