/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
 * Schema.
 * $Id:AlignmentSequence.java 264 2006-12-14 17:42:54Z JimP $
 */

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 AlignmentSequence.
 * 
 * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
 */
public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType 
implements java.io.Serializable
{


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

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

    /**
     * Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     */
    private java.lang.Object _refid;

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


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

    public AlignmentSequence() 
     {
        super();
        _alignmentSequenceAnnotationList = new Vector();
    } //-- uk.ac.vamsas.objects.core.AlignmentSequence()


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

    /**
     * Method addAlignmentSequenceAnnotation
     * 
     * 
     * 
     * @param vAlignmentSequenceAnnotation
     */
    public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
    } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 

    /**
     * Method addAlignmentSequenceAnnotation
     * 
     * 
     * 
     * @param index
     * @param vAlignmentSequenceAnnotation
     */
    public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
        throws java.lang.IndexOutOfBoundsException
    {
        _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
    } //-- void addAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) 

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

    /**
     * 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 AlignmentSequence) {
        
            AlignmentSequence temp = (AlignmentSequence)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._refid != null) {
                if (temp._refid == null) return false;
                else if (!(this._refid.equals(temp._refid))) 
                    return false;
            }
            else if (temp._refid != null)
                return false;
            if (this._alignmentSequenceAnnotationList != null) {
                if (temp._alignmentSequenceAnnotationList == null) return false;
                else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList))) 
                    return false;
            }
            else if (temp._alignmentSequenceAnnotationList != null)
                return false;
            return true;
        }
        return false;
    } //-- boolean equals(java.lang.Object) 

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

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

    /**
     * Method getAlignmentSequenceAnnotationCount
     * 
     * 
     * 
     * @return int
     */
    public int getAlignmentSequenceAnnotationCount()
    {
        return _alignmentSequenceAnnotationList.size();
    } //-- int getAlignmentSequenceAnnotationCount() 

    /**
     * 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 'refid'. The field 'refid' has
     * the following description: Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     * 
     * @return Object
     * @return the value of field 'refid'.
     */
    public java.lang.Object getRefid()
    {
        return this._refid;
    } //-- java.lang.Object getRefid() 

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

    /**
     * Method removeAllAlignmentSequenceAnnotation
     * 
     */
    public void removeAllAlignmentSequenceAnnotation()
    {
        _alignmentSequenceAnnotationList.removeAllElements();
    } //-- void removeAllAlignmentSequenceAnnotation() 

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

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

    /**
     * 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 'refid'. The field 'refid' has the
     * following description: Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     * 
     * @param refid the value of field 'refid'.
     */
    public void setRefid(java.lang.Object refid)
    {
        this._refid = refid;
    } //-- void setRefid(java.lang.Object) 

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

}