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// File: WordReversibleSubstitutionModel.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. 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 _WORDREVERSIBLESUBSTITUTIONMODEL_H_
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#define _WORDREVERSIBLESUBSTITUTIONMODEL_H_
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#include "AbstractWordReversibleSubstitutionModel.h"
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#include <Bpp/Numeric/Matrix/Matrix.h>
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#include <Bpp/BppVector.h>
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* @brief Basal class for words of reversible substitution models.
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* @author Laurent Guéguen
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* Only substitutions with one letter changed are accepted. Hence the
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* equilibrium frequency of each word is the product of the
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* equilibrium frequencies of the letters.</p>
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* If there are @f$n@f$ models, @f$\rho_i@f$ is the rate of
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* model i (@f$\sum_{i=1}^{n} \rho_i = 1@f$) and the rates
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* are defined by relative rates parameters @f$r_i@f$
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* (called "relratei") with:
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* 1 <= i < n, \rho_i = (1-r_1).(1-r_2)...(1-r_{i-1}).r_{i}
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* \rho_n = (1-r_1).(1-r_2)...(1-r_{n-1})
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* \forall 1 <= i < n, r_i = \frac{\rho_i}{1-(\rho_1+...\rho_{i-1})}
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* where @f$\rho_i@f$ stands for the rate of position @f$i@f$.
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class WordReversibleSubstitutionModel :
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public AbstractWordReversibleSubstitutionModel
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*@brief Build a new WordReversibleSubstitutionModel 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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WordReversibleSubstitutionModel(const std::vector<SubstitutionModel*>& modelVector, const std::string& st = "");
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*@brief Build a new WordReversibleSubstitutionModel object from a
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*pointer to an SubstitutionModel and a number of
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* @param pmodel pointer to the substitution model to use in all the
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* positions. It is 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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WordReversibleSubstitutionModel(SubstitutionModel* pmodel, unsigned int num, const std::string& st = "");
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virtual ~WordReversibleSubstitutionModel() {}
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WordReversibleSubstitutionModel* clone() const { return new WordReversibleSubstitutionModel(*this); }
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*@brief Constructor for the derived classes only
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WordReversibleSubstitutionModel(const Alphabet* alph, const std::string& = "");
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virtual void updateMatrices();
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virtual void completeMatrices();
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virtual const RowMatrix<double>& getPij_t(double d) const;
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virtual const RowMatrix<double>& getdPij_dt(double d) const;
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virtual const RowMatrix<double>& getd2Pij_dt2(double d) const;
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virtual std::string getName() const;
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} // end of namespace bpp.
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#endif // _WORDREVERSIBLESUBSTITUTIONMODEL
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src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.h
