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116 lines
5.0 KiB
C++
116 lines
5.0 KiB
C++
// $Id: likeDistProp.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___LIKE_DIST_PROP_EB
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#define ___LIKE_DIST_PROP_EB
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#include "definitions.h"
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#include "countTableComponent.h"
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#include "multipleStochasticProcess.h"
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#include "gammaDistribution.h"
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#include "logFile.h"
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#include <cmath>
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class likeDistPropEB {
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private:
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multipleStochasticProcess * _msp;
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const gammaDistribution* _pProportionDist;
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const MDOUBLE _maxPairwiseDistance;
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const MDOUBLE _minPairwiseDistance;
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const MDOUBLE _toll;
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public:
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const MDOUBLE giveDistance( const vector< vector<countTableComponentGamProportional> >& ctc,const int nodeID,
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MDOUBLE& resL,const MDOUBLE initialGuess= 0.03) const;
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explicit likeDistPropEB(multipleStochasticProcess * msp,
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const gammaDistribution* pProportionDist,
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const MDOUBLE toll =0.0001,
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const MDOUBLE maxPairwiseDistance = 5.0,
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const MDOUBLE minPairwiseDistance = 0.0000001) : _msp(msp) ,_pProportionDist(pProportionDist), _maxPairwiseDistance(maxPairwiseDistance), _minPairwiseDistance(minPairwiseDistance),_toll(toll){
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}
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likeDistPropEB(const likeDistPropEB & other)
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: _msp(other._msp),_pProportionDist(other._pProportionDist),_maxPairwiseDistance(other._maxPairwiseDistance),_minPairwiseDistance(other._minPairwiseDistance),_toll(other._toll){}
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virtual likeDistPropEB* clone() const {return new likeDistPropEB(*this);}
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};
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class C_evallikeDistPropEB_d{ // derivative.
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public:
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C_evallikeDistPropEB_d(const vector< vector<countTableComponentGamProportional> >& ctc,
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multipleStochasticProcess* msp,const gammaDistribution* pProportionDist,const int nodeID) : _ctc(ctc), _msp(msp), _pProportionDist(pProportionDist), _nodeID(nodeID) {};
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private:
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const vector< vector<countTableComponentGamProportional> >& _ctc;
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multipleStochasticProcess* _msp;
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const gammaDistribution* _pProportionDist;
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const int _nodeID;
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public:
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MDOUBLE operator() (MDOUBLE dist) {
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const MDOUBLE epsilonPIJ = 1e-10;
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MDOUBLE sumDL = 0.0;
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for (int gene=0; gene < _msp->getSPVecSize(); ++gene) {
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for (int alph1=0; alph1 < _ctc[gene][_nodeID].alphabetSize(); ++alph1){
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for (int alph2=0; alph2 < _ctc[gene][_nodeID].alphabetSize(); ++alph2){
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for(int globalRateCategor = 0;globalRateCategor < _pProportionDist->categories();++globalRateCategor){
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_msp->getSp(gene)->setGlobalRate(_pProportionDist->rates(globalRateCategor));
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MDOUBLE globalRate = _pProportionDist->rates(globalRateCategor);
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for (int localRateCategor = 0; localRateCategor < _msp->getSp(gene)->categories(); ++localRateCategor) {
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MDOUBLE localRate = _msp->getSp(gene)->rates(localRateCategor);
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MDOUBLE pij= _msp->getSp(gene)->Pij_t(alph1,alph2,dist*globalRate*localRate);
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if (pij<epsilonPIJ) {
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pij = epsilonPIJ;
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}
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MDOUBLE dpij = _msp->getSp(gene)->dPij_dt(alph1,alph2,dist*globalRate*localRate);
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//sumDL+= _ctc[gene][_nodeID].getCounts(alph1,alph2,globalRateCategor,localRateCategor)*dpij*_pProportionDist->ratesProb(globalRateCategor)*sp->ratesProb(localRateCategor)
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// *globalRate*localRate/pij;
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sumDL+= _ctc[gene][_nodeID].getCounts(alph1,alph2,globalRateCategor,localRateCategor)*dpij*globalRate*localRate/pij;
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}
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}
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}
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}
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}
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LOG(12,<<"check bl="<<dist<<" gives sumDL "<<sumDL<<endl);
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return -sumDL;
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};
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};
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class C_evallikeDistPropEB{
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private:
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const vector< vector<countTableComponentGamProportional> >& _ctc;
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multipleStochasticProcess* _msp;
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const gammaDistribution* _pProportionDist;
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const int _nodeID;
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public:
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C_evallikeDistPropEB(const vector< vector<countTableComponentGamProportional> >& ctc,
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multipleStochasticProcess* msp,const gammaDistribution* pProportionDist,const int nodeID):_ctc(ctc), _msp(msp), _pProportionDist(pProportionDist), _nodeID(nodeID) {};
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MDOUBLE operator() (MDOUBLE dist) {
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const MDOUBLE epsilonPIJ = 1e-10;
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MDOUBLE sumL = 0.0;
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for (int gene=0; gene < _msp->getSPVecSize(); ++gene) {
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for (int alph1=0; alph1 < _ctc[gene][_nodeID].alphabetSize(); ++alph1){
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for (int alph2=0; alph2 < _ctc[gene][_nodeID].alphabetSize(); ++alph2){
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for(int globalRateCategor = 0;globalRateCategor < _pProportionDist->categories();++globalRateCategor){
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_msp->getSp(gene)->setGlobalRate(_pProportionDist->rates(globalRateCategor));
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MDOUBLE globalRate = _pProportionDist->rates(globalRateCategor);
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for (int localRateCategor = 0; localRateCategor < _msp->getSp(gene)->categories(); ++localRateCategor) {
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MDOUBLE localRate = _msp->getSp(gene)->rates(localRateCategor);
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MDOUBLE pij= _msp->getSp(gene)->Pij_t(alph1,alph2,dist*globalRate*localRate);
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if (pij<epsilonPIJ) {
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pij = epsilonPIJ;
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}
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sumL += _ctc[gene][_nodeID].getCounts(alph1,alph2,globalRateCategor,localRateCategor)*(log(pij)-log(_msp->getSp(gene)->freq(alph2)));//*_pProportionDist->ratesProb(globalRateCategor)*sp->ratesProb(localRateCategor);
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}
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}
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}
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}
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}
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LOG(8,<<"check bl="<<dist<<" gives sumL "<<sumL<<endl);
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return -sumL;
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};
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};
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#endif
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