/usr/include/libphylo/bblEM.h is in rate4site 3.0.0-5.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | // $Id: bblEM.h 8174 2010-06-20 08:38:12Z cohenofi $
#ifndef ___BBL_EM_H
#define ___BBL_EM_H
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "countTableComponent.h"
#include "computePijComponent.h"
#include "suffStatComponent.h"
#include "unObservableData.h"
#include <vector>
using namespace std;
class bblEM {
public:
explicit bblEM(tree& et,
const sequenceContainer& sc,
const stochasticProcess& sp,
const Vdouble * weights = NULL,
const int maxIterations=50,
const MDOUBLE epsilon=0.05,
const MDOUBLE tollForPairwiseDist=0.001,
unObservableData* unObservableData_p=NULL,
const MDOUBLE* likelihoodLast=NULL);
MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
private:
MDOUBLE compute_bblEM(const int maxIterations,
const MDOUBLE epsilon,
const MDOUBLE tollForPairwiseDist,
const MDOUBLE* likelihoodLast=NULL);
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 doubleRep posProb, const MDOUBLE weig);
void optimizeBranches(const MDOUBLE tollForPairwiseDist);
void allocatePlace();
MDOUBLE _treeLikelihood;
tree& _et;
const sequenceContainer& _sc;
const stochasticProcess& _sp;
vector<countTableComponentGam> _computeCountsV; // for each node - a table of rate*alph*alph
computePijGam _pij;
suffStatGlobalGam _cup;
suffStatGlobalGamPos _cdown;
const Vdouble * _weights;
VdoubleRep _posLike;
unObservableData* _unObservableData_p;
};
#endif
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