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// File: MixedSubstitutionModel.h
// Created by: Laurent Gueguen
//
/*
Copyright or © or Copr. CNRS, (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 _MIXEDSUBSTITUTIONMODEL_H_
#define _MIXEDSUBSTITUTIONMODEL_H_
#include "SubstitutionModel.h"
// #include <Bpp/Seq/Alphabet.all>
#include <vector>
#include <string>
#include <map>
#include <cstring> // C lib for string copy
namespace bpp
{
/**
* @brief Interface for Substitution models, defined as a mixture
* of "simple" substitution models.
* @author Laurent Guéguen
*
*/
class MixedSubstitutionModel :
public virtual SubstitutionModel
{
public:
MixedSubstitutionModel() {};
virtual ~MixedSubstitutionModel(){};
virtual MixedSubstitutionModel* clone() const = 0;
public:
/**
* @brief Returns a specific model from the mixture
*/
virtual const SubstitutionModel* getNModel(size_t i) const = 0;
virtual SubstitutionModel* getNModel(size_t i) = 0;
/**
* @brief Returns the probability of a specific model from the mixture
*/
virtual double getNProbability(size_t i) const = 0;
virtual const std::vector<double>& getProbabilities() const = 0;
/**
* @brief Sets the probability of a specific model from the mixture
*/
virtual void setNProbability(size_t i, double prob) = 0;
virtual size_t getNumberOfModels() const = 0;
/**
* @brief Returns the rates of the submodels.
*/
virtual const std::vector<double>& getVRates() const = 0;
/**
* @brief Returns the rate of a specific submodel.
*/
virtual double getNRate(size_t i) const = 0;
/**
* @brief Sets the rates of the submodels to be proportional to a
* given vector, and normalizes them so that the mean rate of the
* mixture equals rate_.
* @param vd a vector of positive values such that the rates of
* the respective submodels are in the same proportions (ie this
* vector does not need to be normalized).
*/
virtual void setVRates(const Vdouble& vd) = 0;
/**
* @brief Normalizes the rates of the submodels so that the mean
* rate of the mixture equals rate_.
*/
virtual void normalizeVRates() = 0;
/*
*@brief Returns the vector of numbers of the submodels in the
*mixture that match a description.
*
*/
virtual Vint getSubmodelNumbers(std::string& desc) const = 0;
};
} // end of namespace bpp.
#endif // _MIXEDSUBSTITUTIONMODEL_H_
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