/*
* JukesCantorDistanceMatrix.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.evolution.distance;
import dr.evolution.alignment.PatternList;
/**
* compute jukes-cantor corrected distance matrix
*
* @version $Id: JukesCantorDistanceMatrix.java,v 1.4 2005/05/24 20:25:56 rambaut Exp $
*
* @author Andrew Rambaut
* @author Korbinian Strimmer
*/
public class JukesCantorDistanceMatrix extends DistanceMatrix
{
//
// Public stuff
//
/** constructor */
public JukesCantorDistanceMatrix()
{
super();
}
/** constructor taking a pattern source */
public JukesCantorDistanceMatrix(PatternList patterns)
{
super(patterns);
}
/**
* set the pattern source
*/
public void setPatterns(PatternList patterns) {
super.setPatterns(patterns);
final int stateCount = patterns.getStateCount();
const1 = ((double) stateCount - 1) / stateCount;
const2 = ((double) stateCount) / (stateCount - 1) ;
}
/**
* Calculate a pairwise distance
*/
protected double calculatePairwiseDistance(int i, int j) {
final double obsDist = super.calculatePairwiseDistance(i, j);
if (obsDist == 0.0) return 0.0;
if (obsDist >= const1) {
return MAX_DISTANCE;
}
final double expDist = -const1 * Math.log(1.0 - (const2 * obsDist));
if (expDist < MAX_DISTANCE) {
return expDist;
} else {
return MAX_DISTANCE;
}
}
//
// Private stuff
//
//used in correction formula
private double const1, const2;
}