YNGP_M9.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_YNGP_M9_H
#define BPP_PHYL_MODEL_CODON_YNGP_M9_H
 
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
 
#include "YNGP_M.h"
 
namespace bpp
{
class YNGP_M9 :
  public YNGP_M
{
private:
  unsigned int nBeta_, nGamma_;
 
public:
  YNGP_M9(
      std::shared_ptr<const GeneticCode> gc,
      std::unique_ptr<CodonFrequencySetInterface> codonFreqs,
      unsigned int nbBeta,
      unsigned int nbGamma);
 
  YNGP_M9* clone() const override { return new YNGP_M9(*this); }
 
  YNGP_M9(const YNGP_M9& mod2) :
    AbstractParameterAliasable(mod2),
    AbstractWrappedModel(mod2),
    AbstractWrappedTransitionModel(mod2),
    AbstractTotallyWrappedTransitionModel(mod2),
    AbstractBiblioTransitionModel(mod2),
    YNGP_M(mod2),
    nBeta_(mod2.nBeta_),
    nGamma_(mod2.nGamma_)
  {}
 
  YNGP_M9& operator=(const YNGP_M9& mod2)
  {
    YNGP_M::operator=(mod2);
    nBeta_ = mod2.nBeta_;
    nGamma_ = mod2.nGamma_;
    return *this;
  }
 
public:
  std::string getName() const override { return "YNGP_M9"; }
 
  unsigned int getNBeta() const
  {
    return nBeta_;
  }
 
  unsigned int getNGamma() const
  {
    return nGamma_;
  }
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_YNGP_M9_H