SSR.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_SSR_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_SSR_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class SSR :
  public AbstractReversibleNucleotideSubstitutionModel
{
private:
  double beta_, gamma_, delta_, theta_, piA_, piC_, piG_, piT_;
 
public:
  SSR(std::shared_ptr<const NucleicAlphabet> alpha,
      double beta = 1.,
      double gamma = 1.,
      double delta = 1.,
      double theta = 0.5);
 
  virtual ~SSR() {}
 
  SSR* clone() const override { return new SSR(*this); }
 
public:
  std::string getName() const override { return "SSR"; }
 
  void setFreq(std::map<int, double>&) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_SSR_H