/usr/include/libphylo/bblEMProportionalEB.h is in rate4site 3.0.0-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | // $Id: bblEMProportional.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___BBL_EM_PROPORTIONALEB_H
#define ___BBL_EM_PROPORTIONALEB_H
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "multipleStochasticProcess.h"
#include <vector>
using namespace std;
class bblEMProportionalEB {
public:
explicit bblEMProportionalEB(tree& et,
const vector<sequenceContainer>& sc,
multipleStochasticProcess* msp,
const gammaDistribution* pProportionDist,
const bool optimizeSelectedBranches=false,
const vector<Vdouble *> * weights = NULL,
const int maxIterations=50,
const MDOUBLE epsilon=0.05,
const MDOUBLE tollForPairwiseDist=0.0001,
const MDOUBLE* likelihoodLast=NULL);
Vdouble getTreeLikelihood() const {return _treeLikelihoodVec;}
private:
Vdouble compute_bblEMPropEB(const int maxIterations,const MDOUBLE epsilon,const MDOUBLE tollForPairwiseDist,const MDOUBLE* likelihoodLast=NULL);
void allocatePlacePropEB();
void computeUpPropEB();
void bblEM_itPropEB(const MDOUBLE tollForPairwiseDist);
void computeDownPropEB(const int gene, const int pos);
void addCountsPropEB(const int gene, const int pos);
void addCountsPropEB(const int gene,const int pos, tree::nodeP mynode, const VdoubleRep posProb, const MDOUBLE weig);
void optimizeBranchesPropEB(const MDOUBLE tollForPairwiseDist);
Vdouble _treeLikelihoodVec;
tree& _et;
const vector<sequenceContainer>& _sc;
multipleStochasticProcess* _msp;
const gammaDistribution* _pProportionDist;
const vector<Vdouble *> * _weights;
int _numberOfGenes;
vector< vector<countTableComponentGamProportional> > _computeCountsV; // for each gene, for each node - a table of globalRate*localRate*alph*alph - [globalRateCategory][localRateCategory][character]
vector<suffStatGlobalGamProportional> _cup; //[gene][pos][globalRateCategory][localRateCategory][nodeID][character]
vector<suffStatGlobalGamProportionalPos> _cdown; //[gene][globalRateCategory][localRateCategory][nodeID][character]
vector< vector<computePijGam> > _pij;//[gene][globalRateCategory]
VVVdoubleRep _posLike;//[gene][pos][globalRateCategory]
const bool _optimizeSelectedBranches;
};
#endif
|