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107 lines
2.6 KiB
C++
107 lines
2.6 KiB
C++
// $Id: checkcovFanctors.h 6634 2009-07-20 07:00:05Z osnatz $
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#ifndef ____CHECKCOV__FANCTORS
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#define ____CHECKCOV__FANCTORS
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#include "definitions.h"
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#include "tree.h"
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#include "likelihoodComputation.h"
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using namespace likelihoodComputation;
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#include "sequenceContainer.h"
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#include "stochasticProcess.h"
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#include "logFile.h"
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#include <cmath>
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//#define VERBOS
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#ifdef VERBOS
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#include <iostream>
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using namespace std;
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#endif
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class Cevaluate_L_given_r{
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public:
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explicit Cevaluate_L_given_r( const sequenceContainer& sd,
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const tree& t1,
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const stochasticProcess& sp,
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const int pos)
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:_sd(sd),_t1(t1),_pos(pos), _sp(sp) {}
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private:
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const sequenceContainer& _sd;
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const tree& _t1;
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const int _pos;
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const stochasticProcess& _sp;
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public:
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MDOUBLE operator() (const MDOUBLE r) {
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MDOUBLE tmp1= convert(getLofPos(_pos,_t1,_sd,_sp,r));
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#ifdef VERBOS
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LOG(5,<<" r = "<<r<<" l = "<<tmp1<<endl);
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#else
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LOG(12,<<" r = "<<r<<" l = "<<tmp1<<endl);
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#endif
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return -tmp1;
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}
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};
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// THIS FUNCTION IS USED ONLY BY ITAY MAYROSE AND ONLY HE KNOWS WHAT IS INSIDE...
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// ONE DAY HE WILL WRITE .DOC FILES...
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class Cevaluate_Posterior_given_r {
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public:
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explicit Cevaluate_Posterior_given_r( const sequenceContainer& seqContainer,
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const tree& t1,
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const stochasticProcess& sp,
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const MDOUBLE alpha,
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const int pos)
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:m_seqContainer(seqContainer), m_alpha(alpha),m_tree(t1), m_pos(pos), m_sp(sp) {}
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public:
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MDOUBLE operator() (const MDOUBLE r)
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{
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MDOUBLE l= convert(getLofPos(m_pos, m_tree, m_seqContainer, m_sp, r));
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#ifdef VERBOS
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LOG(5,<<" r = "<<r<<" l = "<<l<<endl);
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#endif
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MDOUBLE prior = exp((-m_alpha) * r) * pow(r, m_alpha - 1);
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return -(l * prior);
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}
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private:
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const sequenceContainer& m_seqContainer;
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const MDOUBLE m_alpha;
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const tree& m_tree;
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const int m_pos;
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const stochasticProcess& m_sp;
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};
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// WHEN YOU WANT TWO TREE TO HAVE THE SAME RATE AT A SPECIFIC POSITION.
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class Cevaluate_L_sum_given_r{
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public:
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explicit Cevaluate_L_sum_given_r(const stochasticProcess& sp,
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const sequenceContainer& sd1,
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const sequenceContainer& sd2,
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const tree &inLTree1,
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const tree &inLTree2,
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const int pos)
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:_sp(sp), _sd1(sd1), _sd2(sd2), _tree1(inLTree1),_tree2(inLTree2), _pos(pos){};
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private:
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const stochasticProcess _sp;
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const sequenceContainer _sd1;
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const sequenceContainer _sd2;
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const tree& _tree1;
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const tree& _tree2;
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const int _pos;
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public:
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MDOUBLE operator() (const MDOUBLE r) {
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MDOUBLE tmp1= convert(getLofPos(_pos,_tree1,_sd1,_sp,r));
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MDOUBLE tmp2= convert(getLofPos(_pos,_tree2,_sd2,_sp,r));
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MDOUBLE tmp= tmp1*tmp2;
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return -tmp;
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}
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};
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#endif
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