KroneckerWordSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_KRONECKERWORDSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_KRONECKERWORDSUBSTITUTIONMODEL_H
 
 
#include "AbstractKroneckerWordSubstitutionModel.h"
 
// From bpp-core
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/BppVector.h>
 
namespace bpp
{
class KroneckerWordSubstitutionModel :
  public AbstractKroneckerWordSubstitutionModel
{
public:
  KroneckerWordSubstitutionModel(ModelList& modelList, const std::string& prefix = "");
 
  KroneckerWordSubstitutionModel(ModelList& modelList,
      const std::vector<std::set< size_t>>& vPos,
      const std::string& prefix = "");
 
  KroneckerWordSubstitutionModel(
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      unsigned int num,
      const std::string& prefix = "");
 
  KroneckerWordSubstitutionModel(
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      unsigned int num,
      const std::vector<std::set< size_t>>& vPos,
      const std::string& prefix = "");
 
  virtual ~KroneckerWordSubstitutionModel() {}
 
  KroneckerWordSubstitutionModel* clone() const override
  {
    return new KroneckerWordSubstitutionModel(*this);
  }
 
protected:
  KroneckerWordSubstitutionModel(
      std::shared_ptr<const Alphabet> alph,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix = "");
 
  void completeMatrices_() override {}
 
public:
  virtual std::string getName() const override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_KRONECKERWORDSUBSTITUTIONMODEL_H