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// $Id: goldmanYangModel.cpp 962 2006-11-07 15:13:34Z privmane $
#include "goldmanYangModel.h"
#include "codon.h"
#include "readDatMatrix.h" // for the normalizeQ function.
goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV):
_v(inV),_k(inK),_globalV(_globalV),_codonAlph(inCodonAlph){
homogenousFreq();
_Q.resize(_codonAlph.size());
for (int z=0; z < _Q.size();++z) _Q[z].resize(_codonAlph.size(),0);
updateQ();
}
goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV):
_freq(freq),_v(inV),_k(inK),_globalV(_globalV),_codonAlph(inCodonAlph){
_Q.resize(_codonAlph.size());
for (int z=0; z < _Q.size();++z) _Q[z].resize(_codonAlph.size(),0);
updateQ();
}
void goldmanYangModel::updateQ() {
// building q.
int i,j;
MDOUBLE sum=0.0;
MDOUBLE epsilon=0.00000001;//0.00000000001;
MDOUBLE factor = 1000.0;
for (i=0; i < _Q.size();++i) {
sum=0;
for (j=0; j < _Q.size();++j) {
if (j==i) continue; //same codon
if (codonUtility::codonDiff(i,j,_codonAlph) == codonUtility::tr) {
_Q[i][j] = _k*exp(-(1/factor)*_gcd.getGranthamDistance(codonUtility::aaOf(i,_codonAlph),codonUtility::aaOf(j,_codonAlph))*_v);
if (_Q[i][j]<epsilon) _Q[i][j] = epsilon;
}else if (codonUtility::codonDiff(i,j,_codonAlph) == codonUtility::tv) {
_Q[i][j] = exp(-(1/factor)*_gcd.getGranthamDistance(codonUtility::aaOf(i,_codonAlph),codonUtility::aaOf(j,_codonAlph))*_v);
if (_Q[i][j]<epsilon) _Q[i][j] = epsilon;
}
else _Q[i][j] = 0;//more than one substitution.
_Q[i][j]*=_freq[j];
sum += _Q[i][j];
}
_Q[i][i]=-sum;
}
// check:
/* LOG(5,<<"\n\n\n ===================================== \n");
int a1,a2;
for (a1=0;a1<4;++a1){
for (a2=0;a2<4;++a2){
LOG(5,<<qMatrix[a1][a2]<<"\t");
}
LOG(5,<<endl);
}
*/
if (_globalV == true)
normalizeQ(_Q,_freq);
// check:
/* LOG(5,<<"\n\n\n ===================================== \n");
for (a1=0;a1<4;++a1){
for ( a2=0;a2<4;++a2){
LOG(5,<<qMatrix[a1][a2]<<"\t");
}
LOG(5,<<endl);
}
*/
// updating _q2Pt;
// _Q = qMatrix;
_q2pt.fillFromRateMatrix(_freq,_Q);
}
// original with V and not 1/V
/*
void goldmanYangModel::updateQ() {
// building q.
VVdouble qMatrix(_codonAlph.size());
int i,j,z;
MDOUBLE sum=0.0;
for (z=0; z < qMatrix.size();++z) qMatrix[z].resize(_codonAlph.size(),0);
for (i=0; i < qMatrix.size();++i) {
sum=0;
for (j=0; j < qMatrix.size();++j) {
if (j==i) continue;
if (codonUtility::codonDiff(i,j) == codonUtility::different) {
qMatrix[i][j] =0;
} else if (codonUtility::codonDiff(i,j) == codonUtility::transition) {
qMatrix[i][j] =_k*exp(-_gcd.getGranthamDistance(codonUtility::aaOf(i),codonUtility::aaOf(j))/_v);
} else if (codonUtility::codonDiff(i,j) == codonUtility::transversion) {
qMatrix[i][j] = exp(-_gcd.getGranthamDistance(codonUtility::aaOf(i),codonUtility::aaOf(j))/_v);
}
qMatrix[i][j]*=_freq[j];
sum += qMatrix[i][j];
}
qMatrix[i][i]=-sum;
}
// check:
//LOG(5,<<"\n\n\n ===================================== \n");
//int a1,a2;
//for (a1=0;a1<4;++a1){
// for (a2=0;a2<4;++a2){
// LOG(5,<<qMatrix[a1][a2]<<"\t");
// }
// LOG(5,<<endl);
//}
if (_globalV == true)
normalizeQ(qMatrix,_freq);
//LOG(5,<<"\n\n\n ===================================== \n");
//LOG(5,<<endl<<endl);
//for (a1=0;a1<4;++a1){
// for (a2=0;a2<4;++a2){
// LOG(5,<<qMatrix[a1][a2]<<"\t");
// }
// LOG(5,<<endl);
//}
// updating _q2Pt;
_Q = qMatrix;
_q2pt.fillFromRateMatrix(_freq,qMatrix);
}
*/
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