ProbabilisticSite.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_PROBABILISTICSITE_H
#define BPP_SEQ_PROBABILISTICSITE_H
 
 
#include "CoreSite.h"
#include "ProbabilisticSymbolList.h"
 
namespace bpp
{
class ProbabilisticSiteInterface :
  public virtual CoreSiteInterface,
  public virtual ProbabilisticSymbolListInterface
{
public:
  virtual ~ProbabilisticSiteInterface() {}
 
public:
  virtual ProbabilisticSiteInterface* clone() const = 0;
};
 
class ProbabilisticSite :
  public virtual ProbabilisticSiteInterface,
  public AbstractCoreSite,
  public virtual ProbabilisticSymbolList // Diamond inheritance
{
public:
  ProbabilisticSite(std::shared_ptr<const Alphabet>& alpha) :
    ProbabilisticSymbolList(alpha),
    AbstractCoreSite()
  {}
 
 
  ProbabilisticSite(std::shared_ptr<const Alphabet>& alpha, int position) :
    ProbabilisticSymbolList(alpha),
    AbstractCoreSite(position)
  {}
 
 
  ProbabilisticSite(const Table<double>& site, std::shared_ptr<const Alphabet>& alpha) :
    ProbabilisticSymbolList(site, alpha),
    AbstractCoreSite()
  {}
 
 
  ProbabilisticSite(const Table<double>& site, std::shared_ptr<const Alphabet>& alpha, int position) :
    ProbabilisticSymbolList(site, alpha),
    AbstractCoreSite(position)
  {}
 
 
  ProbabilisticSite(const ProbabilisticSite& site) :
    ProbabilisticSymbolList(site),
    AbstractCoreSite(site)
  {}
 
 
  ProbabilisticSite(const ProbabilisticSiteInterface& site) :
    ProbabilisticSymbolList(site),
    AbstractCoreSite(site.getCoordinate())
  {}
 
 
  ProbabilisticSite& operator=(const ProbabilisticSite& site)
  {
    ProbabilisticSymbolList::operator=(site);
    AbstractCoreSite::operator=(site);
    return *this;
  }
 
  ProbabilisticSite& operator=(const ProbabilisticSiteInterface& site)
  {
    ProbabilisticSymbolList::operator=(site);
    AbstractCoreSite::operator=(site);
    return *this;
  }
 
  ProbabilisticSite* clone() const { return new ProbabilisticSite(*this); }
 
  // class destructor
  virtual ~ProbabilisticSite() {}
 
  double getStateValueAt(size_t sequencePosition, int state) const
  {
    if (sequencePosition  >= size()) throw IndexOutOfBoundsException("ProbabilisticSites::getStateValueAt.", sequencePosition, 0, size() - 1);
    return (*this)[sequencePosition][static_cast<size_t>(state)];
  }
};
} // end of namespace bpp.
#endif // BPP_SEQ_PROBABILISTICSITE_H