com.actelion.research.chem.properties.complexity.ContainerBitArray Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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.chem.properties.complexity;
import java.util.ArrayList;
import java.util.List;
import com.actelion.research.util.Formatter;
import com.actelion.research.util.datamodel.IntArray;
/**
* Contains a list of reusable bit arrays.
*/
public class ContainerBitArray {
private static boolean ELUSIVE = false;
private static final int LIMIT2FULL = 1500 * 1000 * 1000;
/**
* If we reach Integer.MAX_VALUE an error will be thrown.
*/
private static final int CAPACITY_FULL = Integer.MAX_VALUE-1;
private List li;
private IntArray arrAvailable;
private int bits;
private IBitArrayFactory extends IBitArray> bitArrayCreator;
/**
*
* @param bits is the number of available bits in the binary vector.
* @param capacity
*/
public ContainerBitArray(int bits, int capacity) {
if(bits == BitArray128.MAX_NUM_BITS){
bitArrayCreator = new BitArray128Factory();
} else {
throw new RuntimeException("Do not know a factory to construct " + bits + " bits array.");
}
this.bits = bits;
if(capacity > LIMIT2FULL) {
capacity = CAPACITY_FULL;
}
if(isELUSIVE()){
System.out.println("ContainerBitArray(...) capacity " + Formatter.group(capacity) + ".");
}
arrAvailable = new IntArray(capacity);
li = new ArrayList<>(capacity);
addResources(capacity);
}
@SuppressWarnings("unchecked")
public void calculateHash(IBitArray f){
((IBitArrayFactory)bitArrayCreator).calculateHash(f);
}
public int getSizeBinaryArray(){
return bits;
}
public void reset(){
arrAvailable.reset();
for (int i = 0; i < li.size(); i++) {
arrAvailable.add(i);
}
}
private void addResources(int capacity) {
if(li.size() == Integer.MAX_VALUE){
new RuntimeException("Maximum capacity reached").printStackTrace();
return;
}
int indexStart = li.size();
for (int i = 0; i < capacity; i++) {
int index = indexStart+i;
li.add(bitArrayCreator.getNew(index));
arrAvailable.add(index);
if(li.size() == Integer.MAX_VALUE){
new RuntimeException("Maximum capacity reached").printStackTrace();
break;
}
}
}
/**
*
* @return a fresh (reset) instance.
*/
public IBitArray get(){
if(arrAvailable.length()==0){
throw new CapacityReachedError("Maximum capacity " + Formatter.group(arrAvailable.getCapacity()) + " reached!");
}
int index = arrAvailable.removeLast();
IBitArray bitArray = li.get(index);
bitArray.reset();
return bitArray;
}
/**
* The garbage collector. Put BitArray here if not used anymore.
* @param liv
*/
public void receycle(IBitArray liv){
arrAvailable.add(liv.getIndex());
}
public IBitArray getWithCopy(BitArray128 orign){
IBitArray liv = get();
liv.copyIntoThis(orign);
return liv;
}
public int getCapacity(){
return li.size();
}
public int getAvailable(){
return arrAvailable.length();
}
/**
* @return the eLUSIVE
*/
public static boolean isELUSIVE() {
return ELUSIVE;
}
/**
* @param elusive the eLUSIVE to set
*/
public static void setELUSIVE(boolean elusive) {
ELUSIVE = elusive;
}
public static class CapacityReachedError extends RuntimeException {
public CapacityReachedError(String msg) {
super(msg);
}
}
}