DFP07.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_DFP07_H
#define BPP_PHYL_MODEL_CODON_DFP07_H
 
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
 
#include "../AbstractBiblioMixedTransitionModel.h"
#include "../FrequencySet/CodonFrequencySet.h"
#include "../MixtureOfASubstitutionModel.h"
#include "../Protein/ProteinSubstitutionModel.h"
#include "CodonSameAARateSubstitutionModel.h"
 
namespace bpp
{
class DFP07 :
  public AbstractBiblioMixedTransitionModel
{
protected:
  const MixtureOfASubstitutionModel* mixedSubModelPtr_;
 
  size_t synfrom_, synto_;
 
public:
  DFP07(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<ProteinSubstitutionModelInterface> pAAmodel,
      std::unique_ptr<CodonFrequencySetInterface> codonFreqs);
 
  DFP07(const DFP07& mod2) :
    AbstractParameterAliasable(mod2),
    AbstractWrappedModel(mod2),
    AbstractWrappedTransitionModel(mod2),
    AbstractTotallyWrappedTransitionModel(mod2),
    AbstractBiblioTransitionModel(mod2),
    AbstractBiblioMixedTransitionModel(mod2),
    mixedSubModelPtr_(nullptr),
    synfrom_(mod2.synfrom_),
    synto_(mod2.synto_)
  {
    mixedSubModelPtr_ = dynamic_cast<const MixtureOfASubstitutionModel*>(&mixedModel());
  }
 
  virtual DFP07* clone() const override
  {
    return new DFP07(*this);
  }
 
  DFP07& operator=(const DFP07& mod2)
  {
    const auto& eq = AbstractBiblioMixedTransitionModel::operator=(mod2);
 
    synfrom_ = mod2.synfrom_;
    synto_ = mod2.synto_;
 
    mixedSubModelPtr_ = dynamic_cast<const MixtureOfASubstitutionModel*>(&eq.mixedModel());
 
    return *this;
  }
 
  const ProteinSubstitutionModelInterface& proteinModel() const
  {
    return dynamic_cast<const CodonSameAARateSubstitutionModel&>(nModel(0)).proteinModel();
  }
 
  std::string getName() const override { return "DFP07"; }
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_DFP07_H