content: /*
   * Copyright (c) 1997 - 2016
   * Actelion Pharmaceuticals Ltd.
   * Gewerbestrasse 16
   * CH-4123 Allschwil, Switzerland
   *
   * All rights reserved.
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   * modification, are permitted provided that the following conditions are met:
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   * 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
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   * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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   * 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.
   */
  
  package com.actelion.research.util.graph.complete;
  
  import com.actelion.research.util.BurtleHasher;
  
  import java.util.Arrays;
  
  /**
   * SolutionCompleteGraph
   * @author Modest von Korff
   * @version 1.0
   * Oct 1, 2012 MvK: Start implementation
   */
  public class SolutionCompleteGraph extends AMemorizedObject implements Comparable<SolutionCompleteGraph>{
  
  	//
  	// Stores the solution as pairwise node indices
  	//
  
  	// Contains the node index in MolDistHist for base
  	private byte [] heapIndexBase;
  
  	/**
  	 * number of the matching nodes
  	 */
  	private int sizeHeap;
  
  	// Contains the node index in MolDistHist for query
  	private byte [] heapIndexQuery;
  
  	private byte maxIndexNodeQuery;
  	
  	/**
  	 * The index is the index of the node in the query molecule. Not matched query nodes contain a -1.
  	 * The value at 'index' is the index of the node in the base molecule.
  	 * Contains the same information as heapIndexBase and heapIndexQuery. Used for fast lookup.
  	 */
  	private byte [] arrSolution;
  
  	private int hash;
  	
  	private double similarity;
  	
  	private int nodes;
  	
  	public SolutionCompleteGraph() {
  		
  		nodes = -1;
  		
  		arrSolution = new byte [CompleteGraphMatcher.MAX_NUM_NODES];
  		
  		heapIndexBase = new byte [CompleteGraphMatcher.MAX_NUM_NODES];
  		
  		heapIndexQuery = new byte [CompleteGraphMatcher.MAX_NUM_NODES];
  		
  		for (int i = 0; i < arrSolution.length; i++) {
  			arrSolution[i]=CompleteGraphMatcher.DEFAULT_VAL;
  			heapIndexBase[i]=CompleteGraphMatcher.DEFAULT_VAL;
  			heapIndexQuery[i]=CompleteGraphMatcher.DEFAULT_VAL;
  		}
  	}
  	
  	/**
  	 * Adds a pair of nodes to this solution.
  	 * @param indexNodeBase index of the base node in the complete base graph.
  	 * @param indexNodeQuery index of the query node in the complete query graph.
  	 */
  	public void add(byte indexNodeQuery, byte indexNodeBase) {
  		arrSolution[indexNodeQuery]=indexNodeBase;
  		if(indexNodeQuery>maxIndexNodeQuery){
  			maxIndexNodeQuery=indexNodeQuery;
  		}
  		heapIndexBase[sizeHeap]=indexNodeBase;
  		heapIndexQuery[sizeHeap]=indexNodeQuery;
  		sizeHeap++;
  		calcHashCode();
  	}
  	
  	public int compareTo(SolutionCompleteGraph s) {
  		if(similarity > s.similarity){
  			return 1;
  		} else if(similarity < s.similarity){
  			return -1;
  		}
  		return 0;
  	}
  
  	public int getSizeHeap(){
  		return sizeHeap;
  	}
  
  	public byte getIndexBaseFromHeap(int indexOnHeapBase){
  		return heapIndexBase[indexOnHeapBase];
  	}
  	
  	public byte getIndexQueryFromHeap(int indexOnHeapQuery){
  		return heapIndexQuery[indexOnHeapQuery];
  	}
  	
  	public byte getIndexCorrespondingBaseNode(int indexQueryNode) {
  		return arrSolution[indexQueryNode];
  	}
  
  	/**
  	 * The index is the index of the node in the query molecule.
  	 * The value at 'index' is the index of the node in the base molecule.
  	 * Can contain -1 if a node is not mapping.
  	 */
  	public byte [] getSolution (){
  		return arrSolution;
  	}
  
  	public boolean equals(Object obj) {
  		
  		boolean eq = true;
  		SolutionCompleteGraph s = (SolutionCompleteGraph)obj;
  		if(sizeHeap != s.sizeHeap){
  			return false;
  		}
  		if(maxIndexNodeQuery != s.maxIndexNodeQuery){
  			return false;
  		}
  		for (int i = 0; i < maxIndexNodeQuery; i++) {
  			if(arrSolution[i]!=s.arrSolution[i]){
  				eq = false;
  				break;
  			}
  		}
  		
  		return eq;
  	} 
  		
  	public void copyIntoThis(AMemorizedObject a) {
  		SolutionCompleteGraph solution = (SolutionCompleteGraph)a;
  		System.arraycopy(solution.heapIndexBase, 0, heapIndexBase, 0, solution.sizeHeap);
  		System.arraycopy(solution.heapIndexQuery, 0, heapIndexQuery, 0, solution.sizeHeap);
  		System.arraycopy(solution.arrSolution, 0, arrSolution, 0, arrSolution.length);
  		sizeHeap = solution.sizeHeap;
  		hash = solution.hash;
  		similarity = solution.similarity;
  		nodes = solution.nodes;
  		maxIndexNodeQuery = solution.maxIndexNodeQuery;
  	}
  	
      private void calcHashCode(){
      	hash = BurtleHasher.hashlittle(arrSolution, 13, maxIndexNodeQuery+1);
      }
      
  	public int hashCode() {
  		return hash;
  	}
  	
  	public void reset() {
  		for (int i = 0; i < arrSolution.length; i++) {
  			arrSolution[i] = CompleteGraphMatcher.DEFAULT_VAL;
  			heapIndexBase[i] = CompleteGraphMatcher.DEFAULT_VAL;
  			heapIndexQuery[i] = CompleteGraphMatcher.DEFAULT_VAL;
  		}
  		sizeHeap = 0;
  		hash = 0;
  		similarity = 0;
  		nodes = 0;
  		maxIndexNodeQuery = 0;
  	}
  
  	public double getSimilarity() {
  		return similarity;
  	}
  
  	public void setSimilarity(double similarity) {
  		this.similarity = similarity;
  	}
  
  	/**
  	 * Only needed for the toString() method.  
  	 * @param nodes
  	 */
  	public void setNodesQuery(int nodes) {
  		this.nodes = nodes;
  	}
  	
  	public int getNodesQuery() {
  		return nodes;
  	}
  	
  	public String toString() {
  		StringBuilder sb = new StringBuilder();
  		
  		if(sizeHeap>0) {
  			
  			for (int i = 0; i < maxIndexNodeQuery+1; i++) {
  				if(sb.length()>0)
  					sb.append(" ");
  				sb.append(arrSolution[i]);
  			}
  			
  		} else {
  			sb.append(Arrays.toString(arrSolution));	
  		}
  		
  		return sb.toString();
  	}
  }