Binomial.java

/*
 * Binomial.java
 *
 * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST 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.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.math;

/**
 * Binomial coefficients
 *
 * @version $Id: Binomial.java,v 1.11 2005/05/24 20:26:00 rambaut Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 * @author Korbinian Strimmer
 */
public class Binomial
{
	//
	// Public stuff; lnGamma is used, so parameters can be doubles.
	//
	
	public static double logChoose(double n, double k){
		return GammaFunction.lnGamma(n + 1.0) -	GammaFunction.lnGamma(k + 1.0) 
			- GammaFunction.lnGamma(n - k + 1.0);
	}
	
	
	/**
	 * @return Binomial coefficient n choose k
     * @param n total elements
     * @param k chosen elements
	 */
	public static double choose(double n, double k)
	{
		n = Math.floor(n + 0.5);
		k = Math.floor(k + 0.5);

		double lchoose = GammaFunction.lnGamma(n + 1.0) -
		GammaFunction.lnGamma(k + 1.0) - GammaFunction.lnGamma(n - k + 1.0);

		return Math.floor(Math.exp(lchoose) + 0.5);
	}
	
	/**
     * @param n # elements
     * @return n choose 2 (number of distinct ways to choose a pair from n elements)
     */
	public static double choose2(int n)
	{
		// not sure how much overhead there is with try-catch blocks
		// i.e. would an if statement be better?

		try {
			return choose2LUT[n];
		} catch (ArrayIndexOutOfBoundsException e) {
			if( n < 0 ) {
                return 0;
            }
            
			while (maxN < n) {
				maxN += 1000;
			}
			
			initialize();
			return choose2LUT[n];
		}
	}

	private static void initialize() {
		choose2LUT = new double[maxN+1];
		choose2LUT[0] = 0;
		choose2LUT[1] = 0;
		choose2LUT[2] = 1;
		for (int i = 3; i <= maxN; i++) {
			choose2LUT[i] = ((double) (i*(i-1))) * 0.5;
		}
	}

	private static int maxN = 5000;
	private static double[] choose2LUT;
	
	static {
		initialize();
	}
}