YNGP_M8.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_YNGP_M8_H
#define BPP_PHYL_MODEL_CODON_YNGP_M8_H
 
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
 
#include "YNGP_M.h"
 
namespace bpp
{
class YNGP_M8 :
  public YNGP_M
{
private:
  bool neutral_;
 
public:
  YNGP_M8(
      std::shared_ptr<const GeneticCode> gc,
      std::unique_ptr<CodonFrequencySetInterface> codonFreqs,
      unsigned int nbclass,
      bool neutral = false);
 
  YNGP_M8* clone() const override { return new YNGP_M8(*this); }
 
  YNGP_M8(const YNGP_M8& mod2) :
    AbstractParameterAliasable(mod2),
    AbstractWrappedModel(mod2),
    AbstractWrappedTransitionModel(mod2),
    AbstractTotallyWrappedTransitionModel(mod2),
    AbstractBiblioTransitionModel(mod2),
    YNGP_M(mod2),
    neutral_(mod2.neutral_)
  {}
 
  YNGP_M8& operator=(const YNGP_M8& mod2)
  {
    YNGP_M::operator=(mod2);
    neutral_ = mod2.neutral_;
    return *this;
  }
 
  std::string getName() const override { return neutral_ ? "YNGP_M8a" : "YNGP_M8"; }
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_YNGP_M8_H