NucleotideSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_NUCLEOTIDE_NUCLEOTIDESUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_NUCLEOTIDE_NUCLEOTIDESUBSTITUTIONMODEL_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "../SubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
namespace bpp
{
class NucleotideSubstitutionModelInterface :
  public virtual SubstitutionModelInterface
{
public:
  virtual ~NucleotideSubstitutionModelInterface() {}
 
  NucleotideSubstitutionModelInterface* clone() const override = 0;
 
public:
  virtual std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const = 0;
};
 
 
class NucleotideReversibleSubstitutionModelInterface :
  public virtual NucleotideSubstitutionModelInterface,
  public virtual ReversibleSubstitutionModelInterface
{
public:
  virtual ~NucleotideReversibleSubstitutionModelInterface() {}
 
  NucleotideReversibleSubstitutionModelInterface* clone() const override = 0;
};
 
 
class AbstractNucleotideSubstitutionModel :
  public AbstractSubstitutionModel,
  public virtual NucleotideSubstitutionModelInterface
{
public:
  AbstractNucleotideSubstitutionModel(
      std::shared_ptr<const NucleicAlphabet> alpha,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix) :
    AbstractSubstitutionModel(alpha, stateMap, prefix) {}
 
  virtual ~AbstractNucleotideSubstitutionModel() {}
 
  AbstractNucleotideSubstitutionModel* clone() const override = 0;
 
public:
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(alphabet_);
  }
};
 
class AbstractReversibleNucleotideSubstitutionModel :
  public AbstractReversibleSubstitutionModel,
  public virtual NucleotideReversibleSubstitutionModelInterface
{
public:
  AbstractReversibleNucleotideSubstitutionModel(
      std::shared_ptr<const NucleicAlphabet> alpha,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix) :
    AbstractReversibleSubstitutionModel(alpha, stateMap, prefix) {}
 
  virtual ~AbstractReversibleNucleotideSubstitutionModel() {}
 
  AbstractReversibleNucleotideSubstitutionModel* clone() const override = 0;
 
public:
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(alphabet_);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_NUCLEOTIDE_NUCLEOTIDESUBSTITUTIONMODEL_H