EquiprobableSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_EQUIPROBABLESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_EQUIPROBABLESUBSTITUTIONMODEL_H
 
#include <Bpp/Seq/Alphabet/Alphabet.h>
 
#include "AbstractSubstitutionModel.h"
#include "FrequencySet/FrequencySet.h"
 
namespace bpp
{
class EquiprobableSubstitutionModel :
  public AbstractReversibleSubstitutionModel
{
private:
  mutable double exp_;
  mutable RowMatrix<double> p_;
  std::unique_ptr<FrequencySetInterface> freqSet_;
 
public:
  EquiprobableSubstitutionModel(std::shared_ptr<const Alphabet> alpha);
 
  EquiprobableSubstitutionModel(
      std::shared_ptr<const Alphabet> alpha,
      std::unique_ptr<FrequencySetInterface> freqSet,
      bool initFreqs = false);
 
  EquiprobableSubstitutionModel(const EquiprobableSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    AbstractReversibleSubstitutionModel(model),
    exp_(model.exp_),
    p_(model.p_),
    freqSet_(model.freqSet_->clone())
  {}
 
  EquiprobableSubstitutionModel& operator=(const EquiprobableSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    AbstractReversibleSubstitutionModel::operator=(model);
    exp_ = model.exp_;
    p_   = model.p_;
    freqSet_.reset(model.freqSet_->clone());
    return *this;
  }
 
  virtual ~EquiprobableSubstitutionModel() {}
 
  EquiprobableSubstitutionModel* clone() const override { return new EquiprobableSubstitutionModel(*this); }
 
public:
  double Pij_t    (size_t i, size_t j, double d) const override;
  double dPij_dt  (size_t i, size_t j, double d) const override;
  double d2Pij_dt2(size_t i, size_t j, double d) const override;
  const Matrix<double>& getPij_t    (double d) const override;
  const Matrix<double>& getdPij_dt  (double d) const override;
  const Matrix<double>& getd2Pij_dt2(double d) const override;
 
  std::string getName() const override
  {
    if (freqSet_->getNamespace().find("+F.") != std::string::npos)
      return "Equi+F";
    else
      return "Equi";
  }
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    freqSet_->matchParametersValues(parameters);
    freq_ = freqSet_->getFrequencies();
    AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
  }
 
  void setFrequencySet(const FrequencySetInterface& freqSet)
  {
    freqSet_.reset(freqSet.clone());
    resetParameters_();
    addParameters_(freqSet_->getParameters());
  }
 
  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_EQUIPROBABLESUBSTITUTIONMODEL_H