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// File: LLG08_EHO.h
// Created by: Laurent Gueguen
// Created on: jeudi 7 octobre 2010, à 21h 47
//
/*
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 _LLG08_EHO_H_
#define _LLG08_EHO_H_
#include "../MixtureOfSubstitutionModels.h"
#include "ProteinSubstitutionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../AbstractBiblioMixedSubstitutionModel.h"
using namespace std;
namespace bpp
{
/**
* @brief The Le et al (2008) EH0 substitution model for proteins.
* @author Laurent Guéguen
*
* This model is a mixture of three models corresponding to
* extended/helix/other sites in proteins. The models are considered
* in this order.
*
*
* This model includes 4 parameters :
*
* - relrate1 is the relative rate of model of extended sites;
* - relrate2 is the relative rate of helix sites;
* - relproba1 is the proportion of extended sites;
* - relproba2 is the ratio of the proportions of helix sites over the sum of
* the proportion of helix sites plus the proportion of other sites.
*
* 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., Lartillot N., Gascuel O. (2008) Phil. Trans. R. Soc. B 363:3965--3976.
*/
class LLG08_EHO :
public AbstractBiblioMixedSubstitutionModel
{
public:
class EmbeddedModel :
public virtual ProteinSubstitutionModel,
public AbstractReversibleSubstitutionModel
{
private:
double proportion_;
string name_;
public:
EmbeddedModel(const ProteicAlphabet* alpha, string name);
~EmbeddedModel(){}
EmbeddedModel* clone() const { return new EmbeddedModel(*this); }
string getName() const { return name_;}
double getProportion() const { return proportion_;}
};
private:
auto_ptr<MixtureOfSubstitutionModels> pmixmodel_;
public:
/**
* @brief Build a EH0 model, with original equilibrium frequencies, probabilities and rates.
*
* @param alpha A proteic alphabet.
*
*/
LLG08_EHO(const ProteicAlphabet* alpha);
~LLG08_EHO();
LLG08_EHO* clone() const { return new LLG08_EHO(*this); }
LLG08_EHO(const LLG08_EHO&);
LLG08_EHO& operator=(const LLG08_EHO&);
const SubstitutionModel& getModel() const { return *pmixmodel_.get(); }
const MixedSubstitutionModel& getMixedModel() const { return *pmixmodel_.get(); }
std::string getName() const { return "LLG08_EHO"; }
private:
SubstitutionModel& getModel() { return *pmixmodel_.get(); }
MixedSubstitutionModel& getMixedModel() { return *pmixmodel_.get(); }
};
} // end of namespace bpp.
#endif // _LLG08_EHO_H_
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