OneChangeTransitionModel.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ONECHANGETRANSITIONMODEL_H
#define BPP_PHYL_MODEL_ONECHANGETRANSITIONMODEL_H
 
 
#include "AbstractFromSubstitutionModelTransitionModel.h"
 
namespace bpp
{
class OneChangeTransitionModel :
  public AbstractFromSubstitutionModelTransitionModel
{
public:
  OneChangeTransitionModel(std::unique_ptr<SubstitutionModelInterface> originalModel) :
    AbstractParameterAliasable("Onechange."),
    AbstractWrappedModel("Onechange."),
    AbstractWrappedTransitionModel("Onechange."),
    AbstractFromSubstitutionModelTransitionModel(std::move(originalModel), "OneChange.")
  {}
 
  OneChangeTransitionModel(const OneChangeTransitionModel& fmsm) :
    AbstractParameterAliasable(fmsm),
    AbstractWrappedModel(fmsm),
    AbstractWrappedTransitionModel(fmsm),
    AbstractFromSubstitutionModelTransitionModel(fmsm)
  {}
 
  OneChangeTransitionModel& operator=(const OneChangeTransitionModel& fmsm)
  {
    AbstractWrappedModel::operator=(fmsm);
    AbstractWrappedTransitionModel::operator=(fmsm);
    AbstractFromSubstitutionModelTransitionModel::operator=(fmsm);
    return *this;
  }
 
  virtual ~OneChangeTransitionModel() {}
 
  OneChangeTransitionModel* clone() const override { return new OneChangeTransitionModel(*this); }
 
public:
  double Pij_t    (size_t i, size_t j, double t) const override;
  double dPij_dt  (size_t i, size_t j, double t) const override;
  double d2Pij_dt2(size_t i, size_t j, double t) const override;
 
  const Matrix<double>& getPij_t(double t) const override;
 
  const Matrix<double>& getdPij_dt(double t) const override;
 
  const Matrix<double>& getd2Pij_dt2(double t) const override;
 
  double freq(size_t i) const override { return transitionModel().freq(i); }
 
  const Vdouble& getFrequencies() const override { return transitionModel().getFrequencies(); }
 
  const FrequencySetInterface& frequencySet() const override
  {
    return transitionModel().frequencySet();
  }
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount) override
  {
    transitionModel_().setFreqFromData(data, pseudoCount);
  }
 
  virtual void setFreq(std::map<int, double>& m) override
  {
    transitionModel_().setFreq(m);
  }
 
  double getRate() const override { return transitionModel().getRate(); }
 
  void setRate(double rate) override { return transitionModel_().setRate(rate); }
 
  double getInitValue(size_t i, int state) const override
  {
    return model().getInitValue(i, state);
  }
 
  std::string getName() const override
  {
    return "OneChange";
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ONECHANGETRANSITIONMODEL_H