/*
 * 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 Alignment.
 * 
 * @version $Revision$ $Date$
 */
public class Alignment extends org.vamsas.client.object 
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;

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

    /**
     * Field _alignmentAnnotations
     */
    private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;

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

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

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


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

    public Alignment() 
     {
        super();
        _treeList = new Vector();
        _alignmentSequenceList = new Vector();
    } //-- org.vamsas.objects.core.Alignment()


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

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

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

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

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

    /**
     * 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._alignmentAnnotations != null) {
                if (temp._alignmentAnnotations == null) return false;
                else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations))) 
                    return false;
            }
            else if (temp._alignmentAnnotations != 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._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() 

    /**
     * Returns the value of field 'alignmentAnnotations'.
     * 
     * @return AlignmentAnnotations
     * @return the value of field 'alignmentAnnotations'.
     */
    public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
    {
        return this._alignmentAnnotations;
    } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations() 

    /**
     * Method getAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @return AlignmentSequence
     */
    public org.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 (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
    } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int) 

    /**
     * Method getAlignmentSequence
     * 
     * 
     * 
     * @return AlignmentSequence
     */
    public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
    {
        int size = _alignmentSequenceList.size();
        org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
        }
        return mArray;
    } //-- org.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'.
     * 
     * @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 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 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 removeAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @return AlignmentSequence
     */
    public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
    {
        java.lang.Object obj = _alignmentSequenceList.elementAt(index);
        _alignmentSequenceList.removeElementAt(index);
        return (org.vamsas.objects.core.AlignmentSequence) obj;
    } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int) 

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

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

    /**
     * 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) 

    /**
     * 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) 

    /**
     * Sets the value of field 'alignmentAnnotations'.
     * 
     * @param alignmentAnnotations the value of field
     * 'alignmentAnnotations'.
     */
    public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations alignmentAnnotations)
    {
        this._alignmentAnnotations = alignmentAnnotations;
    } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations) 

    /**
     * Method setAlignmentSequence
     * 
     * 
     * 
     * @param index
     * @param vAlignmentSequence
     */
    public void setAlignmentSequence(int index, org.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, org.vamsas.objects.core.AlignmentSequence) 

    /**
     * Method setAlignmentSequence
     * 
     * 
     * 
     * @param alignmentSequenceArray
     */
    public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
    {
        //-- copy array
        _alignmentSequenceList.removeAllElements();
        for (int i = 0; i < alignmentSequenceArray.length; i++) {
            _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
        }
    } //-- void setAlignmentSequence(org.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'.
     * 
     * @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 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 Alignment
     */
    public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
    } //-- org.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() 

}