/*
 * 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 MCview;

import java.util.Vector;

public class Zsort
{
  /**
   * Sorts the Bond list in ascending order of the z-value of the bond start
   * atom
   * 
   * @param bonds
   */
  public void sort(Vector<Bond> bonds)
  {
    sort(bonds, 0, bonds.size() - 1);
  }

  public void sort(Vector<Bond> bonds, int p, int r)
  {
    int q;

    if (p < r)
    {
      q = partition(bonds, p, r);
      sort(bonds, p, q);
      sort(bonds, q + 1, r);
    }
  }

  private int partition(Vector<Bond> bonds, int p, int r)
  {
    float x = bonds.elementAt(p).start[2];
    int i = p - 1;
    int j = r + 1;
    Bond tmp;
    while (true)
    {
      do
      {
        j--;
      } while ((j >= 0) && (bonds.elementAt(j).start[2] > x));

      do
      {
        i++;
      } while ((i < bonds.size()) && (bonds.elementAt(i).start[2] < x));

      if (i < j)
      {
        tmp = bonds.elementAt(i);
        bonds.setElementAt(bonds.elementAt(j), i);
        bonds.setElementAt(tmp, j);
      }
      else
      {
        return j;
      }
    }
  }
}