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82 lines
2.3 KiB
C++
82 lines
2.3 KiB
C++
// $Id: findRateOfGene.cpp 962 2006-11-07 15:13:34Z privmane $
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#include "definitions.h"
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#include "findRateOfGene.h"
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#include "computeUpAlg.h"
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//#define VERBOS
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class findRateOfGene{
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public:
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explicit findRateOfGene(const tree &t,
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const sequenceContainer& sc,
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stochasticProcess& sp,
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const Vdouble * weights): _t(t), _sc(sc),
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_sp(sp),_weights(weights){};
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private:
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const tree& _t;
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const sequenceContainer& _sc;
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stochasticProcess& _sp;
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const Vdouble * _weights;
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public:
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MDOUBLE operator() (const MDOUBLE fac) {
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#ifdef VERBOS
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LOG(5,<<"factor = "<<fac<<endl);
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#endif
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_sp.setGlobalRate(fac);
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MDOUBLE tmp = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_t,_sc,_sp,_weights);
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#ifdef VERBOS
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LOG(5,<<"likelihood = "<<tmp<<endl);
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#endif
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return -tmp;
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}
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};
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MDOUBLE findTheBestFactorFor(const tree &t,
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const sequenceContainer& sc,
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stochasticProcess& sp,
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const Vdouble * weights,
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MDOUBLE & logLresults) {
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#ifdef VERBOS
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LOG(5,<<"xxx in funtion findTheNestFactorFor xxxxxxxxx"<<endl);
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LOG(5,<<"xxx b4 optimization xxxxxxxxx"<<endl);
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MDOUBLE myL = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(t,sc,sp);
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LOG(5,<<" likelihod is: "<<myL<<endl);
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LOG(5,<<" global rate is: "<<sp.getGlobalRate()<<endl);
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LOG(5,<<"\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx \n");
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#endif
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const MDOUBLE ax=0,bx=1.0,cx=4.0,tol=0.01f;
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MDOUBLE res=-1.0;
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logLresults =-brent(ax,bx,cx,
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findRateOfGene(t,sc,sp,weights),
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tol,
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&res);
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#ifdef VERBOS
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LOG(5,<<"rate of gene = "<<res<<endl);
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LOG(5,<<"xxx in funtion findTheNestFactorFor xxxxxxxxx"<<endl);
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LOG(5,<<"xxx after optimization xxxxxxxxx"<<endl);
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myL = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(t,sc,sp);
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LOG(5,<<" likelihod is: "<<myL<<"\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx \n");
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#endif
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sp.setGlobalRate(res);
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return res;}
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void makeAverageRateEqOne(tree& et,vector<stochasticProcess> & spVec){
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MDOUBLE sumGlobalRates=0.0;
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for (int k=0; k < spVec.size(); ++k) {
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sumGlobalRates+=spVec[k].getGlobalRate();
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}
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for (int j=0; j < spVec.size(); ++j) {
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MDOUBLE newGlobalRate = spVec[j].getGlobalRate();
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newGlobalRate*=(spVec.size()/sumGlobalRates);
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spVec[j].setGlobalRate(newGlobalRate);
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}
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et.multipleAllBranchesByFactor(sumGlobalRates/spVec.size());
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}
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