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// File: WordSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: Jan 2009
//
/*
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 _WORDSUBSTITUTIONMODEL_H_
#define _WORDSUBSTITUTIONMODEL_H_
#include "AbstractWordSubstitutionModel.h"
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/BppVector.h>
namespace bpp
{
/**
* @brief Basal class for words of reversible substitution models.
* @author Laurent Guéguen
*
* Only substitutions with one letter changed are accepted. Hence the
* equilibrium frequency of each word is the product of the
* equilibrium frequencies of the letters.</p>
*
* If there are @f$n@f$ models, @f$\rho_i@f$ is the rate of
* model i (@f$\sum_{i=1}^{n} \rho_i = 1@f$) and the rates
* are defined by relative rates parameters @f$r_i@f$
* (called "relratei") with:
* @f[
* 1 <= i < n, \rho_i = (1-r_1).(1-r_2)...(1-r_{i-1}).r_{i}
* @f]
* @f[
* \rho_n = (1-r_1).(1-r_2)...(1-r_{n-1})
* @f]
* and
* @f[
* \forall 1 <= i < n, r_i = \frac{\rho_i}{1-(\rho_1+...\rho_{i-1})}
* @f]
* where @f$\rho_i@f$ stands for the rate of position @f$i@f$.
*/
class WordSubstitutionModel :
public AbstractWordSubstitutionModel
{
public:
/**
* @brief Build a new WordSubstitutionModel object from a
* Vector of pointers to SubstitutionModels.
*
* @param modelVector the Vector of substitution models to use, in
* the order of the positions in the words from left to right. All
* the models must be different objects to avoid parameters
* redundancy, otherwise only the first model is used. The used models
* are owned by the instance.
* @param prefix the Namespace.
*/
WordSubstitutionModel(const std::vector<SubstitutionModel*>& modelVector, const std::string& prefix = "");
/**
* @brief Build a new WordSubstitutionModel object from a
* pointer to an SubstitutionModel and a number of
* desired models.
*
* @param pmodel pointer to the substitution model to use in all the
* positions. It is owned by the instance.
* @param num The number of models involved.
* @param prefix the Namespace.
*/
WordSubstitutionModel(SubstitutionModel* pmodel, unsigned int num, const std::string& prefix = "");
virtual ~WordSubstitutionModel() {}
WordSubstitutionModel* clone() const { return new WordSubstitutionModel(*this); }
protected:
/**
* @brief Constructor for the derived classes only
*/
WordSubstitutionModel(const Alphabet* alph, StateMap* stateMap, const std::string& prefix = "");
virtual void updateMatrices();
virtual void completeMatrices();
public:
virtual const RowMatrix<double>& getPij_t(double d) const;
virtual const RowMatrix<double>& getdPij_dt(double d) const;
virtual const RowMatrix<double>& getd2Pij_dt2(double d) const;
virtual std::string getName() const;
};
} // end of namespace bpp.
#endif // _WORDSUBSTITUTIONMODEL
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