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#include "likelihoodComputation2Codon.h"
#include "wYangModel.h"
#include "definitions.h"
#include "tree.h"
#include "computeUpAlg.h"
#include "likelihoodComputation.h"
#include <cmath>
#include <cassert>
using namespace likelihoodComputation2Codon;
MDOUBLE likelihoodComputation2Codon::getTreeLikelihoodAllPosAlphTheSame(const tree& et,
const sequenceContainer& sc,
const vector<stochasticProcess>& spVec,const distribution * distr){
computePijGam pi;
pi._V.resize(distr->categories());
for (int i=0; i < spVec.size(); ++i) {
pi._V[i].fillPij(et,spVec[i]);
}
suffStatGlobalGam ssc;
computeUpAlg cup;
cup.fillComputeUp(et,sc,pi,ssc);
MDOUBLE res = 0.0;
int k;
for (k=0; k < sc.seqLen(); ++k) {
MDOUBLE lnL = log(likelihoodComputation2Codon::getProbOfPosUpIsFilledSelectionGam(k,//pos,
et,//const tree&
sc,// sequenceContainer& sc,
spVec[0],
ssc[k],//const computePijGam& ,
distr)); //W distribution ,
LOG(20,<<"pos= "<<k<<" lnL= "<<lnL<<endl);
res += lnL;
//if (k==5) exit(0);
}
return res;
}
MDOUBLE likelihoodComputation2Codon::getProbOfPosUpIsFilledSelectionGam(const int pos,const tree& et,
const sequenceContainer& sc,
const stochasticProcess& sp,
const suffStatGlobalGamPos& cup,const distribution * distr){
doubleRep tmp=0.0;
for (int categor = 0; categor < distr->categories(); ++categor) {
doubleRep veryTmp =0;
for (int let =0; let < sc.alphabetSize(); ++let) {
veryTmp+=cup.get(categor,et.getRoot()->id(),let) * sp.freq(let);
}
//cout<<"category= "<<categor<<" fh= "<<veryTmp<<" freqCategor= "<<distr->ratesProb(categor)<<endl;
tmp += veryTmp*distr->ratesProb(categor);
}
assert(tmp>0.0);
return convert(tmp);
}
MDOUBLE likelihoodComputation2Codon::getTreeLikelihoodFromUp2(const tree& et,
const sequenceContainer& sc,
const stochasticProcess& sp,
const suffStatGlobalGam& cup,
Vdouble& posLike, // fill this vector with each position likelihood but without the weights.
const distribution * distr,
const Vdouble * weights) {
posLike.clear();
MDOUBLE like = 0;
//computing the likelihood from up:
for (int pos = 0; pos < sc.seqLen(); ++pos) {
doubleRep tmp=0;
for (int categor = 0; categor < distr->categories(); ++categor) {
doubleRep veryTmp =0;
for (int let =0; let < sc.alphabetSize(); ++let) {
veryTmp+=cup.get(pos,categor,et.getRoot()->id(),let) * sp.freq(let);
}
tmp += veryTmp*distr->ratesProb(categor);
}
assert(tmp>0.0);
like += log(tmp) * (weights?(*weights)[pos]:1);
posLike.push_back(convert(tmp));
}
return like;
}
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