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56 lines
2.3 KiB
C++
56 lines
2.3 KiB
C++
// $Id: bblEMProportional.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___BBL_EM_PROPORTIONALEB_H
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#define ___BBL_EM_PROPORTIONALEB_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 "multipleStochasticProcess.h"
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#include <vector>
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using namespace std;
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class bblEMProportionalEB {
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public:
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explicit bblEMProportionalEB(tree& et,
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const vector<sequenceContainer>& sc,
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multipleStochasticProcess* msp,
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const gammaDistribution* pProportionDist,
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const bool optimizeSelectedBranches=false,
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const vector<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=0.0001,
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const MDOUBLE* likelihoodLast=NULL);
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Vdouble getTreeLikelihood() const {return _treeLikelihoodVec;}
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private:
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Vdouble compute_bblEMPropEB(const int maxIterations,const MDOUBLE epsilon,const MDOUBLE tollForPairwiseDist,const MDOUBLE* likelihoodLast=NULL);
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void allocatePlacePropEB();
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void computeUpPropEB();
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void bblEM_itPropEB(const MDOUBLE tollForPairwiseDist);
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void computeDownPropEB(const int gene, const int pos);
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void addCountsPropEB(const int gene, const int pos);
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void addCountsPropEB(const int gene,const int pos, tree::nodeP mynode, const VdoubleRep posProb, const MDOUBLE weig);
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void optimizeBranchesPropEB(const MDOUBLE tollForPairwiseDist);
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Vdouble _treeLikelihoodVec;
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tree& _et;
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const vector<sequenceContainer>& _sc;
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multipleStochasticProcess* _msp;
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const gammaDistribution* _pProportionDist;
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const vector<Vdouble *> * _weights;
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int _numberOfGenes;
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vector< vector<countTableComponentGamProportional> > _computeCountsV; // for each gene, for each node - a table of globalRate*localRate*alph*alph - [globalRateCategory][localRateCategory][character]
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vector<suffStatGlobalGamProportional> _cup; //[gene][pos][globalRateCategory][localRateCategory][nodeID][character]
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vector<suffStatGlobalGamProportionalPos> _cdown; //[gene][globalRateCategory][localRateCategory][nodeID][character]
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vector< vector<computePijGam> > _pij;//[gene][globalRateCategory]
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VVVdoubleRep _posLike;//[gene][pos][globalRateCategory]
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const bool _optimizeSelectedBranches;
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};
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#endif
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