mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 03:40:25 +08:00
52 lines
1.6 KiB
C++
52 lines
1.6 KiB
C++
// $Id: bblEMProportional.h 9304 2011-02-20 16:53:19Z rubi $
|
|
#ifndef ___BBL_EM_PROPORTIONAL_H
|
|
#define ___BBL_EM_PROPORTIONAL_H
|
|
|
|
#include "definitions.h"
|
|
#include "tree.h"
|
|
#include "stochasticProcess.h"
|
|
#include "sequenceContainer.h"
|
|
|
|
#include <vector>
|
|
using namespace std;
|
|
|
|
|
|
class bblEMProportional {
|
|
public:
|
|
explicit bblEMProportional(tree& et,
|
|
const vector<sequenceContainer>& sc,
|
|
const vector<stochasticProcess>& sp,
|
|
const vector<Vdouble *> * weights = NULL,
|
|
const int maxIterations=50,
|
|
const MDOUBLE epsilon=0.05,
|
|
const MDOUBLE tollForPairwiseDist=0.0001);
|
|
MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
|
|
|
|
|
|
private:
|
|
MDOUBLE compute_bblEMProp(const int maxIterations,const MDOUBLE epsilon,const MDOUBLE tollForPairwiseDist);
|
|
void allocatePlaceProp();
|
|
void computeUpProp();
|
|
void bblEM_itProp(const MDOUBLE tollForPairwiseDist);
|
|
void computeDownProp(const int gene, const int pos);
|
|
void addCountsProp(const int gene, const int pos);
|
|
void addCountsProp(const int gene,const int pos, tree::nodeP mynode, const doubleRep posProb, const MDOUBLE weig);
|
|
void optimizeBranchesProp(const MDOUBLE tollForPairwiseDist);
|
|
|
|
MDOUBLE _treeLikelihood;
|
|
tree& _et;
|
|
const vector<sequenceContainer>& _sc;
|
|
const vector<stochasticProcess>& _sp;
|
|
const vector<Vdouble *> * _weights;
|
|
int _numberOfGenes;
|
|
vector< vector<countTableComponentGam> > _computeCountsV; // for each gene, for each node - a table of rate*alph*alph
|
|
vector<suffStatGlobalGam> _cup;
|
|
vector<suffStatGlobalGamPos> _cdown;
|
|
vector<computePijGam> _pij;
|
|
VVdoubleRep _posLike;
|
|
|
|
|
|
};
|
|
|
|
#endif
|