AbstractCodonFitnessSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H
 
 
# ifndef _ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H_
# define _ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H_
 
# include "CodonSubstitutionModel.h"
#include "../FrequencySet/CodonFrequencySet.h"
namespace bpp
{
class AbstractCodonFitnessSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::unique_ptr<FrequencySetInterface> pfitset_;
 
  std::shared_ptr<const GeneticCode> pgencode_;
 
  std::string fitName_;
 
public:
  AbstractCodonFitnessSubstitutionModel(
      std::unique_ptr<FrequencySetInterface> pfitset,
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix);
 
  AbstractCodonFitnessSubstitutionModel(const AbstractCodonFitnessSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pfitset_(model.pfitset_->clone()),
    pgencode_(model.pgencode_),
    fitName_(model.fitName_)
  {}
 
  AbstractCodonFitnessSubstitutionModel& operator=(const AbstractCodonFitnessSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pfitset_.reset(model.pfitset_->clone());
    pgencode_ = model.pgencode_;
    fitName_ = model.fitName_;
    return *this;
  }
 
  AbstractCodonFitnessSubstitutionModel* clone() const override
  {
    return new AbstractCodonFitnessSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonFitnessSubstitutionModel();
 
public:
  void fireParameterChanged (const ParameterList& parameters) override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  // const FrequencySet& getFreq() const { return *pfitset_; }
 
  void setNamespace (const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    pfitset_->setNamespace(prefix + fitName_);
  }
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  const FrequencySetInterface& fitness() const { return *pfitset_; }
 
  // TODO (jdutheil 30/12/22) not allowed if fully encapsulated.
  // std::shared_ptr<const FrequencySetInterface> getFitness() const { return pfitset_; }
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonFitnessSubstitutionModel::frequencySet. No associated FrequencySet.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
};
} // end of namespace bpp
# endif
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H