CombinationGenerator.java

/*
*   EuroCarbDB, a framework for carbohydrate bioinformatics
*
*   Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
*   indicated by the @author tags or express copyright attribution
*   statements applied by the authors.  
*
*   This copyrighted material is made available to anyone wishing to use, modify,
*   copy, or redistribute it subject to the terms and conditions of the GNU
*   Lesser General Public License, as published by the Free Software Foundation.
*   A copy of this license accompanies this distribution in the file LICENSE.txt.
*
*   This program is distributed in the hope that it will be useful,
*   but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
*   or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
*   for more details.
*
*   Last commit: $Rev: 1147 $ by $Author: glycoslave $ on $Date:: 2009-06-04 #$  
*/

package org.eurocarbdb.application.glycanbuilder;

import java.math.BigInteger;

//--------------------------------------
// Systematically generate combinations.
// from: http://www.merriampark.com/comb.htm
//--------------------------------------

class CombinationGenerator {

  private int[] a;
  private int n;
  private int r;
  private BigInteger numLeft;
  private BigInteger total;

  //------------
  // Constructor
  //------------

  public CombinationGenerator (int n, int r) {
    if (r > n) {
      throw new IllegalArgumentException ();
    }
    if (n < 1) {
      throw new IllegalArgumentException ();
    }
    this.n = n;
    this.r = r;
    a = new int[r];
    BigInteger nFact = getFactorial (n);
    BigInteger rFact = getFactorial (r);
    BigInteger nminusrFact = getFactorial (n - r);
    total = nFact.divide (rFact.multiply (nminusrFact));
    reset ();
  }

  //------
  // Reset
  //------

  public void reset () {
    for (int i = 0; i < a.length; i++) {
      a[i] = i;
    }
    numLeft = new BigInteger (total.toString ());
  }

  //------------------------------------------------
  // Return number of combinations not yet generated
  //------------------------------------------------

  public BigInteger getNumLeft () {
    return numLeft;
  }

  //-----------------------------
  // Are there more combinations?
  //-----------------------------

  public boolean hasMore () {
    return numLeft.compareTo (BigInteger.ZERO) == 1;
  }

  //------------------------------------
  // Return total number of combinations
  //------------------------------------

  public BigInteger getTotal () {
    return total;
  }

  //------------------
  // Compute factorial
  //------------------

  private 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;
  }

  //--------------------------------------------------------
  // Generate next combination (algorithm from Rosen p. 286)
  //--------------------------------------------------------

  public int[] getNext () {

    if (numLeft.equals (total)) {
      numLeft = numLeft.subtract (BigInteger.ONE);
      return a;
    }

    int i = r - 1;
    while (a[i] == n - r + i) {
      i--;
    }
    a[i] = a[i] + 1;
    for (int j = i + 1; j < r; j++) {
      a[j] = a[i] + j - i;
    }

    numLeft = numLeft.subtract (BigInteger.ONE);
    return a;

  }
}