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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.calc.combinatorics;
import com.actelion.research.util.ListUtils;
import com.actelion.research.util.StringFunctions;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* CombinationGenerator
* @author Modest von Korff
* @version 1.0
* Oct 12, 2012 MvK: Start implementation
*/
public class CombinationGenerator {
/**
* Get all possible index combinations, order independent.
* For a list containing the numbers from 0 to
* nObjects for arrays of the size 'sampleSize'.
* @param nObjects so many indices will be permuted.
* @param sampleSize Size of the array containing the permutations.
* @return
*/
public static List getAllOutOf(int nObjects, int sampleSize) {
List li = new ArrayList();
int [] arrCounters = new int [sampleSize];
if(nObjects==sampleSize){
int [] arr = new int [sampleSize];
for (int i = 0; i < arr.length; i++) {
arr[i]=i;
}
li.add(arr);
return li;
}else if (sampleSize==1){
for (int i = 0; i < nObjects; i++) {
int [] arr = new int [1];
arr[0]=i;
li.add(arr);
}
return li;
}else if (sampleSize>nObjects){
return null;
}
// init
for (int i = 0; i < arrCounters.length; i++) {
arrCounters[i]=i;
}
boolean proceed = true;
while(proceed){
int [] arr = new int [sampleSize];
for (int i = 0; i < sampleSize; i++) {
arr[i]=arrCounters[i];
}
li.add(arr);
int depth = sampleSize-1;
arrCounters[depth]++;
boolean counterFieldReset = false;
if(arrCounters[depth]>=nObjects){
counterFieldReset=true;
}
while(counterFieldReset){
counterFieldReset=false;
depth--;
arrCounters[depth]++;
for (int i = depth + 1; i < sampleSize; i++) {
arrCounters[i] = arrCounters[i-1]+1;
if(arrCounters[i] >= nObjects){
counterFieldReset=true;
}
}
if(depth==0)
break;
}
if(counterFieldReset)
proceed = false;
}
return li;
}
/**
*
* @param arrSizeClass, Each value in the array stands for the number of objects.
* @return
*/
public static List> getCombinations(int [] arrSizeClass) {
long capacity = 1;
for (int sizeClass : arrSizeClass) {
capacity *= sizeClass;
}
if(capacity>Integer.MAX_VALUE){
throw new RuntimeException("Number of combinations " + capacity + " above Integer.MAX_VALUE!");
}
List> li = new ArrayList<>((int)capacity);
List> liTmp = new ArrayList<>((int)capacity);
int index=0;
for (int i = 0; i < arrSizeClass[0]; i++) {
List liCombi = new ArrayList<>();
liCombi.add(i);
li.add(liCombi);
}
index++;
while (index liCombi : li) {
for (int i = 0; i < arrSizeClass[index]; i++) {
List liCombiNew = new ArrayList<>(liCombi);
liCombiNew.add(i);
liTmp.add(liCombiNew);
}
}
li.clear();
li.addAll(liTmp);
index++;
}
return li;
}
public static List getCombinations(List li){
int nCombinations = 1;
for (int[] arr : li) {
nCombinations *= arr.length;
}
List liComb = new ArrayList<>(nCombinations);
for (int i = 0; i < nCombinations; i++) {
int [] arrComb = new int[li.size()];
liComb.add(arrComb);
}
int nCombCol=1;
for (int col = 0; col < li.size(); col++) {
nCombCol *= li.get(col).length;
int nRepetitions = nCombinations / nCombCol;
int [] arr = li.get(col);
int indexArr = 0;
int row = 0;
while (row < nCombinations) {
for (int i = 0; i < nRepetitions; i++) {
int [] arrComb = liComb.get(row);
arrComb[col]=arr[indexArr];
row++;
}
indexArr++;
if(indexArr==arr.length) {
indexArr=0;
}
}
}
return liComb;
}
private static void swap(int[] input, int a, int b) {
int tmp = input[a];
input[a] = input[b];
input[b] = tmp;
}
/**
*
* @param elements
* @param n
* @return
*/
public static List getPermutations(int[] elements, int n){
List permutations = new ArrayList();
int[] indexes = new int[n];
int i = 0;
permutations.add(Arrays.copyOf(elements, elements.length));
while (i < n) {
if (indexes[i] < i) {
swap(elements, i % 2 == 0 ? 0: indexes[i], i);
permutations.add(Arrays.copyOf(elements, elements.length));
indexes[i]++;
i = 0;
}
else {
indexes[i] = 0;
i++;
}
}
return permutations;
}
/**
* https://en.wikipedia.org/wiki/Cartesian_product
* generates all possible combinations of elements from a list of lists
* @param
* @param lists
* @return
*/
public static List> cartesianProduct(List> lists) {
List> resultLists = new ArrayList>();
if (lists.size() == 0) {
resultLists.add(new ArrayList());
return resultLists;
} else {
List firstList = lists.get(0);
List> remainingLists = cartesianProduct(lists.subList(1, lists.size()));
for (T condition : firstList) {
for (List remainingList : remainingLists) {
ArrayList resultList = new ArrayList();
resultList.add(condition);
resultList.addAll(remainingList);
resultLists.add(resultList);
}
}
}
return resultLists;
}
public static BigInteger getFactorial (int n) {
BigInteger fact = BigInteger.ONE;
for (int i = n; i > 1; i--) {
fact = fact.multiply (new BigInteger (Integer.toString (i)));
}
return fact;
}
/**
* Calculate binomial coefficient or
* n choose k
*
* @param n
* @param k
* @return
*/
public static BigInteger getBinomialCoefficient(int n, int k){
BigInteger nFac = getFactorial(n);
BigInteger kFac = getFactorial(k);
BigInteger nMinus_k_Fac = getFactorial(n-k);
BigInteger dev = nMinus_k_Fac.multiply(kFac);
BigInteger bc = nFac.divide(dev);
return bc;
}
public static void main(String[] args) {
exampleGetAllOutOf2();
}
public static void examplePermutations() {
int [] a = {4,7,9};
List liComb = getPermutations(a, 3);
for(int [] p : liComb) {
System.out.println(Arrays.toString(p));
}
}
public static void exampleCartesianProduct() {
List> lists = new ArrayList<>();
List l0 = new ArrayList<>();
l0.add(1);
l0.add(2);
l0.add(3);
List l1 = new ArrayList<>(l0);
List l2 = new ArrayList<>(l0);
lists.add(l0);
lists.add(l1);
lists.add(l2);
List> liComb = cartesianProduct(lists);
for(List li : liComb) {
System.out.println(ListUtils.toStringInteger(li));
}
}
public static void exampleCombinations() {
int [] a = {1,2,3};
List> liComb = getCombinations(a);
for(List li : liComb) {
System.out.println(ListUtils.toStringInteger(li));
}
}
public static void exampleGetAllOutOf() {
int object = 4;
int sampleSize = 3;
List liComb = getAllOutOf(object, sampleSize);
for(int [] a : liComb) {
System.out.println(StringFunctions.toString(a, ","));
}
}
public static void exampleGetAllOutOf2() {
int object = 4;
for (int sampleSize = 1; sampleSize < object; sampleSize++) {
List liComb = getAllOutOf(object, sampleSize);
for(int [] a : liComb) {
System.out.println(StringFunctions.toString(a, ","));
}
}
}
}