KCM.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_KCM_H
#define BPP_PHYL_MODEL_CODON_KCM_H
 
 
#include "../AbstractBiblioSubstitutionModel.h"
#include "KroneckerCodonDistanceSubstitutionModel.h"
 
namespace bpp
{
class KCM :
  public AbstractBiblioSubstitutionModel,
  public virtual CodonReversibleSubstitutionModelInterface
{
private:
  std::unique_ptr<KroneckerCodonDistanceSubstitutionModel> pmodel_;
  bool oneModel_;
 
public:
  KCM(std::shared_ptr<const GeneticCode> gc, bool oneModel);
 
  KCM(const KCM& kcm);
 
  KCM& operator=(const KCM&);
 
  virtual ~KCM() {}
 
  KCM* clone() const override { return new KCM(*this); }
 
public:
  std::string getName() const override { return "KCM" + std::string(oneModel_ ? "7" : "19") + ".";}
 
  const SubstitutionModelInterface& substitutionModel() const override { return *pmodel_; }
 
  std::shared_ptr<const GeneticCode> getGeneticCode() const override { return pmodel_->getGeneticCode(); }
 
  double getCodonsMulRate(size_t i, size_t j) const override { return pmodel_->getCodonsMulRate(i, j); }
 
protected:
  SubstitutionModelInterface& substitutionModel_() override { return *pmodel_; }
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("KCM::codonFrequencySet. No FrequencySet available for this model.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
 
  void setFreq(std::map<int, double>& frequencies) override
  {
    AbstractBiblioSubstitutionModel::setFreq(frequencies);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_KCM_H