YN98.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_YN98_H
#define BPP_PHYL_MODEL_CODON_YN98_H
 
 
#include "../AbstractBiblioSubstitutionModel.h"
#include "CodonDistanceFrequenciesSubstitutionModel.h"
 
namespace bpp
{
class YN98 :
  public AbstractBiblioSubstitutionModel,
  public virtual CodonReversibleSubstitutionModelInterface
{
private:
  std::unique_ptr<CodonDistanceFrequenciesSubstitutionModel> pmodel_;
 
public:
  YN98(
      std::shared_ptr<const GeneticCode> gc,
      std::unique_ptr<CodonFrequencySetInterface> codonFreqs);
 
  YN98(const YN98& yn98);
 
  YN98& operator=(const YN98&);
 
  virtual ~YN98() {}
 
  YN98* clone() const override { return new YN98(*this); }
 
public:
  std::string getName() const override { return "YN98"; }
 
  const SubstitutionModelInterface& substitutionModel() const override { return *pmodel_; }
 
  std::shared_ptr<const GeneticCode> getGeneticCode() const override
  {
    return pmodel_->getGeneticCode();
  }
 
  const FrequencySetInterface& frequencySet() const override
  {
    return AbstractWrappedModel::frequencySet();
  }
 
  double getCodonsMulRate(size_t i, size_t j) const override
  {
    return pmodel_->getCodonsMulRate(i, j);
  }
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    return pmodel_->codonFrequencySet();
  }
 
  bool hasCodonFrequencySet() const override
  {
    return pmodel_->hasCodonFrequencySet();
  }
 
  void setFreq(std::map<int, double>& frequencies) override
  {
    AbstractBiblioSubstitutionModel::setFreq(frequencies);
  }
 
  using AbstractBiblioSubstitutionModel::frequencySet;
 
protected:
  SubstitutionModelInterface& substitutionModel_() override { return *pmodel_; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_YN98_H