RN95.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_RN95_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_RN95_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class RN95 :
  public AbstractNucleotideSubstitutionModel
{
private:
  double alpha_, beta_, gamma_, delta_, epsilon_, kappa_, lambda_, sigma_;
 
public:
  RN95(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      double alpha = 1,
      double beta = 1,
      double gamma = 0.25,
      double delta = 0.25,
      double epsilon = 1,
      double kappa = 0.25,
      double lambda = 0.25,
      double sigma = 1);
 
  virtual ~RN95() {}
 
  RN95* clone() const override { return new RN95(*this); }
 
public:
  std::string getName() const override { return "RN95"; }
 
  void setFreq(std::map<int, double>&) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_RN95_H