/*
 * 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 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;

/**
 * This is annotation over the coordinate frame
 *  defined by all the columns in the alignment.
 *  
 * 
 * @version $Revision$ $Date$
 */
public class AlignmentAnnotation extends uk.ac.vamsas.objects.core.RangeAnnotation 
implements java.io.Serializable
{


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

    /**
     * TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     */
    private boolean _graph;

    /**
     * keeps track of state for field: _graph
     */
    private boolean _has_graph;

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


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

    public AlignmentAnnotation() 
     {
        super();
    } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation()


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

    /**
     * Method deleteGraph
     * 
     */
    public void deleteGraph()
    {
        this._has_graph= false;
    } //-- void deleteGraph() 

    /**
     * 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 AlignmentAnnotation) {
        
            AlignmentAnnotation temp = (AlignmentAnnotation)obj;
            if (this._graph != temp._graph)
                return false;
            if (this._has_graph != temp._has_graph)
                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 'graph'. The field 'graph' has
     * the following description: TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     * 
     * @return boolean
     * @return the value of field 'graph'.
     */
    public boolean getGraph()
    {
        return this._graph;
    } //-- boolean getGraph() 

    /**
     * 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 hasGraph
     * 
     * 
     * 
     * @return boolean
     */
    public boolean hasGraph()
    {
        return this._has_graph;
    } //-- boolean hasGraph() 

    /**
     * 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) 

    /**
     * Sets the value of field 'graph'. The field 'graph' has the
     * following description: TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     * 
     * @param graph the value of field 'graph'.
     */
    public void setGraph(boolean graph)
    {
        this._graph = graph;
        this._has_graph = true;
    } //-- void setGraph(boolean) 

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

}