WordSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_WORDSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_WORDSUBSTITUTIONMODEL_H
 
 
#include "AbstractWordSubstitutionModel.h"
 
// From bpp-core
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/BppVector.h>
 
namespace bpp
{
class WordSubstitutionModel :
  public AbstractWordSubstitutionModel
{
public:
  WordSubstitutionModel(ModelList& modelList, const std::string& prefix = "");
 
  WordSubstitutionModel(
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      unsigned int num,
      const std::string& prefix = "");
 
  virtual ~WordSubstitutionModel() {}
 
  WordSubstitutionModel* clone() const override { return new WordSubstitutionModel(*this); }
 
protected:
  WordSubstitutionModel(
      std::shared_ptr<const Alphabet> alphabet,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix = "");
 
  virtual void updateMatrices_() override;
 
  virtual void completeMatrices_() override;
 
public:
  virtual const RowMatrix<double>& getPij_t(double d) const override;
 
  virtual const RowMatrix<double>& getdPij_dt(double d) const override;
 
  virtual const RowMatrix<double>& getd2Pij_dt2(double d) const override;
 
  virtual std::string getName() const override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_WORDSUBSTITUTIONMODEL_H