AbstractCodonFrequenciesSubstitutionModel.h

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//
// File: AbstractCodonFrequenciesSubstitutionModel.h
// Created by: jeudi 15 septembre 2011, à 15h 02
//

/*
   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
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   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
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 */

#ifndef _ABSTRACTCODONFREQUENCIESSUBSTITUTIONMODEL_H_
#define _ABSTRACTCODONFREQUENCIESSUBSTITUTIONMODEL_H_

#include "AbstractCodonSubstitutionModel.h"
#include "../FrequenciesSet/CodonFrequenciesSet.h"

namespace bpp
{
class AbstractCodonFrequenciesSubstitutionModel :
  virtual public CodonSubstitutionModel,
  virtual public AbstractParameterAliasable
{
private:
  FrequenciesSet* pfreqset_;
  std::string freqName_;

public:
  AbstractCodonFrequenciesSubstitutionModel(FrequenciesSet* pfreq,
                                            const std::string& prefix);

  AbstractCodonFrequenciesSubstitutionModel(const AbstractCodonFrequenciesSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pfreqset_(model.pfreqset_->clone()),
    freqName_(model.freqName_)
  {}

  AbstractCodonFrequenciesSubstitutionModel& operator=(const AbstractCodonFrequenciesSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    if (pfreqset_) delete pfreqset_;
    pfreqset_   = model.pfreqset_->clone();
    freqName_   = model.freqName_;
    return *this;
  }

  virtual ~AbstractCodonFrequenciesSubstitutionModel();

  void fireParameterChanged(const ParameterList& parameters);

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

  const FrequenciesSet* getFrequenciesSet() const { return pfreqset_; }

  void setNamespace(const std::string& prefix)
  {
    pfreqset_->setNamespace(prefix + freqName_);
  }

  double getCodonsMulRate(size_t, size_t) const;
};
} // end of namespace bpp.

#endif