AbstractCodonDistanceSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_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 AbstractCodonDistanceSubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::shared_ptr<const AlphabetIndex2> pdistance_;
 
  std::shared_ptr<const GeneticCode> pgencode_;
 
  double alpha_, beta_;
 
  double gamma_;
 
  std::shared_ptr<const StateMapInterface> stateMap_;
 
public:
  AbstractCodonDistanceSubstitutionModel(
      std::shared_ptr<const AlphabetIndex2> pdist,
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix,
      bool paramSynRate = false);
 
  AbstractCodonDistanceSubstitutionModel(const AbstractCodonDistanceSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pdistance_(model.pdistance_),
    pgencode_(model.pgencode_),
    alpha_(model.alpha_),
    beta_(model.beta_),
    gamma_(model.gamma_),
    stateMap_(model.stateMap_)
  {}
 
  AbstractCodonDistanceSubstitutionModel& operator=(
      const AbstractCodonDistanceSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pdistance_ = model.pdistance_;
    pgencode_ = model.pgencode_;
    alpha_ = model.alpha_;
    beta_ = model.beta_;
    gamma_ = model.gamma_;
    stateMap_ = model.stateMap_;
 
    return *this;
  }
 
  AbstractCodonDistanceSubstitutionModel* clone() const override
  {
    return new AbstractCodonDistanceSubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonDistanceSubstitutionModel() {}
 
public:
  void fireParameterChanged(const ParameterList& parameters) override;
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonDistanceSubstitutionModel::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_ABSTRACTCODONDISTANCESUBSTITUTIONMODEL_H