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// File: CodonRateSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: Tue Dec 24 11:03:53 2003
//
/*
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 _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_
#define _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_
#include "AbstractCodonSubstitutionModel.h"
#include "AbstractCodonFrequenciesSubstitutionModel.h"
namespace bpp
{
/**
* @brief Class for substitution models on non stop codons, with
* different parametrized rates on the models, depending on their
* phase and defined through a specific equilibrium distribution.
*
* @author Laurent Guéguen
*
* This class should be used with models which equilibrium
* distribution is fixed, ans does not depend on the parameters.
* Otherwise there may be problems of identifiability of the
* parameters.
*
* See description in AbstractCodonRateSubstitutionModel and
* AbstractCodonFrequenciesSubstitutionModel class.
*
*/
class CodonRateFrequenciesSubstitutionModel :
public AbstractCodonSubstitutionModel,
public AbstractCodonFrequenciesSubstitutionModel
{
public:
/**
* @brief Build a new CodonRateSubstitutionModel object from
* a pointer to NucleotideSubstitutionModels.
* @author Laurent Guéguen
*
* @param gCode pointer to a genetic code, which will be owned by this instance.
* @param pmod pointer to the NucleotideSubstitutionModel to use in the
* three positions. It is owned by the instabce.
* @param pfreq pointer to the FrequenciesSet* equilibrium frequencies
*/
CodonRateFrequenciesSubstitutionModel(
const GeneticCode* gCode,
NucleotideSubstitutionModel* pmod,
FrequenciesSet* pfreq);
/**
* @brief Build a new CodonRateSubstitutionModel object
* from three pointers to NucleotideSubstitutionModels.
*
* @param gCode pointer to a genetic code, which will be owned by this instance.
* @param pmod1, pmod2, pmod3 pointers to the
* NucleotideSubstitutionModel to use in the three positions.
* All the models must be different objects to avoid parameters
* redondancy, otherwise only the first model is used. The used models
* are owned by the instance.
* @param pfreq pointer to the FrequenciesSet* equilibrium frequencies
*/
CodonRateFrequenciesSubstitutionModel(
const GeneticCode* gCode,
NucleotideSubstitutionModel* pmod1,
NucleotideSubstitutionModel* pmod2,
NucleotideSubstitutionModel* pmod3,
FrequenciesSet* pfreq);
virtual ~CodonRateFrequenciesSubstitutionModel(){}
#ifndef NO_VIRTUAL_COV
CodonRateFrequenciesSubstitutionModel*
#else
Clonable*
#endif
clone() const { return new CodonRateFrequenciesSubstitutionModel(*this); }
public:
void fireParameterChanged(const ParameterList& parameterlist);
std::string getName() const;
double getCodonsMulRate(size_t i, size_t j) const;
void setNamespace(const std::string& st);
void setFreq(std::map<int,double>& frequencies);
};
} // end of namespace bpp.
#endif
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