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// File: YN98.h
// Created by: Laurent Gueguen
// Created on: July 2009
//
/*
Copyright or © or Copr. Bio++ Development Team, (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 _YN98_H_
#define _YN98_H_
#include "../AbstractBiblioSubstitutionModel.h"
#include "CodonDistanceFrequenciesSubstitutionModel.h"
namespace bpp
{
/**
* @brief The Yang and Nielsen (1998) substitution model for codons.
* @author Laurent Guéguen
*
* This model has one rate of transitions and one rate of
* transversion. It also allows distinct equilibrium frequencies
* between codons. A multiplicative factor accounts for the selective
* restraints at the amino acid level, depending on the synonymy of
* the amino acids.
*
* For codons @f$i=i_1i_2i_3@f$ and @f$j=j_1j_2j_3@f$, the generator
* term @f$Q_{ij} (i \neq j)@f$ is:
*
* 0 if 2 or 3 of the pair @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ are different.
*
* @f$\mu \pi_j \omega@f$ if exactly 1 of the pairs @f$(i_1,j_1)
* (i_2,j_2) (i_3,j_3) @f$ is different, that difference is a
* transversion and amino acids coded by i and j are different.
*
* @f$\mu \pi_j @f$ if exactly 1 of the pairs @f$(i_1,j_1) (i_2,j_2)
* (i_3,j_3) @f$ is different, that difference is a transversion and
* amino acids coded by i and j are the same.
*
* @f$\mu \kappa \pi_j \omega@f$ if exactly 1 of the pairs
* @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ is different, that difference
* is a transition and amino acids coded by i and j are different.
*
* @f$\mu \kappa \pi_j @f$ if exactly 1 of the pairs @f$(i_1,j_1)
* (i_2,j_2) (i_3,j_3) @f$ is different, that difference is a
* transition and amino acids coded by @f$i@f$ and @f$j@f$ are the
* same.
*
* @f$\mu@f$ is a normalization factor.
*
* This model includes 2 parameters (@f$\kappa@f$ and @f$\omega@f$).
* The codon frequencies @f$\pi_j@f$ are either observed or infered.
*
* Reference:
* - Yang Z. and Nielsen R. (1998), _Journal of Molecular Evolution_ 46:409--418.
*/
class YN98 :
public AbstractBiblioSubstitutionModel,
public virtual CodonSubstitutionModel,
public virtual ReversibleSubstitutionModel
{
private:
std::auto_ptr<CodonDistanceFrequenciesSubstitutionModel> pmodel_;
public:
YN98(const GeneticCode* gc, FrequenciesSet* codonFreqs);
YN98(const YN98& yn98);
YN98& operator=(const YN98&);
virtual ~YN98() {}
YN98* clone() const { return new YN98(*this); }
public:
std::string getName() const { return "YN98"; }
const SubstitutionModel& getModel() const { return *pmodel_.get(); }
const GeneticCode* getGeneticCode() const { return pmodel_->getGeneticCode(); }
double getCodonsMulRate(size_t i, size_t j) const { return pmodel_->getCodonsMulRate(i, j); }
private:
SubstitutionModel& getModel() { return *pmodel_.get(); }
};
} // end of namespace bpp.
#endif // _YN98_H_
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