/usr/include/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h is in libbpp-core-dev 2.0.3-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 | //
// File: RescaledHmmLikelihood.h
// Created by: Julien Dutheil
// Created on: Fri Oct 26 11:57 2007
//
/*
Copyright or © or Copr. CNRS, (November 16, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _RESCALEDHMMLIKELIHOOD_H_
#define _RESCALEDHMMLIKELIHOOD_H_
#include "HmmLikelihood.h"
#include "../AbstractParametrizable.h"
#include "../Matrix/Matrix.h"
//From the STL:
#include <vector>
#include <memory>
namespace bpp {
/**
* @brief A simple implementation of hidden Markov models recursion.
*
* This implementation uses the rescaling method described in Durbin et al "Biological sequence analysis", Cambridge University Press.
* It also offer the possibility to specify "breakpoints", where the chain will be reset to the equilibrium frequencies.
*/
class RescaledHmmLikelihood:
public virtual HmmLikelihood,
public AbstractParametrizable
{
private:
/**
* @brief The alphabet describing the hidden states.
*/
std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;
/**
* @brief The likelihood array.
*
* likelihood_[i * nbStates_ + j] corresponds to Pr(x1...xi, yi=j),
* where the x are the observed states, and y the hidden states.
*/
std::vector<double> likelihood_;
std::vector<double> scales_;
double logLik_;
std::vector<unsigned int> breakPoints_;
unsigned int nbStates_, nbSites_;
public:
/**
* @brief Build a new RescaledHmmLikelihood object.
*
* @warning the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null
* and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and
* deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to
* be destroyed with this object.
*/
RescaledHmmLikelihood(
HmmStateAlphabet* hiddenAlphabet,
HmmTransitionMatrix* transitionMatrix,
HmmEmissionProbabilities* emissionProbabilities,
const std::string& prefix) throw (Exception);
RescaledHmmLikelihood(const RescaledHmmLikelihood& lik):
AbstractParametrizable(lik),
hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
likelihood_(lik.likelihood_),
scales_(lik.scales_),
logLik_(lik.logLik_),
breakPoints_(lik.breakPoints_),
nbStates_(lik.nbStates_),
nbSites_(lik.nbSites_)
{
// Now adjust pointers:
transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
}
RescaledHmmLikelihood& operator=(const RescaledHmmLikelihood& lik)
{
AbstractParametrizable::operator =(lik);
hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
likelihood_ = lik.likelihood_;
scales_ = lik.scales_;
logLik_ = lik.logLik_;
breakPoints_ = lik.breakPoints_;
nbStates_ = lik.nbStates_;
nbSites_ = lik.nbSites_;
// Now adjust pointers:
transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
return *this;
}
virtual ~RescaledHmmLikelihood() {}
#ifndef NO_VIRTUAL_COV
RescaledHmmLikelihood*
#else
Clonable*
#endif
clone() const { return new RescaledHmmLikelihood(*this); }
public:
const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }
const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }
const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }
void setBreakPoints(const std::vector<unsigned int>& breakPoints) {
breakPoints_ = breakPoints;
computeForward_();
}
const std::vector<unsigned int>& getBreakPoints() const { return breakPoints_; }
void setParameters(const ParameterList& pl) throw (Exception)
{
setParametersValues(pl);
}
double getValue() const throw (Exception) { return -logLik_; }
double getLogLikelihood() const { return logLik_; }
void fireParameterChanged(const ParameterList& pl);
void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (Exception);
protected:
void computeForward_();
void computeBackward_(std::vector< std::vector<double> >& b) const;
};
}
#endif //_RESCALEDHMMLIKELIHOOD_H_
|