SubstitutionMapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_SUBSTITUTIONMAPPING_H
#define BPP_PHYL_MAPPING_SUBSTITUTIONMAPPING_H
 
#include <Bpp/Clonable.h>
 
#include "Mapping.h"
 
// From the STL:
#include <vector>
#include <memory>
 
namespace bpp
{
class SubstitutionMapping :
  public virtual MappingInterface
{
public:
  SubstitutionMapping() {}
  virtual ~SubstitutionMapping() {}
 
  SubstitutionMapping* clone() const override = 0;
 
public:
  virtual size_t getNumberOfSubstitutionTypes() const = 0;
  virtual void setNumberOfSubstitutionTypes(size_t numberOfTypes) = 0;
 
  virtual double& operator()(unsigned int branchId, size_t siteIndex, size_t type) = 0;
  virtual const double& operator()(unsigned int branchId, size_t siteIndex, size_t type) const = 0;
};
 
 
class AbstractSubstitutionMapping :
  virtual public SubstitutionMapping,
  virtual public AbstractMapping
{
private:
  size_t numberOfTypes_;
 
public:
  AbstractSubstitutionMapping() : AbstractMapping(), numberOfTypes_(0){}
 
  AbstractSubstitutionMapping(const AbstractSubstitutionMapping& absm) :
    AbstractMapping(absm), numberOfTypes_(absm.numberOfTypes_) {}
 
  AbstractSubstitutionMapping* clone() const = 0;
 
  AbstractSubstitutionMapping& operator=(const AbstractSubstitutionMapping& absm)
  {
    AbstractMapping::operator=(absm);
    numberOfTypes_ = absm.numberOfTypes_;
 
    return *this;
  }
 
  virtual ~AbstractSubstitutionMapping() {}
 
  size_t getNumberOfSubstitutionTypes() const
  {
    return numberOfTypes_;
  }
 
  virtual void setNumberOfSubstitutionTypes(size_t numberOfTypes)
  {
    numberOfTypes_ = numberOfTypes;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_SUBSTITUTIONMAPPING_H