
com.actelion.research.chem.mcs.MatchListContainer Maven / Gradle / Ivy
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 hsMatchList;
private LinkedList liIndexAvailable;
private LinkedList liIndexUsed;
private List liMatches;
public MatchListContainer(int maxNumAtomsMolecule) {
int maximumCapacity = (int)(maxNumAtomsMolecule * fractionCapacity);
arrMatchList = new MatchList[maximumCapacity];
liIndexAvailable = new LinkedList();
liIndexUsed = new LinkedList();
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();
liMatches = new ArrayList();
}
public void reset() {
hsMatchList.clear();
for(int index : liIndexUsed) {
arrMatchList[index].reset();
liIndexAvailable.add(index);
}
liIndexUsed.clear();
liMatches = new ArrayList();
}
/**
*
* @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 getMatchList(){
return liMatches;
}
public boolean isMaxCapacityReached(){
return liIndexAvailable.isEmpty();
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy