//
// File: LLG08_EX3.h
// Created by: Laurent Gueguen
// Created on: jeudi 21 octobre 2010, à 13h 50
//

/*
  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_EX3_H_
#define _LLG08_EX3_H_

#include "../MixtureOfSubstitutionModels.h"
#include "ProteinSubstitutionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../AbstractBiblioMixedSubstitutionModel.h"

using namespace std;

namespace bpp
{
/**
 * @brief The Le et al  (2008) EX3 substitution model for proteins.
 * @author Laurent Guéguen
 *
 * This model is a mixture of three models corresponding to
 * buried/intermediate/highly exposed sites in proteins. The models
 * are considered in this order.
 *
 *
 * This model includes 4 parameters :
 *
 * - relrate1 is the relative rate of model of buried sites;
 * - relrate2 is the relative rate of intermediate sites;
 * - relproba1 is the proportion  of buried sites;
 * - relproba2 is the ratio of the proportions of intermediate sites
 * over the sum of the proportion of intermediate sites plus the
 * proportion of highly exposed 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_EX3 :
    public AbstractBiblioMixedSubstitutionModel
  {
  public:
    class EmbeddedModel :
      public AbstractReversibleProteinSubstitutionModel
    {
    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_;}
    };

  public:
    /**
     * @brief Build a  EX3 model, with original equilibrium frequencies, probabilities and rates.
     *
     * @param alpha A proteic alphabet.
     *
     */

    LLG08_EX3(const ProteicAlphabet* alpha);

    LLG08_EX3* clone() const { return new LLG08_EX3(*this); }

    LLG08_EX3(const LLG08_EX3& mod2) : AbstractBiblioMixedSubstitutionModel(mod2)
    {}

    LLG08_EX3& operator=(const LLG08_EX3& mod2)
    {
      AbstractBiblioMixedSubstitutionModel::operator=(mod2);
      return *this;
    }

    std::string getName() const { return "LLG08_EX3"; }
  
  };
} // end of namespace bpp.

#endif  // _LLG08_EX3_H_

