SubstitutionMapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _LEGACY_SUBSTITUTION_MAPPING_H_
#define _LEGACY_SUBSTITUTION_MAPPING_H_
 
#include "Mapping.h"
 
#include <Bpp/Clonable.h>
 
// From the STL:
#include <vector>
#include <memory>
 
namespace bpp
{
class LegacySubstitutionMappingInterface :
  public virtual LegacyMappingInterface
{
public:
  LegacySubstitutionMappingInterface() {}
  virtual ~LegacySubstitutionMappingInterface() {}
 
  LegacySubstitutionMappingInterface* clone() const override = 0;
 
public:
  virtual size_t getNumberOfSubstitutionTypes() const = 0;
 
  virtual double& operator()(size_t nodeIndex, size_t siteIndex, size_t type) = 0;
  virtual const double& operator()(size_t nodeIndex, size_t siteIndex, size_t type) const = 0;
};
 
 
class LegacyAbstractSubstitutionMapping :
  public virtual LegacySubstitutionMappingInterface,
  public LegacyAbstractMapping
{
public:
  LegacyAbstractSubstitutionMapping(const Tree& tree) : LegacyAbstractMapping(tree){}
 
  LegacyAbstractSubstitutionMapping(const LegacyAbstractSubstitutionMapping& absm) = default;
 
  LegacyAbstractSubstitutionMapping* clone() const override = 0;
 
  LegacyAbstractSubstitutionMapping& operator=(const LegacyAbstractSubstitutionMapping& absm) = default;
 
  virtual ~LegacyAbstractSubstitutionMapping() {}
};
} // end of namespace bpp.
 
#endif // _LEGACY_SUBSTITUTION_MAPPING_H_