/*
* TN93.java
*
* Copyright (c) 2002-2016 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.evomodel.substmodel.nucleotide;
import dr.evomodel.substmodel.BaseSubstitutionModel;
import dr.evomodel.substmodel.EigenDecomposition;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evolution.datatype.Nucleotides;
import dr.inference.model.Parameter;
import dr.util.Author;
import dr.util.Citable;
import dr.util.Citation;
import java.util.Collections;
import java.util.List;
/**
* Tamura-Nei model of nucleotide evolution
*
* @author Marc A. Suchard
*/
public class TN93 extends BaseSubstitutionModel implements Citable {
private Parameter kappaParameter1 = null;
private Parameter kappaParameter2 = null;
public TN93(Parameter kappaParameter1, Parameter kappaParameter2, FrequencyModel freqModel) {
super("TN93", Nucleotides.INSTANCE, freqModel);
this.kappaParameter1 = kappaParameter1;
addVariable(kappaParameter1);
kappaParameter1.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.kappaParameter2 = kappaParameter2;
addVariable(kappaParameter2);
kappaParameter2.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
}
public final double getKappa1() {
return kappaParameter1.getParameterValue(0);
}
public final double getKappa2() {
return kappaParameter2.getParameterValue(0);
}
protected void frequenciesChanged() {
}
protected void ratesChanged() {
}
protected void setupRelativeRates(double[] rates) {
double kappa1 = getKappa1();
double kappa2 = getKappa2();
rates[0] = 1.0;
rates[1] = kappa1;
rates[2] = 1.0;
rates[3] = 1.0;
rates[4] = kappa2;
rates[5] = 1.0;
}
public synchronized EigenDecomposition getEigenDecomposition() {
if (eigenDecomposition == null) {
double[] evec = new double[stateCount * stateCount];
double[] ivec = new double[stateCount * stateCount];
double[] eval = new double[stateCount];
eigenDecomposition = new EigenDecomposition(evec, ivec, eval);
ivec[2 * stateCount + 1] = 1; // left eigenvectors 3 = (0,1,0,-1); 4 = (1,0,-1,0)
ivec[2 * stateCount + 3] = -1;
ivec[3 * stateCount + 0] = 1;
ivec[3 * stateCount + 2] = -1;
evec[0 * stateCount + 0] = 1; // right eigenvector 1 = (1,1,1,1)'
evec[1 * stateCount + 0] = 1;
evec[2 * stateCount + 0] = 1;
evec[3 * stateCount + 0] = 1;
}
if (updateMatrix) {
double[] evec = eigenDecomposition.getEigenVectors();
double[] ivec = eigenDecomposition.getInverseEigenVectors();
double[] pi = freqModel.getFrequencies();
double piR = pi[0] + pi[2];
double piY = pi[1] + pi[3];
// left eigenvector #1
ivec[0 * stateCount + 0] = pi[0]; // or, evec[0] = pi;
ivec[0 * stateCount + 1] = pi[1];
ivec[0 * stateCount + 2] = pi[2];
ivec[0 * stateCount + 3] = pi[3];
// left eigenvector #2
ivec[1 * stateCount + 0] = pi[0] * piY;
ivec[1 * stateCount + 1] = -pi[1] * piR;
ivec[1 * stateCount + 2] = pi[2] * piY;
ivec[1 * stateCount + 3] = -pi[3] * piR;
// right eigenvector #2
evec[0 * stateCount + 1] = 1.0 / piR;
evec[1 * stateCount + 1] = -1.0 / piY;
evec[2 * stateCount + 1] = 1.0 / piR;
evec[3 * stateCount + 1] = -1.0 / piY;
// right eigenvector #3
evec[1 * stateCount + 2] = pi[3] / piY;
evec[3 * stateCount + 2] = -pi[1] / piY;
// right eigenvector #4
evec[0 * stateCount + 3] = pi[2] / piR;
evec[2 * stateCount + 3] = -pi[0] / piR;
// eigenvectors
double[] eval = eigenDecomposition.getEigenValues();
final double kappa1 = getKappa1();
final double kappa2 = getKappa2();
final double beta = -1.0 / (2.0 * (piR * piY + kappa1 * pi[0] * pi[2] + kappa2 * pi[1] * pi[3]));
final double A_R = 1.0 + piR * (kappa1 - 1);
final double A_Y = 1.0 + piY * (kappa2 - 1);
eval[1] = beta;
eval[2] = beta * A_Y;
eval[3] = beta * A_R;
updateMatrix = false;
}
return eigenDecomposition;
}
@Override
public Citation.Category getCategory() {
return Citation.Category.SUBSTITUTION_MODELS;
}
@Override
public String getDescription() {
return "Tamura-Nei nucleotide substitution model";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(CITATION);
}
public static Citation CITATION = new Citation(
new Author[]{
new Author("K", "Tamura"),
new Author("M", "Nei")
},
"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees",
1993,
"Mol Biol Evol",
10, 512, 526
);
}