K80.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_K80_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_K80_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class K80 :
  public AbstractReversibleNucleotideSubstitutionModel
{
private:
  double kappa_, r_;
  mutable double l_, k_, exp1_, exp2_;
  mutable RowMatrix<double> p_;
 
public:
  K80(std::shared_ptr<const NucleicAlphabet> alpha, double kappa = 1.);
 
  virtual ~K80() {}
 
  K80* clone() const override { return new K80(*this); }
 
public:
  double Pij_t    (size_t i, size_t j, double d) const override;
  double dPij_dt  (size_t i, size_t j, double d) const override;
  double d2Pij_dt2(size_t i, size_t j, double d) const override;
  const Matrix<double>& getPij_t    (double d) const override;
  const Matrix<double>& getdPij_dt  (double d) const override;
  const Matrix<double>& getd2Pij_dt2(double d) const override;
 
  std::string getName() const override { return "K80"; }
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override {}
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_K80_H