SequenceData.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_SEQUENCEDATA_H
#define BPP_SEQ_CONTAINER_SEQUENCEDATA_H
 
#include <Bpp/Clonable.h>
 
#include "../Alphabet/Alphabet.h"
#include "../Commentable.h"
#include "../CoreSequence.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
template<class HashType = std::string>
class TemplateSequenceDataInterface :
  public virtual Clonable,
  public virtual Commentable
{
public:
  TemplateSequenceDataInterface() {}
  virtual ~TemplateSequenceDataInterface() {}
 
  TemplateSequenceDataInterface<HashType>* clone() const override = 0;
 
public:
  virtual const Alphabet& alphabet() const = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
 
  virtual size_t getNumberOfSequences() const = 0;
 
  virtual std::vector<HashType> getSequenceKeys() const = 0;
 
  virtual void setSequenceKeys(const std::vector<HashType>& sequenceKeys) = 0;
 
  virtual double getStateValueAt(size_t sitePosition, const HashType& sequenceKey, int state) const = 0;
 
  virtual double operator()(size_t sitePosition, const HashType& sequenceKey, int state) const = 0;
 
  virtual double getStateValueAt(size_t sitePosition, size_t sequencePosition, int state) const = 0;
 
  virtual double operator()(size_t sitePosition, size_t sequencePosition, int state) const = 0;
 
  virtual void clear() = 0;
 
  virtual TemplateSequenceDataInterface<HashType>* createEmptyContainer() const = 0;
 
  virtual bool hasSequence(const HashType& sequenceKey) const = 0;
 
 
  virtual const CoreSequenceInterface& sequence(const HashType& sequenceKey) const = 0;
 
  virtual void deleteSequence(const HashType& sequenceKey) = 0;
 
  virtual const CoreSequenceInterface& sequence(size_t sequencePosition) const = 0;
 
  virtual void deleteSequence(size_t sequencePosition) = 0;
 
  virtual const HashType& sequenceKey(size_t sequencePosition) const = 0;
 
  virtual size_t getSequencePosition(const HashType& sequenceKey) const = 0;
 
  virtual std::vector<std::string> getSequenceNames() const = 0;
 
  virtual void setSequenceNames(const std::vector<std::string>& names, bool updateKeys) = 0;
 
  virtual std::vector<Comments> getSequenceComments() const = 0;
};
 
using SequenceDataInterface = TemplateSequenceDataInterface<std::string>;
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_SEQUENCEDATA_H