AbstractCodonAAFitnessSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONAAFITNESSSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONAAFITNESSSUBSTITUTIONMODEL_H
 
 
# ifndef _ABSTRACTCODON_AA_FITNESSSUBSTITUTIONMODEL_H_
# define _ABSTRACTCODON_AA_FITNESSSUBSTITUTIONMODEL_H_
 
# include "CodonSubstitutionModel.h"
 
#include "../FrequencySet/ProteinFrequencySet.h"
 
namespace bpp
{
class AbstractCodonAAFitnessSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::shared_ptr<FrequencySetInterface> pfitset_;
 
  std::shared_ptr<const GeneticCode> pgencode_;
 
  std::string fitName_;
 
  std::shared_ptr<const StateMapInterface> stateMap_;
 
  std::shared_ptr<const StateMapInterface> protStateMap_;
 
  double Ns_;
 
public:
  AbstractCodonAAFitnessSubstitutionModel(
      std::shared_ptr<FrequencySetInterface> pfitset,
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix);
 
  AbstractCodonAAFitnessSubstitutionModel(const AbstractCodonAAFitnessSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pfitset_(model.pfitset_->clone()),
    pgencode_(model.pgencode_),
    fitName_(model.fitName_),
    stateMap_(model.stateMap_),
    protStateMap_(pfitset_->getStateMap()),
    Ns_(1)
  {}
 
  AbstractCodonAAFitnessSubstitutionModel& operator=(const AbstractCodonAAFitnessSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pfitset_.reset(model.pfitset_->clone());
    pgencode_ = model.pgencode_;
    fitName_ = model.fitName_;
    stateMap_ = model.stateMap_;
    protStateMap_ = pfitset_->getStateMap();
    Ns_ = 1;
 
    return *this;
  }
 
  AbstractCodonAAFitnessSubstitutionModel* clone() const override
  {
    return new AbstractCodonAAFitnessSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonAAFitnessSubstitutionModel();
 
public:
  void fireParameterChanged(const ParameterList& parameters) override;
 
  void setFreq(std::map<int, double>& frequencies) override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonAAFitnessSubstitutionModel::codonFrequencySet. This model does not take codon frequencies. See aaFitness.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
 
  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& aaFitness() const { return *pfitset_; }
 
  std::shared_ptr<const FrequencySetInterface> getAAFitness() const { return pfitset_; }
 
  void addNsParameter()
  {
    addParameter_(new Parameter(getNamespace() + "Ns", 1, std::make_shared<IntervalConstraint>(NumConstants::MILLI(), 100, true, true)));
  }
};
} // end of namespace bpp
 
# endif // _ABSTRACTCODON_AA_FITNESSSUBSTITUTIONMODEL_H_
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONAAFITNESSSUBSTITUTIONMODEL_H