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// $Id: tamura92.cpp 962 2006-11-07 15:13:34Z privmane $
#include "tamura92.h"
#include "errorMsg.h"
// This implementation was copied from the Bio++ Phyl library (by Julien Dutheil) - file T92.cpp
tamura92::tamura92(const MDOUBLE theta,
const MDOUBLE TrTv)
: _theta(theta), _TrTv(TrTv) {
_freq.resize(4);
changeTheta(theta);
}
void tamura92::changeTheta(const MDOUBLE theta) {
_theta = theta;
_freq[0] = _freq[3] = (1.0 - theta) / 2.0;
_freq[1] = _freq[2] = theta / 2.0;
}
const MDOUBLE tamura92::Pij_t(const int i, const int j, const MDOUBLE t) const {
double k = (_TrTv + 1.0) / 2.0;
double r = 2.0 / (1.0 + 2.0 * _theta * _TrTv - 2.0 * _theta * _theta * _TrTv);
double l = r * t;
double exp1 = exp(-l);
double exp2 = exp(-k * l);
switch(i) {
//A
case 0 : {
switch(j) {
case 0 : return _freq[0] * (1.0 + exp1) + _theta * exp2; //A
case 1 : return _freq[1] * (1.0 - exp1); //C
case 2 : return _freq[2] * (1.0 + exp1) - _theta * exp2; //G
case 3 : return _freq[3] * (1.0 - exp1); //T, U
}
}
//C
case 1 : {
switch(j) {
case 0 : return _freq[0] * (1.0 - exp1); //A
case 1 : return _freq[1] * (1.0 + exp1) + (1. - _theta) * exp2; //C
case 2 : return _freq[2] * (1.0 - exp1); //G
case 3 : return _freq[3] * (1.0 + exp1) - (1. - _theta) * exp2; //T, U
}
}
//G
case 2 : {
switch(j) {
case 0 : return _freq[0] * (1.0 + exp1) - (1. - _theta) * exp2; //A
case 1 : return _freq[1] * (1.0 - exp1); //C
case 2 : return _freq[2] * (1.0 + exp1) + (1. - _theta) * exp2; //G
case 3 : return _freq[3] * (1.0 - exp1); //T, U
}
}
//T, U
case 3 : {
switch(j) {
case 0 : return _freq[0] * (1.0 - exp1); //A
case 1 : return _freq[1] * (1.0 + exp1) - _theta * exp2; //C
case 2 : return _freq[2] * (1.0 - exp1); //G
case 3 : return _freq[3] * (1.0 + exp1) + _theta * exp2; //T, U
}
}
}
return -1;
}
const MDOUBLE tamura92::dPij_dt(const int i,const int j, const MDOUBLE t) const {
double k = (_TrTv + 1.0) / 2.0;
double r = 2.0 / (1.0 + 2.0 * _theta * _TrTv - 2.0 * _theta * _theta * _TrTv);
double l = r * t;
double exp1 = exp(-l);
double exp2 = exp(-k * l);
switch(i) {
//A
case 0 : {
switch(j) {
case 0 : return r * (_freq[0] * - exp1 + _theta * -k * exp2); //A
case 1 : return r * (_freq[1] * exp1); //C
case 2 : return r * (_freq[2] * - exp1 - _theta * -k * exp2); //G
case 3 : return r * (_freq[3] * exp1); //T, U
}
}
//C
case 1 : {
switch(j) {
case 0 : return r * (_freq[0] * exp1); //A
case 1 : return r * (_freq[1] * - exp1 + (1.0 - _theta) * -k * exp2); //C
case 2 : return r * (_freq[2] * exp1); //G
case 3 : return r * (_freq[3] * - exp1 - (1.0 - _theta) * -k * exp2); //T, U
}
}
//G
case 2 : {
switch(j) {
case 0 : return r * (_freq[0] * - exp1 - (1.0 - _theta) * -k * exp2); //A
case 1 : return r * (_freq[1] * exp1); //C
case 2 : return r * (_freq[2] * - exp1 + (1.0 - _theta) * -k * exp2); //G
case 3 : return r * (_freq[3] * exp1); //T, U
}
}
//T, U
case 3 : {
switch(j) {
case 0 : return r * (_freq[0] * exp1); //A
case 1 : return r * (_freq[1] * - exp1 - _theta * -k * exp2); //C
case 2 : return r * (_freq[2] * exp1); //G
case 3 : return r * (_freq[3] * - exp1 + _theta * -k * exp2); //T, U
}
}
}
return -1;
}
const MDOUBLE tamura92::d2Pij_dt2(const int i,const int j, const MDOUBLE t) const {
double k = (_TrTv + 1.0) / 2.;
double k2 = k * k;
double r = 2.0 / (1.0 + 2.0 * _theta * _TrTv - 2.0 * _theta * _theta * _TrTv);
double l = r * t;
double r2 = r * r;
double exp1 = exp(-l);
double exp2 = exp(-k * l);
switch(i) {
//A
case 0 : {
switch(j) {
case 0 : return r2 * (_freq[0] * exp1 + _theta * k2 * exp2); //A
case 1 : return r2 * (_freq[1] * - exp1); //C
case 2 : return r2 * (_freq[2] * exp1 - _theta * k2 * exp2); //G
case 3 : return r2 * (_freq[3] * - exp1); //T, U
}
}
//C
case 1 : {
switch(j) {
case 0 : return r2 * (_freq[0] * - exp1); //A
case 1 : return r2 * (_freq[1] * exp1 + (1.0 - _theta) * k2 * exp2); //C
case 2 : return r2 * (_freq[2] * - exp1); //G
case 3 : return r2 * (_freq[3] * exp1 - (1.0 - _theta) * k2 * exp2); //T, U
}
}
//G
case 2 : {
switch(j) {
case 0 : return r2 * (_freq[0] * exp1 - (1.0 - _theta) * k2 * exp2); //A
case 1 : return r2 * (_freq[1] * - exp1); //C
case 2 : return r2 * (_freq[2] * exp1 + (1.0 - _theta) * k2 * exp2); //G
case 3 : return r2 * (_freq[3] * - exp1); //T, U
}
}
//T, U
case 3 : {
switch(j) {
case 0 : return r2 * (_freq[0] * - exp1); //A
case 1 : return r2 * (_freq[1] * exp1 - _theta * k2 * exp2); //C
case 2 : return r2 * (_freq[2] * - exp1); //G
case 3 : return r2 * (_freq[3] * exp1 + _theta * k2 * exp2); //T, U
}
}
}
return -1;
}
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