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55 lines
2.0 KiB
C++
55 lines
2.0 KiB
C++
#ifndef ___R4SP_BBL_LS
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#define ___R4SP_BBL_LS
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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 "gammaDistribution.h"
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#include "likelihoodComputation.h"
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#include <vector>
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using namespace std;
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#define MAX_BRANCH_LENGTH 10.0
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/*
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This class optimize the branches using "naive" line search methodology.
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go over each branch and optimize it using brent.
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In one iteration it optimze seperatly all branches.
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This procedure continues until convergence is reached or until the maximum number of iteration is reached.
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*/
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class bblLSProportionalEB {
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public:
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explicit bblLSProportionalEB(tree& et, const vector<sequenceContainer>& sc, multipleStochasticProcess* msp, const gammaDistribution* pProportionDist, Vdouble& treeLikelihoodVec, const bool optimizeSelectedBranches=false, int maxIter=50, MDOUBLE epsilon=0.05);
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~bblLSProportionalEB() {};
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Vdouble getTreeLikelihoodVec() const {return _treeLikelihoodVec;}
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private:
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Vdouble optimizeBranches(tree& et, const vector<sequenceContainer>& sc, multipleStochasticProcess* msp, const gammaDistribution* pProportionDist, Vdouble& treeLikelihoodVec, const bool optimizeSelectedBranches=false, int maxIter=50, MDOUBLE epsilon=0.05);
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private:
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Vdouble _treeLikelihoodVec;
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};
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class evalR4SPBranch{
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public:
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explicit evalR4SPBranch(tree::nodeP pNode, tree& et, const vector<sequenceContainer>& sc, multipleStochasticProcess* msp, const gammaDistribution* pProportionDist)
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:_pNode(pNode),_et(et), _sc(sc), _msp(msp), _pProportionDist(pProportionDist){};
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private:
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tree::nodeP _pNode;
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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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public:
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MDOUBLE operator() (MDOUBLE bl) {
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_pNode->setDisToFather(bl);
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Vdouble likeVec = likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(_et,_sc,_msp,_pProportionDist);
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MDOUBLE res = sumVdouble(likeVec);
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return -res;
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}
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};
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#endif
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