SiteContainer.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_SITECONTAINER_H
#define BPP_SEQ_CONTAINER_SITECONTAINER_H
 
#include "AlignmentData.h"
#include "SequenceContainer.h"
#include "../Site.h"
#include "../ProbabilisticSite.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
template<class SiteType, class SequenceType, class HashType>
class TemplateSiteContainerInterface :
  public virtual TemplateAlignmentDataInterface<HashType>,
  public virtual TemplateSequenceContainerInterface<SequenceType, HashType>
{
public:
  TemplateSiteContainerInterface() {}
  virtual ~TemplateSiteContainerInterface() {}
 
  TemplateSiteContainerInterface<SiteType, SequenceType, HashType>* clone() const override = 0;
 
  TemplateSiteContainerInterface<SiteType, SequenceType, HashType>* createEmptyContainer() const override = 0;
 
public:
  virtual const SiteType& site(size_t sitePosition) const override = 0;
 
  virtual void setSite(size_t sitePosition, std::unique_ptr<SiteType>& site, bool checkCoordinate = true) = 0;
 
  virtual void addSite(std::unique_ptr<SiteType>& site, bool checkCoordinate) = 0;
 
  virtual void addSite(std::unique_ptr<SiteType>& site, size_t sitePosition, bool checkCoordinate) = 0;
 
  virtual std::unique_ptr<SiteType> removeSite(size_t sitePosition) = 0;
 
  virtual void deleteSite(size_t sitePosition) = 0;
 
  virtual void deleteSites(size_t sitePosition, size_t length) override = 0;
 
  virtual size_t getNumberOfSites() const override = 0;
 
  virtual void reindexSites() override = 0;
};
 
// Aliases:
using SiteContainerInterface = TemplateSiteContainerInterface<Site, Sequence, std::string>;
using ProbabilisticSiteContainerInterface = TemplateSiteContainerInterface<ProbabilisticSite, ProbabilisticSequence, std::string>;
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_SITECONTAINER_H