/usr/include/libphylo/checkcovFanctors.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 | // $Id: checkcovFanctors.h 6634 2009-07-20 07:00:05Z osnatz $
#ifndef ____CHECKCOV__FANCTORS
#define ____CHECKCOV__FANCTORS
#include "definitions.h"
#include "tree.h"
#include "likelihoodComputation.h"
using namespace likelihoodComputation;
#include "sequenceContainer.h"
#include "stochasticProcess.h"
#include "logFile.h"
#include <cmath>
//#define VERBOS
#ifdef VERBOS
#include <iostream>
using namespace std;
#endif
class Cevaluate_L_given_r{
public:
explicit Cevaluate_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= convert(getLofPos(_pos,_t1,_sd,_sp,r));
#ifdef VERBOS
LOG(5,<<" r = "<<r<<" l = "<<tmp1<<endl);
#else
LOG(12,<<" r = "<<r<<" l = "<<tmp1<<endl);
#endif
return -tmp1;
}
};
// THIS FUNCTION IS USED ONLY BY ITAY MAYROSE AND ONLY HE KNOWS WHAT IS INSIDE...
// ONE DAY HE WILL WRITE .DOC FILES...
class Cevaluate_Posterior_given_r {
public:
explicit Cevaluate_Posterior_given_r( const sequenceContainer& seqContainer,
const tree& t1,
const stochasticProcess& sp,
const MDOUBLE alpha,
const int pos)
:m_seqContainer(seqContainer), m_alpha(alpha),m_tree(t1), m_pos(pos), m_sp(sp) {}
public:
MDOUBLE operator() (const MDOUBLE r)
{
MDOUBLE l= convert(getLofPos(m_pos, m_tree, m_seqContainer, m_sp, r));
#ifdef VERBOS
LOG(5,<<" r = "<<r<<" l = "<<l<<endl);
#endif
MDOUBLE prior = exp((-m_alpha) * r) * pow(r, m_alpha - 1);
return -(l * prior);
}
private:
const sequenceContainer& m_seqContainer;
const MDOUBLE m_alpha;
const tree& m_tree;
const int m_pos;
const stochasticProcess& m_sp;
};
// WHEN YOU WANT TWO TREE TO HAVE THE SAME RATE AT A SPECIFIC POSITION.
class Cevaluate_L_sum_given_r{
public:
explicit Cevaluate_L_sum_given_r(const stochasticProcess& sp,
const sequenceContainer& sd1,
const sequenceContainer& sd2,
const tree &inLTree1,
const tree &inLTree2,
const int pos)
:_sp(sp), _sd1(sd1), _sd2(sd2), _tree1(inLTree1),_tree2(inLTree2), _pos(pos){};
private:
const stochasticProcess _sp;
const sequenceContainer _sd1;
const sequenceContainer _sd2;
const tree& _tree1;
const tree& _tree2;
const int _pos;
public:
MDOUBLE operator() (const MDOUBLE r) {
MDOUBLE tmp1= convert(getLofPos(_pos,_tree1,_sd1,_sp,r));
MDOUBLE tmp2= convert(getLofPos(_pos,_tree2,_sd2,_sp,r));
MDOUBLE tmp= tmp1*tmp2;
return -tmp;
}
};
#endif
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