Site.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_SITE_H
#define BPP_SEQ_SITE_H
 
 
#include "CoreSite.h"
#include "IntSymbolList.h"
#include "SiteExceptions.h"
 
namespace bpp
{
class SiteInterface :
  public virtual CoreSiteInterface,
  public virtual IntSymbolListInterface
{
public:
  virtual ~SiteInterface() {}
 
public:
  SiteInterface* clone() const override = 0;
 
  virtual bool operator==(const SiteInterface& site)
  {
    // Verify that site's size, position and content are equals
    if (site.size() != size())
      return false;
    if (site.getCoordinate() != getCoordinate())
    {
      return false;
    }
    else
    {
      for (size_t i = 0; i < site.size(); ++i)
      {
        if (site[i] != operator[](i))
          return false;
      }
      return true;
    }
  }
 
  virtual bool operator<(const SiteInterface& site)
  {
    return site.getCoordinate() < getCoordinate();
  }
};
 
class Site :
  public virtual SiteInterface,
  public AbstractCoreSite,
  public IntSymbolList
{
public:
  Site(std::shared_ptr<const Alphabet>& alphabet) :
    AbstractTemplateSymbolList(alphabet),
    AbstractCoreSite(),
    IntSymbolList(alphabet)
  {}
 
  Site(std::shared_ptr<const Alphabet>& alphabet, int coordinate) :
    AbstractTemplateSymbolList(alphabet),
    AbstractCoreSite(coordinate),
    IntSymbolList(alphabet)
  {}
 
  Site(const std::vector<std::string>& site, std::shared_ptr<const Alphabet>& alphabet) :
    AbstractTemplateSymbolList(alphabet),
    AbstractCoreSite(),
    IntSymbolList(site, alphabet)
  {}
 
  Site(const std::vector<std::string>& site, std::shared_ptr<const Alphabet>& alphabet, int coordinate) :
    AbstractTemplateSymbolList(alphabet),
    AbstractCoreSite(coordinate),
    IntSymbolList(site, alphabet)
  {}
 
  Site(const std::vector<int>& site, std::shared_ptr<const Alphabet>& alphabet) :
    AbstractTemplateSymbolList(site, alphabet),
    AbstractCoreSite(),
    IntSymbolList(site, alphabet)
  {}
 
  Site(const std::vector<int>& site, std::shared_ptr<const Alphabet> alphabet, int coordinate) :
    AbstractTemplateSymbolList(site, alphabet),
    AbstractCoreSite(coordinate),
    IntSymbolList(site, alphabet)
  {}
 
  Site(const Site& site) :
    AbstractTemplateSymbolList(site),
    AbstractCoreSite(site.getCoordinate()),
    IntSymbolList(site)
  {}
 
  Site& operator=(const Site& s)
  {
    AbstractTemplateSymbolList::operator=(s);
    AbstractCoreSite::operator=(s);
    IntSymbolList::operator=(s);
    return *this;
  }
 
  virtual ~Site() {}
 
public:
  Site* clone() const { return new Site(*this); }
  double getStateValueAt(size_t sequencePosition, int state) const
  {
    if (sequencePosition  >= size()) throw IndexOutOfBoundsException("Site::getStateValueAt.", sequencePosition, 0, size() - 1);
    return getAlphabet()->isResolvedIn((*this)[sequencePosition], state) ? 1. : 0.;
  }
};
} // end of namespace bpp.
 
#endif // BPP_SEQ_SITE_H