/*
* AbstractCodonModel.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.codon;
import dr.evomodel.substmodel.BaseSubstitutionModel;
import dr.evomodel.substmodel.EigenSystem;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evolution.datatype.AminoAcids;
import dr.evolution.datatype.Codons;
import dr.evolution.datatype.GeneticCode;
import dr.evolution.datatype.Nucleotides;
/**
* @author Marc A. Suchard
*/
public abstract class AbstractCodonModel extends BaseSubstitutionModel {
/** kappa */
// protected Parameter kappaParameter;
/**
* omega
*/
// protected Parameter omegaParameter;
protected byte[] rateMap;
protected Codons codonDataType;
protected GeneticCode geneticCode;
// public AbstractCodonModel(Codons codonDataType, Parameter omegaParameter, Parameter kappaParameter,
// FrequencyModel freqModel) {
// this(codonDataType, omegaParameter, kappaParameter, freqModel,
// new DefaultEigenSystem(codonDataType.getStateCount()));
// }
public AbstractCodonModel(String name, Codons codonDataType, FrequencyModel freqModel, EigenSystem eigenSystem) {
super(name, codonDataType, freqModel, eigenSystem);
this.codonDataType = codonDataType;
this.geneticCode = codonDataType.getGeneticCode();
constructRateMap();
updateMatrix = true;
}
/*public AbstractCodonModel(Codons codonDataType,
FrequencyModel freqModel, EigenSystem eigenSystem) {
super("GY94", codonDataType, freqModel, eigenSystem);
this.codonDataType = codonDataType;
this.geneticCode = codonDataType.getGeneticCode();
constructRateMap();
updateMatrix = true;
}*/
protected void frequenciesChanged() {
}
protected void ratesChanged() {
}
abstract protected void setupRelativeRates(double[] rates);
/**
* Construct a map of the rate classes in the rate matrix using the current
* genetic code. Classes:
* 0: codon changes in more than one codon position (or stop codons)
* 1: synonymous transition
* 2: synonymous transversion
* 3: non-synonymous transition
* 4: non-synonymous transversion
*/
protected void constructRateMap() {
// Refactored into static function, since CodonProductChains need this functionality
rateMap = Codons.constructRateMap(rateCount, stateCount, codonDataType, geneticCode);
}
public void printRateMap() {
int u, v, i1, j1, k1, i2, j2, k2;
byte rateClass;
int[] codon;
int cs1, cs2, aa1, aa2;
System.out.print("\t");
for (v = 0; v < stateCount; v++) {
codon = codonDataType.getTripletStates(v);
i2 = codon[0];
j2 = codon[1];
k2 = codon[2];
System.out.print("\t" + Nucleotides.INSTANCE.getChar(i2));
System.out.print(Nucleotides.INSTANCE.getChar(j2));
System.out.print(Nucleotides.INSTANCE.getChar(k2));
}
System.out.println();
System.out.print("\t");
for (v = 0; v < stateCount; v++) {
codon = codonDataType.getTripletStates(v);
i2 = codon[0];
j2 = codon[1];
k2 = codon[2];
cs2 = codonDataType.getState(i2, j2, k2);
aa2 = geneticCode.getAminoAcidState(codonDataType.getCanonicalState(cs2));
System.out.print("\t" + AminoAcids.INSTANCE.getChar(aa2));
}
System.out.println();
for (u = 0; u < stateCount; u++) {
codon = codonDataType.getTripletStates(u);
i1 = codon[0];
j1 = codon[1];
k1 = codon[2];
System.out.print(Nucleotides.INSTANCE.getChar(i1));
System.out.print(Nucleotides.INSTANCE.getChar(j1));
System.out.print(Nucleotides.INSTANCE.getChar(k1));
cs1 = codonDataType.getState(i1, j1, k1);
aa1 = geneticCode.getAminoAcidState(codonDataType.getCanonicalState(cs1));
System.out.print("\t" + AminoAcids.INSTANCE.getChar(aa1));
for (v = 0; v < stateCount; v++) {
codon = codonDataType.getTripletStates(v);
i2 = codon[0];
j2 = codon[1];
k2 = codon[2];
cs2 = codonDataType.getState(i2, j2, k2);
aa2 = geneticCode.getAminoAcidState(codonDataType.getCanonicalState(cs2));
rateClass = -1;
if (i1 != i2) {
if ((i1 == 0 && i2 == 2) || (i1 == 2 && i2 == 0) || // A <-> G
(i1 == 1 && i2 == 3) || (i1 == 3 && i2 == 1)) { // C <-> T
rateClass = 1; // Transition at position 1
} else {
rateClass = 2; // Transversion at position 1
}
}
if (j1 != j2) {
if (rateClass == -1) {
if ((j1 == 0 && j2 == 2) || (j1 == 2 && j2 == 0) || // A <-> G
(j1 == 1 && j2 == 3) || (j1 == 3 && j2 == 1)) { // C <-> T
rateClass = 1; // Transition
} else {
rateClass = 2; // Transversion
}
} else
rateClass = 0; // Codon changes at more than one position
}
if (k1 != k2) {
if (rateClass == -1) {
if ((k1 == 0 && k2 == 2) || (k1 == 2 && k2 == 0) || // A <-> G
(k1 == 1 && k2 == 3) || (k1 == 3 && k2 == 1)) { // C <-> T
rateClass = 1; // Transition
} else {
rateClass = 2; // Transversion
}
} else
rateClass = 0; // Codon changes at more than one position
}
if (rateClass != 0) {
if (aa1 != aa2) {
rateClass += 2; // Is a non-synonymous change
}
}
System.out.print("\t" + rateClass);
}
System.out.println();
}
}
}