/*
* SMMDistanceMatrix.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;
/**
* @author Chieh-Hsi Wu
* Date: 31/07/2009
* Time: 4:37:38 PM
* This class is used to calculate the distance between different microsatellite alleles
*/
public class SMMDistanceMatrix extends DistanceMatrix{
/**
* constructor taking a pattern source
*
* @param patterns a pattern of a microsatellite locus
*/
public SMMDistanceMatrix(PatternList patterns) {
super(patterns);
}
protected double calculatePairwiseDistance(int taxon1, int taxon2) {
int[] pattern = patterns.getPattern(0);
int state1 = pattern[taxon1];
int state2 = pattern[taxon2];
double distance = 0.0;
if (!dataType.isAmbiguousState(state1) && !dataType.isAmbiguousState(state2))
distance = Math.abs(state1 - state2);
return distance;
}
}