gBGC.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_GBGC_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_GBGC_H
 
#include <Bpp/Numeric/Constraints.h>
 
#include "../AbstractSubstitutionModel.h"
#include "NucleotideSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
// From Utils:
 
using namespace std;
 
namespace bpp
{
class gBGC :
  public AbstractNucleotideSubstitutionModel
{
private:
  std::unique_ptr<NucleotideSubstitutionModelInterface> model_;
  std::string nestedPrefix_;
 
  double B_;
 
public:
  gBGC(
      std::shared_ptr<const NucleicAlphabet>,
      std::unique_ptr<NucleotideSubstitutionModelInterface>,
      double B = 0);
 
  gBGC(const gBGC&);
 
  gBGC& operator=(const gBGC& gbgc);
 
  gBGC* clone() const override { return new gBGC(*this); }
 
  virtual ~gBGC() {}
 
public:
  std::string getName() const override
  {
    return model_->getName() + "+gBGC";
  }
 
  size_t getNumberOfStates() const override { return model_->getNumberOfStates(); }
 
  void fireParameterChanged(const ParameterList&) override;
 
  const SubstitutionModelInterface& nestedModel() const { return *model_; }
 
  void setNamespace(const std::string&) override;
 
protected:
  void updateMatrices_() override;
};
}
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_GBGC_H