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// File: MG94.h
// Created by: Laurent Gueguen
// Created on: July 2009
//
/*
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 _MG94_H_
#define _MG94_H_
#include "../AbstractBiblioSubstitutionModel.h"
#include "CodonDistancePhaseFrequenciesSubstitutionModel.h"
namespace bpp
{
/**
* @brief The Muse and Gaut (1994) substitution model for codons.
* @author Laurent Guéguen
*
* This model has one ratio @f$\rho@f$ of synonymous substitution rate
* over non-synonymous substitution rate. It allows distinct
* equilibrium frequencies between nucleotides.
*
* 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$\mu \rho \pi_{j_k} @f$ if exactly 1 of the pairs
* @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ is different (@f$k@f$), and that
* difference is synonymous.
*
* @f$\mu \pi_{j_k} @f$ if exactly 1 of the pairs
* @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ is different (@f$k@f$), and that
* difference is non-synonymous.
*
* @f$\mu@f$ is a normalization factor.
*
* This model includes one parameter (@f$\rho@f$). The codon
* frequencies @f$\pi_j@f$ are either observed or infered.
*
* Reference:
* - Muse S.V. and Gaut B.S. (1994), Molecular_ Biology And Evolution_ 11(5) 715--724.
*/
class MG94 :
public AbstractBiblioSubstitutionModel,
virtual public ReversibleSubstitutionModel
{
private:
std::auto_ptr<CodonDistancePhaseFrequenciesSubstitutionModel> pmodel_;
public:
MG94(const GeneticCode* gc, FrequenciesSet* codonFreqs);
MG94(const MG94& mg94);
MG94& operator=(const MG94& mg94);
~MG94();
#ifndef NO_VIRTUAL_COV
MG94*
#else
Clonable*
#endif
clone() const { return new MG94(*this); }
public:
std::string getName() const { return "MG94"; }
const SubstitutionModel& getModel() const { return *pmodel_.get(); }
private:
SubstitutionModel& getModel() { return *pmodel_.get(); }
};
} // end of namespace bpp.
#endif // _MG94_H_
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