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// File: CodonRateSubstitutionModel.h
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// Created by: Laurent Gueguen
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// Created on: Tue Dec 24 11:03:53 2003
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_
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#define _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_
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#include "AbstractCodonSubstitutionModel.h"
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#include "AbstractCodonFrequenciesSubstitutionModel.h"
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* @brief Class for substitution models on non stop codons, with
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* different parametrized rates on the models, depending on their
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* phase and defined through a specific equilibrium distribution.
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* @author Laurent Guéguen
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* This class should be used with models which equilibrium
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* distribution is fixed, ans does not depend on the parameters.
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* Otherwise there may be problems of identifiability of the
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* See description in AbstractCodonRateSubstitutionModel and
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* AbstractCodonFrequenciesSubstitutionModel class.
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class CodonRateFrequenciesSubstitutionModel :
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public AbstractCodonSubstitutionModel,
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public AbstractCodonFrequenciesSubstitutionModel
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*@brief Build a new CodonRateSubstitutionModel object from
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*a pointer to NucleotideSubstitutionModels.
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* @author Laurent Guéguen
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*@param palph pointer to a CodonAlphabet
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*@param pmod pointer to the NucleotideSubstitutionModel to use in the
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* three positions. It is owned by the instabce.
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*@param pfreq pointer to the FrequenciesSet* equilibrium frequencies
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CodonRateFrequenciesSubstitutionModel(const CodonAlphabet* palph,
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NucleotideSubstitutionModel* pmod,
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FrequenciesSet* pfreq);
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*@brief Build a new CodonRateSubstitutionModel object
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*from three pointers to NucleotideSubstitutionModels.
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*@param palph pointer to a CodonAlphabet
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*@param pmod1, pmod2, pmod3 pointers to the
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* NucleotideSubstitutionModel to use in the three positions.
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* All the models must be different objects to avoid parameters
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* redondancy, otherwise only the first model is used. The used models
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* are owned by the instance.
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*@param pfreq pointer to the FrequenciesSet* equilibrium frequencies
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CodonRateFrequenciesSubstitutionModel(const CodonAlphabet* palph,
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NucleotideSubstitutionModel* pmod1,
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NucleotideSubstitutionModel* pmod2,
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NucleotideSubstitutionModel* pmod3,
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FrequenciesSet* pfreq);
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~CodonRateFrequenciesSubstitutionModel(){}
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#ifndef NO_VIRTUAL_COV
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CodonRateFrequenciesSubstitutionModel*
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clone() const { return new CodonRateFrequenciesSubstitutionModel(*this); }
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void fireParameterChanged(const ParameterList& parameterlist);
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std::string getName() const;
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double getCodonsMulRate(unsigned int, unsigned int) const;
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void setNamespace(const std::string& st);
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void setFreq(std::map<int,double>& frequencies);
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} // end of namespace bpp.
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src/Bpp/Phyl/Model/CodonRateFrequenciesSubstitutionModel.h
