GTR.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_GTR_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_GTR_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class GTR :
  public AbstractReversibleNucleotideSubstitutionModel
{
protected:
  double a_, b_, c_, d_, e_, piA_, piC_, piG_, piT_, theta_, theta1_, theta2_, p_;
 
public:
  GTR(
      std::shared_ptr<const NucleicAlphabet> alpha,
      double a = 1.,
      double b = 1.,
      double c = 1.,
      double d = 1.,
      double e = 1.,
      double piA = 0.25,
      double piC = 0.25,
      double piG = 0.25,
      double piT = 0.25);
 
  virtual ~GTR() {}
 
  GTR* clone() const override { return new GTR(*this); }
 
public:
  std::string getName() const override { return "GTR"; }
 
  void setFreq(std::map<int, double>& freqs) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_GTR_H