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// File: LGL08_CAT.h
// Created by: Mathieu Groussin
// Created on: Tuesday 11 December 2012
//
/*
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 _LGL08_CAT_H_
#define _LGL08_CAT_H_
#include "../MixtureOfSubstitutionModels.h"
#include "ProteinSubstitutionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../AbstractBiblioMixedSubstitutionModel.h"
using namespace std;
namespace bpp
{
/**
* @brief The Le et al (2008) CAT substitution model for proteins.
* @author Mathieu Groussin
*
* This model is a mixture of N profiles empirically built with an EM algorithm
* (see ref). The submodels are called C1, C2, ..., CN. For each model, exchangeabilities are equal (F81 model).
*
*
* This model includes 2N-2 parameters :
*
* - relrate1, ..., relrate(N-1) are the relative rates of model C1, ..., C(N-1);
* - relproba1, ..., relproba(N-1) are the relative proportions of model C1, ..., C(N-1);
*
* Important: See the relation between these parameters and the
* rates and probabilities of the models in the description of
* MixtureOfSubstitutionModels class.
*
* Reference:
*
* Le S.Q., Gascuel O. & Lartillot N. (2008) Bioinformatics 24:2317–2323.
*/
class LGL08_CAT :
public AbstractBiblioMixedSubstitutionModel
{
public:
class EmbeddedModel :
public virtual ProteinSubstitutionModel,
public AbstractReversibleSubstitutionModel
{
private:
double proportion_;
string name_;
public:
EmbeddedModel(const ProteicAlphabet* alpha, string name, unsigned int nbCat = 10);
~EmbeddedModel(){}
EmbeddedModel* clone() const { return new EmbeddedModel(*this); }
string getName() const { return name_;}
double getProportion() const { return proportion_;}
};
private:
std::auto_ptr<MixtureOfSubstitutionModels> pmixmodel_;
public:
/**
* @brief Build a CAT model, with original equilibrium frequencies, probabilities and rates.
*
* @param alpha A proteic alphabet.
* @param nbCat number of profiles
*
*/
LGL08_CAT(const ProteicAlphabet* alpha, unsigned int nbCat = 10);
~LGL08_CAT();
LGL08_CAT* clone() const { return new LGL08_CAT(*this); }
LGL08_CAT(const LGL08_CAT&);
LGL08_CAT& operator=(const LGL08_CAT&);
const SubstitutionModel& getModel() const { return *pmixmodel_.get(); }
const MixedSubstitutionModel& getMixedModel() const { return *pmixmodel_.get(); }
std::string getName() const { return "LGL08_CAT"; }
private:
SubstitutionModel& getModel() { return *pmixmodel_.get(); }
MixedSubstitutionModel& getMixedModel() { return *pmixmodel_.get(); }
};
} // end of namespace bpp.
#endif // _LGL08_CAT_H_
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