/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 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;
  }

  /**
   * replaces oldref with newref in the alignment order.
   * 
   * @param oldref
   * @param newref
   * @return true if oldref was contained in order and replaced with newref
   */
  public boolean updateSequence(SequenceI oldref, SequenceI newref)
  {
    int found = Order.indexOf(oldref);
    if (found > -1)
    {
      Order.setElementAt(newref, found);
    }
    return found > -1;
  }

  /**
   * Exact equivalence of two AlignmentOrders
   * 
   * @param o
   * @return true if o orders the same sequenceI objects in the same way
   */
  public boolean equals(AlignmentOrder o)
  {
    return equals(o, true);
  }

  /**
   * Exact equivalence of two AlignmentOrders // TODO: Weak SequenceI
   * equivalence - will throw Error at moment
   * 
   * @param o
   * @param identity -
   *                false - use weak equivalence (refers to same or different
   *                parts of same sequence)
   * @return true if o orders equivalent sequenceI objects in the same way
   */
  public boolean equals(AlignmentOrder o, boolean identity)
  {
    if (o != this)
    {
      if (o == null)
      {
        return false;
      }
      if (Order != null && o.Order != null
              && Order.size() == o.Order.size())
      {
        if (!identity)
        {
          throw new Error("Weak sequenceI equivalence not yet implemented.");
        }
        else
        {
          for (int i = 0, j = o.Order.size(); i < j; i++)
          {
            if (Order.elementAt(i) != o.Order.elementAt(i))
            {
              return false;
            }
          }
        }
      }
      else
      {
        return false;
      }
    }
    return true;
  }

  /**
   * Consistency test for alignmentOrders
   * 
   * @param o
   * @return true if o contains or is contained by this and the common SequenceI
   *         objects are ordered in the same way
   */
  public boolean isConsistent(AlignmentOrder o)
  {
    return isConsistent(o, true);
  }

  /**
   * Consistency test for alignmentOrders
   * 
   * @param o //
   *                TODO: Weak SequenceI equivalence - will throw Error at
   *                moment
   * @param identity -
   *                false - use weak equivalence (refers to same or different
   *                parts of same sequence)
   * @return true if o contains or is contained by this and the common SequenceI
   *         objects are ordered in the same way
   */
  public boolean isConsistent(AlignmentOrder o, boolean identity)
  {
    if (o != this)
    {
      if (o == null)
      {
        return false;
      }
      if (Order != null && o.Order != null)
      {
        Vector c, s;
        if (o.Order.size() > Order.size())
        {
          c = o.Order;
          s = Order;
        }
        else
        {
          c = Order;
          s = o.Order;
        }
        if (!identity)
        {
          throw new Error("Weak sequenceI equivalence not yet implemented.");
        }
        else
        {
          // test if c contains s and order in s is conserved in c
          int last = -1;
          for (int i = 0, j = s.size(); i < j; i++)
          {
            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by
                                                  // incremental position search
            if (pos > last)
            {
              last = pos;
            }
            else
            {
              return false;
            }
          }
        }
      }
      else
      {
        return false;
      }
    }
    return true;
  }
  /**
   * 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
   *  }
   */
}