/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

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 List<SequenceI> Order = null;

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

  /**
   * AlignmentOrder
   * 
   * @param anOrder
   */
  public AlignmentOrder(List<SequenceI> anOrder)
  {
    Order = anOrder;
  }

  /**
   * AlignmentOrder
   * 
   * @param orderFrom
   *          AlignmentI
   */
  public AlignmentOrder(AlignmentI orderFrom)
  {
    Order = new ArrayList<SequenceI>();

    for (SequenceI seq : orderFrom.getSequences())
    {
      Order.add(seq);
    }
  }

  /**
   * Creates a new AlignmentOrder object.
   * 
   * @param orderFrom
   *          DOCUMENT ME!
   */
  public AlignmentOrder(SequenceI[] orderFrom)
  {
    Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
  }

  /**
   * 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(List<SequenceI> Order)
  {
    this.Order = Order;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public List<SequenceI> 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.set(found, newref);
    }
    return found > -1;
  }

  /**
   * Exact equivalence of two AlignmentOrders
   * 
   * @param o
   * @return true if o orders the same sequenceI objects in the same way
   */
  @Override
  public boolean equals(Object o)
  {
    if (o == null || !(o instanceof AlignmentOrder))
    {
      return false;
    }
    return equals((AlignmentOrder) 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.get(i) != o.Order.get(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)
      {
        List<SequenceI> 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.get(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 }
   */
}