SequenceContainer.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_SEQUENCECONTAINER_H
#define BPP_SEQ_CONTAINER_SEQUENCECONTAINER_H
 
#include "SequenceData.h"
#include "SequenceContainerExceptions.h"
#include "../Sequence.h"
#include "../ProbabilisticSequence.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
template<class SequenceType, class HashType = std::string>
class TemplateSequenceContainerInterface :
  public virtual TemplateSequenceDataInterface<HashType>
{
public:
  TemplateSequenceContainerInterface() {}
  virtual ~TemplateSequenceContainerInterface() {}
 
public:
  virtual TemplateSequenceContainerInterface<SequenceType, HashType>*
  createEmptyContainer() const override = 0;
 
  virtual const SequenceType& sequence(const HashType& sequenceKey) const override = 0;
 
  virtual void setSequence(const HashType& sequenceKey, std::unique_ptr<SequenceType>& sequencePtr) = 0;
 
  virtual void addSequence(const HashType& sequenceKey, std::unique_ptr<SequenceType>& sequencePtr) = 0;
 
  virtual std::unique_ptr<SequenceType> removeSequence(const HashType& sequenceKey) = 0;
 
  virtual const typename SequenceType::ElementType& valueAt(const HashType& sequenceKey, size_t sitePosition) const = 0;
 
  virtual typename SequenceType::ElementType& valueAt(const HashType& sequenceKey, size_t sitePosition) = 0;
 
  virtual const SequenceType& sequence(size_t sequencePosition) const override = 0;
 
  virtual void setSequence(size_t sequencePosition, std::unique_ptr<SequenceType>& sequencePtr) = 0;
 
  virtual void setSequence(size_t sequencePosition, std::unique_ptr<SequenceType>& sequencePtr, const HashType& sequenceKey) = 0;
 
  virtual void insertSequence(size_t sequencePosition, std::unique_ptr<SequenceType>& sequencePtr, const HashType& sequenceKey) = 0;
 
  virtual std::unique_ptr<SequenceType> removeSequence(size_t sequencePosition) = 0;
 
  virtual const typename SequenceType::ElementType& valueAt(size_t sequencePosition, size_t sitePosition) const = 0;
 
  virtual typename SequenceType::ElementType& valueAt(size_t sequencePosition, size_t sitePosition) = 0;
};
 
// Aliases:
using SequenceContainerInterface = TemplateSequenceContainerInterface<Sequence>;
using ProbabilisticSequenceContainerInterface = TemplateSequenceContainerInterface<ProbabilisticSequence>;
 
template<class T>
class SwitchDeleter
{
private:
  bool doDelete_;
 
public:
  SwitchDeleter() : doDelete_(true) {}
 
public:
  void operator()(T* ptr) const
  {
    if (doDelete_) delete ptr;
  }
 
  void on() { doDelete_ = true; }
  void off() { doDelete_ = false; }
 
  bool isOn() const { return doDelete_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_SEQUENCECONTAINER_H