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AtomContainerPermutor.java

/*
 *  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1
 *  of the License, or (at your option) any later version.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  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 Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
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package org.openscience.cdk.graph;

import java.util.Iterator;

import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.tools.LoggingTool;

/**
 * The permutation code here is based on a pseudo code example 
 * on a tutorial site created and maintained by Phillip P. Fuchs:
 * <a href="http://www.geocities.com/permute_it/pseudo2.html">http://www.geocities.com/permute_it/pseudo2.html</a>.
 * 
 *@author         steinbeck
 * @cdk.githash
 *@cdk.created    2005-05-04
 *@cdk.keyword    permutation
 */
00047 public abstract class AtomContainerPermutor implements Iterator
{
      final static boolean debug = true;
      static int debugCounter = 0;
      int N, i, j;
      int[] bookkeeping;
      Object[] objects;
      
      private static LoggingTool logger = new LoggingTool(AtomContainerPermutor.class);

      AtomContainer atomContainer;
      
      public void setAtomContainer(AtomContainer ac)
      {
            this.atomContainer = ac;
      }

      public void initBookkeeping()
      {
            bookkeeping = new int[N + 1];
            for (int f = 0; f <= N ; f++)
            {
                  bookkeeping[f] = f;     
            }
            i = 1;
            
      }
      
      public Object next()
      {
            bookkeeping[i] = bookkeeping[i] - 1;
            if (isOdd(i)) j = bookkeeping[i];
            else j = 0;
            swap(i, j);
            i = 1;
            while(bookkeeping[i] == 0)
            {
                  bookkeeping[i] = i;
                  i++;
            }
            return makeResult();    
      }
      
      public boolean hasNext()
      {
            if (i < N) return true;
            return false;
      }
      
      public void remove()
      {
            // stupid method. not implemented.  
      }
      
      void swap(int x, int y)
      {
            logger.debug("swapping order of " + x + " and " + y);
            Object o = objects[x];
            objects[x] = objects[y];
            objects[y] = o;
      }
      
      void initObjectArray()
      {
            //
      }
      
      AtomContainer makeResult()
      {
            return null;
      }
      
      /**
        * Returns true if this number is odd.
        */
00122         boolean isOdd(int x) 
      {
                return (x & 1 ) == 1;
        }
}


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