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52 lines
1.6 KiB
C++
52 lines
1.6 KiB
C++
// $Id: bblEMProportional.h 9304 2011-02-20 16:53:19Z rubi $
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#ifndef ___BBL_EM_PROPORTIONAL_H
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#define ___BBL_EM_PROPORTIONAL_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 <vector>
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using namespace std;
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class bblEMProportional {
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public:
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explicit bblEMProportional(tree& et,
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const vector<sequenceContainer>& sc,
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const vector<stochasticProcess>& sp,
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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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MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
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private:
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MDOUBLE compute_bblEMProp(const int maxIterations,const MDOUBLE epsilon,const MDOUBLE tollForPairwiseDist);
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void allocatePlaceProp();
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void computeUpProp();
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void bblEM_itProp(const MDOUBLE tollForPairwiseDist);
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void computeDownProp(const int gene, const int pos);
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void addCountsProp(const int gene, const int pos);
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void addCountsProp(const int gene,const int pos, tree::nodeP mynode, const doubleRep posProb, const MDOUBLE weig);
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void optimizeBranchesProp(const MDOUBLE tollForPairwiseDist);
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MDOUBLE _treeLikelihood;
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tree& _et;
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const vector<sequenceContainer>& _sc;
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const vector<stochasticProcess>& _sp;
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const vector<Vdouble *> * _weights;
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int _numberOfGenes;
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vector< vector<countTableComponentGam> > _computeCountsV; // for each gene, for each node - a table of rate*alph*alph
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vector<suffStatGlobalGam> _cup;
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vector<suffStatGlobalGamPos> _cdown;
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vector<computePijGam> _pij;
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VVdoubleRep _posLike;
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};
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#endif
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