GY94.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_GY94_H
#define BPP_PHYL_MODEL_CODON_GY94_H
 
#include <Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h>
 
#include "../AbstractBiblioSubstitutionModel.h"
#include "CodonDistanceFrequenciesSubstitutionModel.h"
 
namespace bpp
{
class GY94 :
  public AbstractBiblioSubstitutionModel,
  public virtual ReversibleSubstitutionModelInterface
{
private:
  std::shared_ptr<const GranthamAAChemicalDistance> gacd_;
  std::unique_ptr<CodonDistanceFrequenciesSubstitutionModel> pmodel_;
 
public:
  GY94(
      std::shared_ptr<const GeneticCode> gc,
      std::unique_ptr<CodonFrequencySetInterface> codonFreqs);
 
  virtual ~GY94();
 
  GY94(const GY94& gy94);
 
  GY94& operator=(const GY94& gy94);
 
  GY94* clone() const override { return new GY94(*this); }
 
public:
  std::string getName() const override { return "GY94"; }
 
  const SubstitutionModelInterface& substitutionModel() const override { return *pmodel_; }
 
  std::shared_ptr<const GeneticCode> getGeneticCode() const { return pmodel_->getGeneticCode(); }
 
  double getCodonsMulRate(size_t i, size_t j) const { return pmodel_->getCodonsMulRate(i, j); }
 
protected:
  SubstitutionModelInterface& substitutionModel_() override { return *pmodel_; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_GY94_H