AlignmentData.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_ALIGNMENTDATA_H
#define BPP_SEQ_CONTAINER_ALIGNMENTDATA_H
 
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/VectorTools.h>
#include "SequenceData.h"
#include "../CoreSite.h"
 
// From the STL:
#include <string>
namespace bpp
{
template<class HashType = std::string>
class TemplateAlignmentDataInterface :
  public virtual TemplateSequenceDataInterface<HashType>
{
public:
  TemplateAlignmentDataInterface() {}
  virtual ~TemplateAlignmentDataInterface() {}
 
  TemplateAlignmentDataInterface* clone() const override = 0;
 
 
  virtual const CoreSiteInterface& site(size_t siteIndex) const = 0;
 
  virtual void deleteSites(size_t siteIndex, size_t length) = 0;
 
  virtual size_t getNumberOfSites() const = 0;
 
  virtual void reindexSites() = 0;
 
  virtual Vint getSiteCoordinates() const = 0;
 
  virtual void setSiteCoordinates(const Vint& vCoordinates) = 0;
};
 
using AlignmentDataInterface = TemplateAlignmentDataInterface<std::string>;
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_ALIGNEDVALUESCONTAINER_H