AbstractKroneckerCodonSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTKRONECKERCODONSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTKRONECKERCODONSUBSTITUTIONMODEL_H
 
 
#include "../AbstractKroneckerWordSubstitutionModel.h"
#include "../Nucleotide/NucleotideSubstitutionModel.h"
#include "CodonSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
 
// From the STL:
#include <memory>
#include <set>
 
namespace bpp
{
class AbstractKroneckerCodonSubstitutionModel :
  public virtual CodonSubstitutionModelInterface,
  public virtual AbstractKroneckerWordSubstitutionModel
{
private:
  std::shared_ptr<const GeneticCode> gCode_;
 
public:
  AbstractKroneckerCodonSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
      const std::string& st);
 
  AbstractKroneckerCodonSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod,
      const std::vector<std::set<size_t>>& vPos,
      const std::string& st);
 
  AbstractKroneckerCodonSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
      const std::string& st);
 
  AbstractKroneckerCodonSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
      std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3,
      const std::vector<std::set< size_t>>& vPos,
      const std::string& st);
 
  virtual ~AbstractKroneckerCodonSubstitutionModel() {}
 
  AbstractKroneckerCodonSubstitutionModel(const AbstractKroneckerCodonSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    AbstractKroneckerWordSubstitutionModel(model),
    gCode_(model.gCode_)
  {}
 
  AbstractKroneckerCodonSubstitutionModel& operator=(const AbstractKroneckerCodonSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    AbstractKroneckerWordSubstitutionModel::operator=(model);
    gCode_ = model.gCode_;
    return *this;
  }
 
  AbstractKroneckerCodonSubstitutionModel* clone() const override = 0;
 
protected:
  void completeMatrices_() override;
 
public:
  std::shared_ptr<const GeneticCode> getGeneticCode() const override { return gCode_; }
 
  virtual double getCodonsMulRate(size_t i, size_t j) const override { return 1.; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTKRONECKERCODONSUBSTITUTIONMODEL_H