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