AbstractCodonBGCSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONBGCSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONBGCSUBSTITUTIONMODEL_H
 
#include <Bpp/Numeric/AbstractParameterAliasable.h>
 
#include "CodonSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
 
namespace bpp
{
class AbstractCodonBGCSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::shared_ptr<const GeneticCode> pgencode_;
 
  double B_, S_;
 
  std::shared_ptr<const StateMapInterface> stateMap_;
 
public:
  AbstractCodonBGCSubstitutionModel(
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix);
 
  AbstractCodonBGCSubstitutionModel(const AbstractCodonBGCSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pgencode_(model.pgencode_),
    B_(model.B_),
    S_(model.S_),
    stateMap_(model.stateMap_)
  {}
 
  AbstractCodonBGCSubstitutionModel& operator=(
      const AbstractCodonBGCSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pgencode_ = model.pgencode_;
    B_ = model.B_;
    S_ = model.S_;
    stateMap_ = model.stateMap_;
 
    return *this;
  }
 
  AbstractCodonBGCSubstitutionModel* clone() const override
  {
    return new AbstractCodonBGCSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonBGCSubstitutionModel() {}
 
public:
  void fireParameterChanged(const ParameterList& parameters) override;
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonBGCSubstitutionModel::frequencySet. No associated FrequencySet.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
 
  void setFreq(std::map<int, double>& frequencies) override {}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONBGCSUBSTITUTIONMODEL_H