AbstractCodonClusterAASubstitutionModel.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONCLUSTERAASUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTCODONCLUSTERAASUBSTITUTIONMODEL_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 AbstractCodonClusterAASubstitutionModel :
  public virtual CoreCodonSubstitutionModelInterface,
  public virtual AbstractParameterAliasable
{
private:
  std::shared_ptr<const GeneticCode> pgencode_;
 
  double omegaR_, omegaC_;
 
  std::vector<uint> assign_;
 
  std::shared_ptr<const StateMapInterface> stateMap_;
 
public:
  AbstractCodonClusterAASubstitutionModel(
      std::shared_ptr<const GeneticCode> pgencode,
      const std::string& prefix,
      const std::vector<uint>& assign = {1, 2, 3, 3, 3, 2, 2, 1, 2, 4, 4, 2, 4, 4, 1, 3, 3, 2, 2, 1});
 
  AbstractCodonClusterAASubstitutionModel(const AbstractCodonClusterAASubstitutionModel& model) :
    AbstractParameterAliasable(model),
    pgencode_(model.pgencode_),
    omegaR_(model.omegaR_),
    omegaC_(model.omegaC_),
    assign_(model.assign_),
    stateMap_(model.stateMap_)
  {}
 
  AbstractCodonClusterAASubstitutionModel& operator=(
      const AbstractCodonClusterAASubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    pgencode_ = model.pgencode_;
    omegaR_ = model.omegaR_;
    omegaC_ = model.omegaC_;
    assign_ = model.assign_;
    stateMap_ = model.stateMap_;
 
    return *this;
  }
 
  AbstractCodonClusterAASubstitutionModel* clone() const override
  {
    return new AbstractCodonClusterAASubstitutionModel(*this);
  }
 
  virtual ~AbstractCodonClusterAASubstitutionModel() {}
 
public:
  void fireParameterChanged(const ParameterList& parameters) override;
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
  const CodonFrequencySetInterface& codonFrequencySet() const override
  {
    throw NullPointerException("AbstractCodonClusterAASubstitutionModel::frequencySet. No associated FrequencySet.");
  }
 
  bool hasCodonFrequencySet() const override
  {
    return false;
  }
 
  const std::vector<uint>& getAssign() const
  {
    return assign_;
  }
 
  void setFreq(std::map<int, double>& frequencies) override {}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTCODONCLUSTERAASUBSTITUTIONMODEL_H