/*
* EmpiricalAminoAcidModel.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.oldevomodel.substmodel;
import dr.evolution.datatype.AminoAcids;
import dr.inference.model.Parameter;
/**
* <b>A general model of sequence substitution</b>. A general reversible class for any
* data type.
*
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id: EmpiricalAminoAcidModel.java,v 1.15 2005/05/24 20:25:58 rambaut Exp $
*/
public class EmpiricalAminoAcidModel extends AbstractAminoAcidModel {
/**
* constructor
*
* @param rateMatrix EmpiricalRateMatrix
* @param freqModel the frequency model
*/
public EmpiricalAminoAcidModel(EmpiricalRateMatrix rateMatrix, FrequencyModel freqModel) {
super(rateMatrix.getName(), freqModel);
if (freqModel == null) {
areFrequenciesConstant = true;
double[] freqs = rateMatrix.getEmpiricalFrequencies();
this.freqModel = new FrequencyModel(AminoAcids.INSTANCE, new Parameter.Default(freqs));
}
this.rateMatrix = rateMatrix;
}
protected void frequenciesChanged() {
// Nothing to precalculate
}
protected void ratesChanged() {
// Nothing to precalculate
}
protected void setupRelativeRates() {
double[] rates = rateMatrix.getEmpiricalRates();
System.arraycopy(rates, 0, relativeRates, 0, relativeRates.length);
}
// *****************************************************************
// Interface Model
// *****************************************************************
protected void storeState() {
} // nothing to do
protected void restoreState() {
updateMatrix = !areFrequenciesConstant;
}
protected void acceptState() {
} // nothing to do
private EmpiricalRateMatrix rateMatrix;
private boolean areFrequenciesConstant = false;
}