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// File: AbstractCodonDistanceSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: jeudi 15 septembre 2011, à 21h 11
//
/*
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 _ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H_
#define _ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H_
#include "CodonSubstitutionModel.h"
#include <Bpp/Numeric/AbstractParameterAliasable.h>
// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
namespace bpp
{
/**
* @brief Abstract class for modelling of non-synonymous abd
* synonymous substitution rates in codon models.
*
* @author Laurent Guéguen
*
* If a distance @f$d@f$ between amino-acids is defined, the
* non-synonymous rate is multiplied with, if the coded amino-acids
* are @f$x@f$ and @f$y@f$, @f$\beta*\exp(-\alpha.d(x,y))@f$ with
* non-negative parameter \c "alpha" and positive parameter \c
* "beta".
*
* If such a distance is not defined, the non-synonymous substitution
* rate is multiplied with @f$\beta@f$ with positive parameter \c
* "beta" (ie @f$d=0@f$).
*
* If paramSynRate is true, the synonymous substitution rate is
* multiplied with @f$\gamma@f$ (with optional positive parameter \c
* "gamma"), else it is multiplied with 1.
*
*
* References:
* - Goldman N. and Yang Z. (1994), _Molecular Biology And Evolution_ 11(5) 725--736.
* _ Kosakovsky Pond, S. and Muse, S.V. (2005), _Molecular Biology And Evolution_,
* 22(12), 2375--2385.
* - Mayrose, I. and Doron-Faigenboim, A. and Bacharach, E. and Pupko T.
* (2007), Bioinformatics, 23, i319--i327.
*
*/
class AbstractCodonDistanceSubstitutionModel :
public virtual CodonSubstitutionModel,
public virtual AbstractParameterAliasable
{
private:
const GeneticCode* geneticCode_;
const AlphabetIndex2* pdistance_;
double alpha_, beta_;
double gamma_;
public:
/**
*@brief Build a new AbstractCodonDistanceSubstitutionModel object from
* a pointer to NucleotideSubstitutionModel.
*
*@param palph pointer to a GeneticCode
*@param pdist optional pointer to a distance between amino-acids
*@param prefix the Namespace
*@param paramSynRate is true iff synonymous rate is parametrised
* (default=false).
*/
AbstractCodonDistanceSubstitutionModel(
const GeneticCode* palph,
const AlphabetIndex2* pdist,
const std::string& prefix,
bool paramSynRate = false);
AbstractCodonDistanceSubstitutionModel(
const AbstractCodonDistanceSubstitutionModel& model) :
AbstractParameterAliasable(model),
geneticCode_(model.geneticCode_),
pdistance_(model.pdistance_),
alpha_(model.alpha_),
beta_(model.beta_),
gamma_(model.gamma_)
{}
AbstractCodonDistanceSubstitutionModel& operator=(
const AbstractCodonDistanceSubstitutionModel& model)
{
AbstractParameterAliasable::operator=(model);
geneticCode_ = model.geneticCode_;
pdistance_ = model.pdistance_;
alpha_ = model.alpha_;
beta_ = model.beta_;
gamma_ = model.gamma_;
return *this;
}
~AbstractCodonDistanceSubstitutionModel() {}
public:
void fireParameterChanged(const ParameterList& parameters);
const GeneticCode* getGeneticCode() const { return geneticCode_; }
public:
double getCodonsMulRate(size_t i, size_t j) const;
};
} // end of namespace bpp.
#endif
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