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// File: AbstractWordSubstitutionModel.h
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// Created by: Laurent Gueguen
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// Created on: Jan 2009
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Copyright or © or Copr. Bio++ Development Team, (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 _ABSTRACTWORDSUBSTITUTIONMODEL_H_
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#define _ABSTRACTWORDSUBSTITUTIONMODEL_H_
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#include "AbstractSubstitutionModel.h"
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* @brief Abstract Basal class for words of substitution models.
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* @author Laurent Guéguen
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* Objects of this class are built from several substitution models.
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* Each model corresponds to a position in the word. No model is
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* 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.
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* For example, if there are @f$n@f$ models and \f$\rho_i\f$ is the rate of
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* model i (@f$\sum_{i=1}^{n} \rho_i = 1@f$):
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* Q_{abc \rightarrow abd} &=& \rho_2 Q^{(2)}_{c \rightarrow d}\\
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* Q_{abc \rightarrow aed} &=& 0\\
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* Q_{abc \rightarrow abc} &=& \rho_0 Q^{(0)}_{a \rightarrow a} + \rho_1 Q^{(1)}_{b \rightarrow b} + \rho_2 Q^{(2)}_{c \rightarrow c})
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* The parameters of this word model are the same as the ones of the
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* models used. Their names have a new suffix, "phi_" where i stands
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* for the position (i.e. the phase) in the word.
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class AbstractWordSubstitutionModel :
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public virtual AbstractSubstitutionModel
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* @ brief boolean flag to check if a specific WordAlphabet has been built
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std::vector<SubstitutionModel*> VSubMod_;
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std::vector<std::string> VnestedPrefix_;
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std::vector<double> Vrate_;
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static Alphabet* extractAlph(const std::vector<SubstitutionModel*>& modelVector);
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void updateMatrices();
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* @brief Called by updateMatrices to handle specific modifications
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* for inheriting classes
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virtual void completeMatrices() = 0;
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* @brief Build a new AbstractWordSubstitutionModel object from a
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* vector of pointers to SubstitutionModels.
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* @param modelVector the vector of substitution models to use, in
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* the order of the positions in the words from left to right. All
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* the models must be different objects to avoid parameters
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* redundancy, otherwise only the first model is used. The used models
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* are owned by the instance.
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* @param st the Namespace.
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AbstractWordSubstitutionModel(
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const std::vector<SubstitutionModel*>& modelVector,
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const std::string& st);
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* @brief Build a new AbstractWordSubstitutionModel object from a
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* pointer to an SubstitutionModel and a number of
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* @param pmodel A pointer to the substitution model to use in all
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* the positions. It will be owned by the instance.
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* @param num The number of models involved.
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* @param st the Namespace.
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AbstractWordSubstitutionModel(
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SubstitutionModel* pmodel,
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const std::string& st);
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AbstractWordSubstitutionModel(const AbstractWordSubstitutionModel&);
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AbstractWordSubstitutionModel& operator=(const AbstractWordSubstitutionModel&);
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virtual ~AbstractWordSubstitutionModel();
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void setNamespace(const std::string& prefix);
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*@brief Constructor for the derived classes only
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AbstractWordSubstitutionModel(const Alphabet* alph, const std::string&);
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virtual unsigned int getNumberOfStates() const;
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*@brief Estimation of the parameters of the models so that the
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*equilibrium frequencies match the given ones.
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*@param freqs map of the frequencies
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* When there is one submodel for all the positions, the submodel
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* parameters are fit on the means of the frequencies on each
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* position. Otherwise, each model is fit on the frequencies on its
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* corresponding position in the word.
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virtual void setFreq(std::map<int, double>& freqs);
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} // end of namespace bpp.
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#endif // ABSTRACTWORDSUBSTITUTIONMODEL_
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src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
