/*
* SimpleMutator.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.wrightfisher;
import dr.math.MathUtils;
import dr.math.Poisson;
/**
* @author Alexei Drummond
*/
public class SimpleMutator extends Mutator {
public SimpleMutator(double muRate, int stateSize) {
this.stateSize = stateSize;
this.muRate = muRate;
}
public Mutation[] mutate(byte[] sequence, byte[] childSequence) {
if (genomeLength != sequence.length) {
genomeLength = sequence.length;
poissonMean = genomeLength * muRate;
}
int mutationCount = Poisson.nextPoisson(poissonMean);
Mutation[] mutations = new Mutation[mutationCount];
System.arraycopy(sequence, 0, childSequence, 0, genomeLength);
byte newState;
for (int i = 0; i < mutationCount; i++) {
int pos = MathUtils.nextInt(genomeLength);
newState = (byte)MathUtils.nextInt(stateSize-1);
if (newState == sequence[i]) {
newState = (byte)((newState + 1) % stateSize);
}
childSequence[pos] = newState;
mutations[i] = new Mutation(pos, newState);
}
return mutations;
}
double muRate = 0.01;
double poissonMean = -1;
int genomeLength = -1;
int stateSize = 2;
}