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59 lines
1.6 KiB
C++
59 lines
1.6 KiB
C++
// $Id: bblEM.h 8174 2010-06-20 08:38:12Z cohenofi $
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#ifndef ___BBL_EM_H
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#define ___BBL_EM_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 "countTableComponent.h"
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#include "computePijComponent.h"
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#include "suffStatComponent.h"
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#include "unObservableData.h"
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#include <vector>
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using namespace std;
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class bblEM {
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public:
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explicit bblEM(tree& et,
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const 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=0.001,
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unObservableData* unObservableData_p=NULL,
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const MDOUBLE* likelihoodLast=NULL);
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MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
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private:
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MDOUBLE compute_bblEM(const int maxIterations,
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const MDOUBLE epsilon,
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const MDOUBLE tollForPairwiseDist,
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const MDOUBLE* likelihoodLast=NULL);
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void bblEM_it(const MDOUBLE tollForPairwiseDist);
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void computeDown(const int pos);
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void computeUp();
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void addCounts(const int pos);
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void addCounts(const int pos, tree::nodeP mynode, const doubleRep posProb, const MDOUBLE weig);
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void optimizeBranches(const MDOUBLE tollForPairwiseDist);
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void allocatePlace();
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MDOUBLE _treeLikelihood;
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tree& _et;
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const sequenceContainer& _sc;
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const stochasticProcess& _sp;
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vector<countTableComponentGam> _computeCountsV; // for each node - a table of rate*alph*alph
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computePijGam _pij;
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suffStatGlobalGam _cup;
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suffStatGlobalGamPos _cdown;
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const Vdouble * _weights;
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VdoubleRep _posLike;
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unObservableData* _unObservableData_p;
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};
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#endif
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