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74 lines
2.5 KiB
C++
74 lines
2.5 KiB
C++
// $Id: bblEM2USSRV.h 1504 2007-01-15 14:04:44Z osnatz $
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//copy of bblEM of the codon model + changes
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#ifndef ___BBL_EM_2_USSRV
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#define ___BBL_EM_2_USSRV
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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 "ussrvModel.h"
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#include "computeUpAlg.h"
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#include "computeDownAlg.h"
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#include "computeCounts.h"
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#include "treeIt.h"
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#include "fromCountTableComponentToDistance2USSRV.h"
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#include "likelihoodComputation2USSRV.h"
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#include "someUtil.h"
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#include <vector>
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using namespace std;
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// @@@@ maybe should inherit from bblEM
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class bblEM2USSRV {
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public:
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explicit bblEM2USSRV(tree& et,
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const sequenceContainer& sc,
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const sequenceContainer& baseSc,
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const ussrvModel &model,
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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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MDOUBLE getTreeLikelihood() const {return _treeLikelihood;}
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private:
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MDOUBLE compute_bblEM(int maxIterations,
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MDOUBLE epsilon,
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MDOUBLE tollForPairwiseDist);
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void bblEM_it(MDOUBLE tollForPairwiseDist);
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void computeDown(int pos);
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void computeUp();
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void addCounts(int pos);
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void addCounts(int pos, tree::nodeP mynode, doubleRep posProb, MDOUBLE weig);
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void optimizeBranches(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 sequenceContainer& _baseSc;
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const ussrvModel& _model;
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vector<countTableComponentGam> _computeCountsBaseV; // for each node - a table of rate*alph*alph (see below)
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vector<countTableComponentHom> _computeCountsSsrvV; // for each node - a table of rate*alph*alph (see below)
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computePijGam _pijBase;
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computePijHom _pijSSRV;
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suffStatGlobalGam _cupBase;
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suffStatGlobalHom _cupSSRV;
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suffStatGlobalGamPos _cdownBase;
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suffStatGlobalHomPos _cdownSSRV;
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const Vdouble * _weights;
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VdoubleRep _posLike;
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};
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// _computeCountsV is a vector containing for each node a countTableComponentGam.
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// countTableComponentGam is a vector containing for each rate category a table of size alphabet*alphabet
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// (VVdouble) which should be pre-filled with Pij(x,y,rk) from equation (17) in the EM-BBL theory summary.
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// Pij(x,y,rk) represents the probability of observing x and y along a branch ti at position j with rate from
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// category k.
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// For this reason, we need to initialize this class and calculate it again for every position.
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#endif // bblEM2USSRV
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