content: /*
   * 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.
   *
   * @author Modest v. Korff
   */
  
  package com.actelion.research.chem.descriptor.flexophore;
  
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.List;
  
  public class ClusterNode implements Comparable<ClusterNode> {
  	
  	private int indexCenter;
  	
  	private List<Integer> liIndexMember;
  	
  	private int rmsd;
  	
  	public ClusterNode(int indexCenter) {
  		this.indexCenter = indexCenter;
  		
  		liIndexMember = new ArrayList<Integer>();
  		
  		rmsd = 0;
  	}
  	
  	public void add(int index){
  		liIndexMember.add(index);
  	}
  	
  	public int compareTo(ClusterNode cl) {
  		return Double.compare(rmsd, cl.rmsd);
  	}
  	
  	@Override
  	public boolean equals(Object obj) {
  		boolean bEqual = true;
  		
  		ClusterNode cl = (ClusterNode)obj;
  		
  		if(liIndexMember.size()!=cl.liIndexMember.size()){
  			return false;
  		}
  		
  		List<Integer> l1 = new ArrayList<Integer>(liIndexMember);
  		l1.add(indexCenter);
  		
  		List<Integer> l2 = new ArrayList<Integer>(cl.liIndexMember);
  		l2.add(cl.indexCenter);
  		
  		Collections.sort(l1);
  		
  		Collections.sort(l2);
  		
  		for (int i = 0; i < l1.size(); i++) {
  			int v1 = l1.get(i);
  			int v2 = l2.get(i);
  			
  			if(v1!=v2){
  				bEqual=false;
  				break;
  			}
  		}
  		
  		return bEqual;
  	}
  
  	public int getIndexCenter() {
  		return indexCenter;
  	}
  
  	public int getRMSD() {
  		return rmsd;
  	}
  	
  	/**
  	 * Sum of squared distances of the center to the other cluster members
  	 * @param rmsd
  	 */ 
  	public void setRMSD(int rmsd) {
  		this.rmsd = rmsd;
  	}
  	
  	public static int getRMSD(ClusterNode cluster, DistHist mdh){
  		int rmsd=0;
  		
  		List<Integer> liIndex = cluster.getClusterMember();
  		
  		for (int i = 0; i < liIndex.size(); i++) {
  			int dist = mdh.getMinDist(cluster.getIndexCenter(), liIndex.get(i));
  			rmsd+=dist*dist;
  		}
  		
  		return rmsd;
  	}
  
  	public List<Integer> getClusterMember() {
  		return liIndexMember;
  	}
  	
  	public boolean isCluster(){
  		if(liIndexMember.size()>0)
  			return true;
  		else
  			return false;
  	}
  
  }
  