content: 
  package com.actelion.research.chem.mcs;
  
  import java.util.ArrayList;
  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 PossibleMappingsFrag2Mol {
  	
  	private PossibleMappingsFrag2Mol parent;
  	
  	private int indexProcessingArray;
  	
  	// Index of the fragment atom.
  	private int indexAtomFrag;
  	
  	// Ring bond to an object with a lower index in the array
  	private final int [] arrIndexCounterAtomFragRingClosure;
  	
  	private int ringClosures;
  	
  	// Array for the mapping molecule atom indices.
  	private final int [] arrIndexAtomMolMapping;
  	
  	private int sizeArrayMappingMolecules;
  	
  	private final List<PossibleMappingsFrag2Mol> liChild;
  	
  	public PossibleMappingsFrag2Mol(int indexProcessingArray, int capacityMappings) {
  		
  		this.indexProcessingArray=indexProcessingArray;
  		
  		indexAtomFrag=-1;
  		
  		arrIndexCounterAtomFragRingClosure = new int [SubStructSearchExhaustiveTreeWalker.LEN_RING_CLOSURES];
  		
  		arrIndexAtomMolMapping = new int [capacityMappings];
  		
  		sizeArrayMappingMolecules=0;
  		
  		ringClosures=0;
  		
  		liChild = new ArrayList<PossibleMappingsFrag2Mol>();
  	}
  	
  	public void reset(){
  		
  		parent=null;
  		
  		indexAtomFrag=-1;
  		
  		ringClosures=0;
  		
  		sizeArrayMappingMolecules=0;
  		
  		liChild.clear();
  		
  	}
  	
  	public void resetMappingMolecules(){
  		sizeArrayMappingMolecules=0;
  	}
  	
  	public PossibleMappingsFrag2Mol(int indexProcessingArray) {
  		this(indexProcessingArray, SubStructSearchExhaustiveTreeWalker.LEN_MAPPING_BLOCK);
  	}
  
  	public void addChild(PossibleMappingsFrag2Mol child){
  		child.setParent(this);
  		liChild.add(child);
  	}
  	
  	public void addIndexMappingAtomMolecule(int indexMolAtom){
  		arrIndexAtomMolMapping[sizeArrayMappingMolecules]=indexMolAtom;
  		sizeArrayMappingMolecules++;
  	}
  	
  	public void addIndexCounterAtomFragmentRingClosure(int indexCounterAtomFragmentRingClosure){
  		arrIndexCounterAtomFragRingClosure[ringClosures]=indexCounterAtomFragmentRingClosure;
  		ringClosures++;
  	}
  	
  	public int getIndexCounterAtomFragmentRingClosure(int i) {
  		return arrIndexCounterAtomFragRingClosure[i];
  	}
  	
  	public int getRingClosures() {
  		return ringClosures;
  	}
  	
  	public int getIndexAtomFrag() {
  		return indexAtomFrag;
  	}
  
  	public int getChilds() {
  		return liChild.size();
  	}
  	
  	public PossibleMappingsFrag2Mol getChild(int indexChild) {
  		return liChild.get(indexChild);
  	}
  
  	public boolean empty(){
  		return (sizeArrayMappingMolecules==0) ? true : false;
  	}
  	
  	public int getIndexProcessingArray() {
  		return indexProcessingArray;
  	}
  	
  
  	public int pollIndexMappingAtomMolecule(){
  		
  		int indexAtomMol = arrIndexAtomMolMapping[sizeArrayMappingMolecules-1];
  		
  		sizeArrayMappingMolecules--;
  		
  		return indexAtomMol;
  		
  	}
  	
  	public PossibleMappingsFrag2Mol getParent(){
  		return parent;
  	}
  	
  	private void setParent(PossibleMappingsFrag2Mol parent){
  		this.parent=parent;
  	}
  	
  	public String toString() {
  		StringBuilder sb = new StringBuilder();
  		
  		if(parent!=null){
  			sb.append("Parent " + parent.indexAtomFrag);
  			sb.append(", fragment atom " + indexAtomFrag);
  		} else {
  			sb.append("No parent, fragment atom " + indexAtomFrag);
  		}
  		
  		sb.append(", mapping mol atms ");
  		for (int i = 0; i < sizeArrayMappingMolecules; i++) {
  			sb.append(arrIndexAtomMolMapping[i]);
  			if(i<sizeArrayMappingMolecules-1){
  				sb.append(",");
  			}
  		}
  		
  		sb.append(".");
  		
  		return sb.toString();
  	}
  
  	public void setIndexAtomFrag(int indexAtomFrag) {
  		this.indexAtomFrag = indexAtomFrag;
  	}
  
  }