AbstractCodonPhaseFrequenciesSubstitutionModel.h

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//
// File: AbstractCodonPhaseFrequenciesSubstitutionModel.h
// Created by: vendredi 23 septembre 2011, à 16h 29
//

/*
   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".

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 */

#ifndef _ABSTRACTCODONPHASEFREQUENCIESSUBSTITUTIONMODEL_H_
#define _ABSTRACTCODONPHASEFREQUENCIESSUBSTITUTIONMODEL_H_

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

namespace bpp
{
class AbstractCodonPhaseFrequenciesSubstitutionModel :
  public virtual CodonSubstitutionModel,
  public virtual AbstractParameterAliasable
{
private:
  WordFrequenciesSet* posfreqset_;
  std::string freqName_;

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

  AbstractCodonPhaseFrequenciesSubstitutionModel(const AbstractCodonPhaseFrequenciesSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    posfreqset_(model.posfreqset_->clone()),
    freqName_(model.freqName_)
  {}

  AbstractCodonPhaseFrequenciesSubstitutionModel& operator=(const AbstractCodonPhaseFrequenciesSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    if (posfreqset_)
      delete posfreqset_;
    posfreqset_   = model.posfreqset_->clone();
    freqName_   = model.freqName_;

    return *this;
  }

  virtual ~AbstractCodonPhaseFrequenciesSubstitutionModel();

  void fireParameterChanged(const ParameterList& parameters);

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

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

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

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

#endif