AbstractCodonDistanceSubstitutionModel.h

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//
// File: AbstractCodonDistanceSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: jeudi 15 septembre 2011, à 21h 11
//

/*
   Copyright or © or Copr. Bio++ Development Team, (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
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 */

#ifndef _ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H_
#define _ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H_

#include "CodonSubstitutionModel.h"
#include <Bpp/Numeric/AbstractParameterAliasable.h>


// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>

namespace bpp
{
class AbstractCodonDistanceSubstitutionModel :
  public virtual CodonSubstitutionModel,
  public virtual AbstractParameterAliasable
{
private:
  const AlphabetIndex2* pdistance_;

  double alpha_, beta_;

  double gamma_;
public:
  AbstractCodonDistanceSubstitutionModel(
    const AlphabetIndex2* pdist,
    const std::string& prefix,
    bool paramSynRate = false);

  AbstractCodonDistanceSubstitutionModel(const AbstractCodonDistanceSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pdistance_(model.pdistance_),
    alpha_(model.alpha_),
    beta_(model.beta_),
    gamma_(model.gamma_)
  {}

  AbstractCodonDistanceSubstitutionModel& operator=(
    const AbstractCodonDistanceSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pdistance_ = model.pdistance_;
    alpha_ = model.alpha_;
    beta_ = model.beta_;
    gamma_ = model.gamma_;
    return *this;
  }

  virtual ~AbstractCodonDistanceSubstitutionModel() {}

public:
  void fireParameterChanged(const ParameterList& parameters);

public:
  double getCodonsMulRate(size_t i, size_t j) const;
};

} // end of namespace bpp.

#endif