TripletSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_TRIPLETSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_TRIPLETSUBSTITUTIONMODEL_H
 
 
#include "../Nucleotide/NucleotideSubstitutionModel.h"
#include "../WordSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
 
namespace bpp
{
class TripletSubstitutionModel :
  public WordSubstitutionModel
{
public:
  TripletSubstitutionModel(
      std::shared_ptr<const CodonAlphabet> palph,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod);
 
  TripletSubstitutionModel(
      std::shared_ptr<const CodonAlphabet> palph,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3);
 
  virtual ~TripletSubstitutionModel() {}
 
  TripletSubstitutionModel* clone() const override { return new TripletSubstitutionModel(*this);}
 
public:
  std::string getName() const override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_TRIPLETSUBSTITUTIONMODEL_H