/*
* PCACodonModel.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.Codons;
import dr.oldevomodelxml.substmodel.PCACodonModelParser;
import dr.inference.model.Parameter;
/**
* PCA model of codon evolution
*
* @author Stefan Zoller
*/
public class PCACodonModel extends AbstractCodonModel {
// principal components, means, scale factors
protected AbstractPCARateMatrix rateMatrix;
protected byte[] rateMap;
private Parameter pcFactors;
/**
* constructor
*
* @param codonDataType Data type as Codons.UNIVERSAL
* @param pcaType Rate matrix with PCs, means, scale factors
* @param pcaDimensionParameter Scalars for PCs
* @param freqModel Frequency model
*/
public PCACodonModel(Codons codonDataType,
AbstractPCARateMatrix pcaType,
Parameter pcaDimensionParameter,
FrequencyModel freqModel)
{
super(PCACodonModelParser.PCA_CODON_MODEL, codonDataType, freqModel);
this.rateMatrix = pcaType;
// initialize scalars for principal components
this.pcFactors = pcaDimensionParameter;
double[] startFacs = pcaType.getStartFacs();
double facSum = 0.0;
for(int i=0; i<pcFactors.getDimension(); i++) {
facSum += startFacs[i];
}
for(int i=0; i<pcFactors.getDimension(); i++) {
pcFactors.setParameterValueQuietly(i, startFacs[i]/facSum);
}
addVariable(pcFactors);
pcFactors.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0,
pcFactors.getDimension()));
}
// setup substitution matrix
public void setupRelativeRates() {
double[] m = rateMatrix.getMeans();
double[] sc = rateMatrix.getScales();
for (int i = 0; i < rateCount; i++) {
relativeRates[i] = m[i];
}
for(int j = 0; j < pcFactors.getDimension(); j++) {
double[] pc = rateMatrix.getPCAt(j);
double f = pcFactors.getParameterValue(j);
for (int i = 0; i < rateCount; i++) {
relativeRates[i] += f*pc[i]*sc[i];
}
}
for (int i = 0; i < rateCount; i++) {
if(relativeRates[i]<0) {
relativeRates[i] = 0.0;
}
}
}
protected void ratesChanged() {
}
protected void frequenciesChanged() {
}
/**
* Getter and setter for Parameter pcFactor
*/
public double getPcFactor(int dim) {
return pcFactors.getParameterValue(dim);
}
public double[] getPcFactor() {
return pcFactors.getParameterValues();
}
public void setPcFactor(int dim, double fac) {
pcFactors.setParameterValue(dim, fac);
updateMatrix = true;
}
public void setPcFactor(double[] fac) {
for(int i=0; i<pcFactors.getDimension(); i++) {
pcFactors.setParameterValue(i, fac[i]);
}
updateMatrix = true;
}
// **************************************************************
// XHTMLable IMPLEMENTATION
// **************************************************************
public String toXHTML() {
StringBuffer buffer = new StringBuffer();
buffer.append("<em>PCA Codon Model</em>");
return buffer.toString();
}
static String format1 = "%2.1e";
static String format2 = "%2.4e";
public String printQ() {
double[][] myQ = getQ();
if (myQ != null) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < myQ.length; i++) {
for(int j = 0; j < myQ[0].length; j++) {
sb.append(String.format(format1, myQ[i][j]));
sb.append("\t");
}
sb.append("\n");
}
return sb.toString();
} else {
return "No Q ready.";
}
}
public String printRelRates() {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < relativeRates.length; i++) {
sb.append(String.format(format2, relativeRates[i]));
sb.append("\t");
}
sb.append("\n");
return sb.toString();
}
}