/usr/include/libphylo/checkcovFanctorsWithFactors.h is in rate4site 3.0.0-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | // $Id: checkcovFanctorsWithFactors.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ____CHECKCOV__FANCTORS_WITH_FACTORS
#define ____CHECKCOV__FANCTORS_WITH_FACTORS
#include "definitions.h"
#include "tree.h"
#include "likelihoodComputation.h"
#include "likelihoodComputationFactors.h" //<-new.
using namespace likelihoodComputation;
#include "sequenceContainer.h"
#include "stochasticProcess.h"
//#define VERBOS
#ifdef VERBOS
#include <iostream>
using namespace std;
#endif
// USING FACTORS: THE IDEA HERE IS THAT WHEN WE HAVE TOO MANY SEQUENCES,
// WE MUST TAKE SPECIAL CARE TO USE "FACTORS" AT INTERNAL NODES, TO AVOID UNDERFLOW.
// HERE WE ALSO RETURN LOG LIKELIHOOD OF A POSITION AND NOT THE LIKELIHOOD ITSELF.
class Cevaluate_LOG_L_given_r{
public:
explicit Cevaluate_LOG_L_given_r( const sequenceContainer& sd,
const tree& t1,
const stochasticProcess& sp,
const int pos)
:_sd(sd),_t1(t1),_pos(pos), _sp(sp){}
private:
const sequenceContainer& _sd;
const tree& _t1;
const int _pos;
const stochasticProcess& _sp;
public:
MDOUBLE operator() (const MDOUBLE r) {
MDOUBLE tmp1= getLOG_LofPos(_pos,_t1,_sd,_sp,r);
#ifdef VERBOS
LOG(5,<<" r = "<<r<<" l = "<<tmp1<<endl);
#endif
return -tmp1;
}
};
#endif
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