CodonDistancePhaseFrequenciesSubstitutionModel.h

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//
// File: CodonDistancePhaseFrequenciesSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: lundi 19 septembre 2011, à 11h 47
//

/*
   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 _CODONDISTANCEPHASEFREQUENCIESSUBSTITUTIONMODEL_H_
#define _CODONDISTANCEPHASEFREQUENCIESSUBSTITUTIONMODEL_H_

#include "AbstractCodonSubstitutionModel.h"
#include "AbstractCodonDistanceSubstitutionModel.h"
#include "AbstractCodonPhaseFrequenciesSubstitutionModel.h"

namespace bpp
{
class CodonDistancePhaseFrequenciesSubstitutionModel :
    public AbstractCodonSubstitutionModel,
    public AbstractCodonDistanceSubstitutionModel,
    public AbstractCodonPhaseFrequenciesSubstitutionModel
{
public:
  CodonDistancePhaseFrequenciesSubstitutionModel(
      const GeneticCode* gCode,
      NucleotideSubstitutionModel* pmod,
      FrequenciesSet* pfreq,
      const AlphabetIndex2* pdist = 0);

  CodonDistancePhaseFrequenciesSubstitutionModel(
      const GeneticCode* gCode,
      NucleotideSubstitutionModel* pmod1,
      NucleotideSubstitutionModel* pmod2,
      NucleotideSubstitutionModel* pmod3,
      FrequenciesSet* pfreq,
      const AlphabetIndex2* pdist = 0);

  virtual ~CodonDistancePhaseFrequenciesSubstitutionModel() {}

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

public:
  void fireParameterChanged(const ParameterList& parameterlist);

  std::string getName() const;

  double getCodonsMulRate(size_t i, size_t j) const;

  void setNamespace(const std::string&);

  void setFreq(std::map<int,double>& frequencies);
};

} // end of namespace bpp.

#endif