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// File: AbstractCodonFrequenciesReversibleSubstitutionModel.h
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// Created by: Laurent Gueguen
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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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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 _ABSTRACTCODONFREQUENCIESREVERSIBLESUBSTITUTIONMODEL_H_
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#define _ABSTRACTCODONFREQUENCIESREVERSIBLESUBSTITUTIONMODEL_H_
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#include "AbstractWordReversibleSubstitutionModel.h"
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#include "FrequenciesSet.h"
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#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
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* @brief Class for reversible substitution models on codons
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* parametrized by the equilibrium frequencies. The basic
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* substitution model is the K80 model. </p>
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* @author Laurent Guéguen
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* Objects of this class are built from three reversible substitution
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* models of NucleicAlphabets. No model is directly accessible. </p>
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* Only substitutions with one letter changed are accepted. </p>
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* There is one substitution per word per unit of time
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* on the equilibrium frequency, and each position has its specific rate.</p>
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class AbstractCodonFrequenciesReversibleSubstitutionModel :
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public AbstractWordReversibleSubstitutionModel
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FrequenciesSet* pfreqset_;
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std::string freqPrefix_;
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*AbstractCodonFrequenciesReversibleSubstitutionModel object from
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*three instances of the K80 model.
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*@param palph pointer to a CodonAlphabet
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*@param pfreq pointer to the AbstractFrequenciesSet equilibrium frequencies.
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* It is owned by the instance.
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*@param prefix the Namespace
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AbstractCodonFrequenciesReversibleSubstitutionModel(
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const CodonAlphabet* palph,
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FrequenciesSet* pfreq,
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const std::string& prefix) throw (Exception);
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AbstractCodonFrequenciesReversibleSubstitutionModel(const AbstractCodonFrequenciesReversibleSubstitutionModel& wrsm) :
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AbstractWordReversibleSubstitutionModel(wrsm),
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pfreqset_(wrsm.pfreqset_->clone()),
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freqPrefix_(wrsm.freqPrefix_)
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AbstractCodonFrequenciesReversibleSubstitutionModel& operator=(const AbstractCodonFrequenciesReversibleSubstitutionModel& wrsm)
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AbstractWordReversibleSubstitutionModel::operator=(wrsm);
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if (pfreqset_) delete pfreqset_;
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pfreqset_ = wrsm.pfreqset_->clone();
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freqPrefix_ = wrsm.freqPrefix_;
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virtual ~AbstractCodonFrequenciesReversibleSubstitutionModel();
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void fireParameterChanged(const ParameterList& parameters);
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void setFreq(std::map<int, double>& frequencies);
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const FrequenciesSet& getFreq() const { return *pfreqset_; }
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void setNamespace(const std::string& prefix)
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AbstractWordReversibleSubstitutionModel::setNamespace(prefix);
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pfreqset_->setNamespace(prefix + "freq_" + freqPrefix_);
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virtual void completeMatrices();
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} // end of namespace bpp.