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90 lines
3.2 KiB
C++
90 lines
3.2 KiB
C++
// $Id: bblEM.h 4478 2008-07-17 17:09:55Z cohenofi $
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#ifndef ___BBL_EM_GL__FIXED_ROOT
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#define ___BBL_EM_GL__FIXED_ROOT
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/********************************************************************************************
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Class::bblEM (with variation: bblEMfixRoot, bblEM2codon)
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compute_bblEM
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allocatePlace (one more level for fixRoot - in computeDownAlg and countsTableVec)
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bblEM_it (called at each iteration of BBL)
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foreach pos{
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computeDown (use variants for fix root - fillComputeDownNonReversible
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vector<suffStatGlobalGamPos> _cdown; //_cdown[categ][letter@root][nodeid][letter][prob])
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addCounts
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addCountsFixedRoot (based on computeUp and computeDown... fill _computeCountsV)
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use class::computeCounts (but no duplicated class!!!)
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}
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optimizeBranches
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foreach node{
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class::fromCountTableComponentToDistance (with variation: ...fixRoot, ...2Codon)
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computeDistance() + set - based on
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class::likeDist (with variation: ...fixRoot, ...2Codon)
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giveDistance()
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giveDistanceBrent()
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C_evallikeDist and C_evallikeDist_d
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.... computation based on counts{alph1,alph2, root, rate(sp)}: sumL+= _ctc.getCounts(alph1,alph2,rateCategor)*(log( _sp.Pij_t(alph1,alph2,dist*rate) )-log(_sp.freq(alph2)))
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}
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*********************************************************************************************/
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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 "gainLossAlphabet.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 bblEMfixRoot {
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public:
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explicit bblEMfixRoot(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 addCountsFixedRoot(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< vector< countTableComponentGam > > _computeCountsV; // _computeCountsV [node] [letter@root] [rate][alph][alph]
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computePijGam _pij;
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suffStatGlobalGam _cup; //_cup[pos][categ][nodeid][letter][prob]
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//suffStatGlobalGamPos _cdown; // for each pos: computeDown(pos); addCounts(pos);
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vector<suffStatGlobalGamPos> _cdown; //_cdown[categ][letter@root][nodeid][letter][prob] - since fillComputeDownNonReversible uses this assumption
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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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