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
{
  public AlignmentOrder()
  {
  }

  public void setType(int Type)
  {
    this.Type = Type;
  }

  public int getType()
  {
    return Type;
  }

  public void setName(String Name)
  {
    this.Name = Name;
  }

  public String getName()
  {
    return Name;
  }

  public void setOrder(Vector Order)
  {
    this.Order = Order;
  }

  public Vector getOrder()
  {

    return Order;
  }
// 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;
  }
 */
  public static final int FILE = 0;
  public static final int MSA = 1;
  public static final int USER = 2;

  private int Type = 0;
  private String Name;
  private Vector Order = null;

  /**
   * 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));
  }
  public AlignmentOrder(SequenceI[] orderFrom) {
    Order = new Vector();
    for (int i=0,ns=orderFrom.length; i<ns; i++)
      Order.addElement(orderFrom[i]);
  }



  /**
   * 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

  } */

}