LG10_EX_EHO.h

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//
// File: LG10_EX_EHO.h
// Created by: Mathieu Groussin
// Created on: Thursday 28 Mar 2013
//

/*
 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
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 */

#ifndef _LG10_EX_EHO_H_
#define _LG10_EX_EHO_H_

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

using namespace std;

namespace bpp
{
class LG10_EX_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:
  std::auto_ptr<MixtureOfSubstitutionModels> pmixmodel_;

public:
  LG10_EX_EHO(const ProteicAlphabet* alpha);

  ~LG10_EX_EHO();

  LG10_EX_EHO* clone() const { return new LG10_EX_EHO(*this); }

  LG10_EX_EHO(const LG10_EX_EHO&);

  LG10_EX_EHO& operator=(const LG10_EX_EHO&);

  const SubstitutionModel& getModel() const { return *pmixmodel_.get(); }

  const MixedSubstitutionModel& getMixedModel() const { return *pmixmodel_.get(); }
  
  std::string getName() const { return "LG10_EX_EHO"; }

private:
  SubstitutionModel& getModel() { return *pmixmodel_.get(); }
  
  MixedSubstitutionModel& getMixedModel() { return *pmixmodel_.get(); }
  
};
} // end of namespace bpp.

#endif  // _LG10_EX_EHO_H_