AnonymousSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ANONYMOUSSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_ANONYMOUSSUBSTITUTIONMODEL_H
 
 
#include "AbstractSubstitutionModel.h"
 
namespace bpp
{
/*
 * @brief Substitution Model with no name nor predefined generator
 * sets, and provides a non-const setGenerator() function to fill
 * the generator directly.
 *
 * Directly inherits from AbstractSubstitutionModel, hence uses the
 * computation methods developed in it.
 */
class AnonymousSubstitutionModel :
  public AbstractSubstitutionModel
{
public:
  AnonymousSubstitutionModel(
      std::shared_ptr<const Alphabet> alpha,
      std::shared_ptr<const StateMapInterface> stateMap) :
    AbstractParameterAliasable("Anonymous"),
    AbstractSubstitutionModel(alpha, stateMap, "Anonymous")
  {}
 
  virtual ~AnonymousSubstitutionModel() {}
 
  AnonymousSubstitutionModel* clone() const override
  {
    return new AnonymousSubstitutionModel(*this);
  }
 
public:
  std::string getName() const override { return "Anonymous"; }
 
  Matrix<double>& setGenerator() { return generator_; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ANONYMOUSSUBSTITUTIONMODEL_H