content: package com.actelion.research.chem.mcs;
  
  import java.util.ArrayList;
  import java.util.HashSet;
  import java.util.LinkedList;
  import java.util.List;
  
  /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its contributors may be used to endorse or promote products
  *    derived from this software without specific prior written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  */
  class MatchListContainer {
  	
  	private static final double fractionCapacity = 0.25; 
  	
  	private MatchList [] arrMatchList;
  	
  	private HashSet<MatchList> hsMatchList;
  	
  	private LinkedList<Integer> liIndexAvailable;
  	
  	private LinkedList<Integer> liIndexUsed;
  	
  	private List<int []> liMatches; 
  	
  	public MatchListContainer(int maxNumAtomsMolecule) {
  		
  		int maximumCapacity = (int)(maxNumAtomsMolecule * fractionCapacity);
  		
  		arrMatchList = new MatchList[maximumCapacity];
  		
  		liIndexAvailable = new LinkedList<Integer>();
  		
  		liIndexUsed = new LinkedList<Integer>();
  		
  		int nInteger = (maxNumAtomsMolecule+Integer.SIZE-1) / Integer.SIZE;
  		
  		for (int i = 0; i < arrMatchList.length; i++) {
  			arrMatchList[i]=new MatchList(nInteger);
  			liIndexAvailable.add(i);
  		}
  		
  		hsMatchList = new HashSet<MatchList>();
  		
  		liMatches = new ArrayList<int[]>();
  	}
  	
  	public void reset() {
  		
  		hsMatchList.clear();
  		
  		for(int index : liIndexUsed) {
  			arrMatchList[index].reset();
  			liIndexAvailable.add(index);
  		}
  		
  		liIndexUsed.clear();
  		
  		liMatches = new ArrayList<int[]>();
  	}
  	
  	/**
  	 * 
  	 * @param arrMatchListFragment match list with length=number of atoms in fragment. 
  	 * The fields contain the matching atom indices of the molecule.
  	 */
  	public void add(int [] arrMatchListFragment) {
  		
  //		if(liIndexAvailable.isEmpty()){
  //			throw new RuntimeException("Maximum capacity ("+arrMatchList.length+")of match list exceeded.");
  //		}
  //		
  //		int index = liIndexAvailable.poll();
  //		
  //		arrMatchList[index].set(arrMatchListFragment);
  //		
  //		if(hsMatchList.add(arrMatchList[index])){
  //			
  //			liIndexUsed.add(index);
  //			
  //			liMatches.add(arrMatchListFragment);
  //			
  //		} else {
  //			
  //			arrMatchList[index].reset();
  //			
  //			liIndexAvailable.add(index);
  //		}
  		
  		
  		liMatches.add(arrMatchListFragment);
  	}
  	
  	public List<int[]> getMatchList(){
  		return liMatches;
  	}
  	
  	public boolean isMaxCapacityReached(){
  		return liIndexAvailable.isEmpty();
  	}
  }
  