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Open Source Chemistry Library
/*
* 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.
*/
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{
//
// 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.
* 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.
*/
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();
}
}