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//copy of bblEM of the lib + changing to codon model
#ifndef ___BBL_EM_2_CODON_H
#define ___BBL_EM_2_CODON_H
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "countTableComponent.h"
#include "computePijComponent.h"
#include "suffStatComponent.h"
#include <vector>
using namespace std;
class bblEM2codon {
public:
explicit bblEM2codon(tree& et,
const sequenceContainer& sc,
const vector<stochasticProcess> &spVec,
const distribution *in_distr,
const Vdouble * weights = NULL,
const int maxIterations=50,
const MDOUBLE epsilon=0.05,
const MDOUBLE tollForPairwiseDist=0.001);
MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
virtual ~bblEM2codon();
private:
MDOUBLE compute_bblEM(const int maxIterations,
const MDOUBLE epsilon,
const MDOUBLE tollForPairwiseDist);
void bblEM_it(const MDOUBLE tollForPairwiseDist);
void computeDown(const int pos);
void computeUp();
void addCounts(const int pos);
void addCounts(const int pos, tree::nodeP mynode, const MDOUBLE posProb, const MDOUBLE weig);
void optimizeBranches(const MDOUBLE tollForPairwiseDist);
void allocatePlace();
MDOUBLE _treeLikelihood;
tree& _et;
const sequenceContainer& _sc;
const vector<stochasticProcess>& _spVec;
const distribution *_distr;
vector<countTableComponentGam> _computeCountsV; // for each node - a table of rate*alph*alph
computePijGam _pij;
suffStatGlobalGam _cup;
suffStatGlobalGamPos _cdown;
const Vdouble * _weights;
Vdouble _posLike;
};
#endif
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