T92.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_T92_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_T92_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class T92 :
  public AbstractReversibleNucleotideSubstitutionModel
{
private:
  double kappa_, theta_, k_, r_, piA_, piC_, piG_, piT_;
  mutable double exp1_, exp2_, l_;
  mutable RowMatrix<double> p_;
 
public:
  T92(std::shared_ptr<const NucleicAlphabet> alpha, double kappa = 1., double theta = 0.5);
 
  virtual ~T92() {}
 
  T92* clone() const override { return new T92(*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 "T92"; }
 
  void setFreq(std::map<int, double>& freqs) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_T92_H