D1WalkSubstitutionModel.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_D1WALKSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_D1WALKSUBSTITUTIONMODEL_H
 
#include <Bpp/Seq/Alphabet/IntegerAlphabet.h>
 
#include "AbstractSubstitutionModel.h"
 
 
namespace bpp
{
class D1WalkSubstitutionModel :
  public AbstractReversibleSubstitutionModel
{
private:
  std::shared_ptr<FullFrequencySet> freqSet_;
 
public:
  D1WalkSubstitutionModel(std::shared_ptr<const IntegerAlphabet> alpha, unsigned short method = 1);
 
  D1WalkSubstitutionModel(const D1WalkSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    AbstractReversibleSubstitutionModel(model),
    freqSet_(model.freqSet_->clone())
  {}
 
  D1WalkSubstitutionModel& operator=(const D1WalkSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    AbstractReversibleSubstitutionModel::operator=(model);
    freqSet_ = std::shared_ptr<FullFrequencySet>(model.freqSet_->clone());
    return *this;
  }
 
  virtual ~D1WalkSubstitutionModel() {}
 
  D1WalkSubstitutionModel* clone() const override { return new D1WalkSubstitutionModel(*this); }
 
public:
  std::string getName() const override
  {
    return "D1Walk";
  }
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    freqSet_->matchParametersValues(parameters);
    AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
  }
 
  const FrequencySetInterface& frequencySet() const override
  {
    return *freqSet_;
  }
 
  void setFreq(std::map<int, double>& freq) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_D1WALKSUBSTITUTIONMODEL_H