/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.datamodel;

import java.util.*;


/**
 * <p>Title: </p>
 *
 * <p>Description: </p>
 *
 * <p>Copyright: Copyright (c) 2004</p>
 *
 * <p>Company: Dundee University</p>
 *
 * @author not attributable
 * @version 1.0
 */
public class AlignmentOrder
{
    // JBPNote : this method would return a vector containing all sequences in seqset
    // with those also contained in order at the beginning of the vector in the order
    // given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
    // should be here for completeness.

    /*  public Vector getOrder(AlignmentI seqset)
       {
         Vector perm = new Vector(seqset.getHeight());
         for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
      perm.setElement(i,...).
         return Order;
       }
     */

    /** DOCUMENT ME!! */
    public static final int FILE = 0;

    /** DOCUMENT ME!! */
    public static final int MSA = 1;

    /** DOCUMENT ME!! */
    public static final int USER = 2;
    private int Type = 0;
    private String Name;
    private Vector Order = null;

    /**
     * Creates a new AlignmentOrder object.
     */
    public AlignmentOrder()
    {
    }

    /**
     * AlignmentOrder
     *
     * @param anOrder Vector
     */
    public AlignmentOrder(Vector anOrder)
    {
        Order = anOrder;
    }

    /**
     * AlignmentOrder
     *
     * @param orderFrom AlignmentI
     */
    public AlignmentOrder(AlignmentI orderFrom)
    {
        Order = new Vector();

        for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
        {
            Order.addElement(orderFrom.getSequenceAt(i));
        }
    }

    /**
     * Creates a new AlignmentOrder object.
     *
     * @param orderFrom DOCUMENT ME!
     */
    public AlignmentOrder(SequenceI[] orderFrom)
    {
        Order = new Vector();

        for (int i = 0, ns = orderFrom.length; i < ns; i++)
        {
            Order.addElement(orderFrom[i]);
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param Type DOCUMENT ME!
     */
    public void setType(int Type)
    {
        this.Type = Type;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public int getType()
    {
        return Type;
    }

    /**
     * DOCUMENT ME!
     *
     * @param Name DOCUMENT ME!
     */
    public void setName(String Name)
    {
        this.Name = Name;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String getName()
    {
        return Name;
    }

    /**
     * DOCUMENT ME!
     *
     * @param Order DOCUMENT ME!
     */
    public void setOrder(Vector Order)
    {
        this.Order = Order;
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public Vector getOrder()
    {
        return Order;
    }

    /**
     * AlignmentOrder
     *
     * @param orderThis AlignmentI
     * @param byThat AlignmentI
     */

    /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
     {
       // Vector is an ordering of this alignment using the order of sequence objects in byThat,
       // where ids and unaligned sequences must match

     } */
}