AbstractSequenceContainer.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_ABSTRACTSEQUENCECONTAINER_H
#define BPP_SEQ_CONTAINER_ABSTRACTSEQUENCECONTAINER_H
 
#include <Bpp/Exceptions.h>
 
#include "../Alphabet/Alphabet.h"
#include "../Sequence.h"
#include "../Commentable.h"
#include "SequenceContainer.h"
 
namespace bpp
{
template<class SequenceType, class HashType = std::string>
class AbstractTemplateSequenceContainer :
  public virtual TemplateSequenceContainerInterface<SequenceType, HashType>,
  public SimpleCommentable
{
protected:
  std::shared_ptr<const Alphabet> alphabet_;
 
public:
  AbstractTemplateSequenceContainer(std::shared_ptr<const Alphabet> alphabet) :
    SimpleCommentable(), alphabet_(alphabet)
  {}
 
  AbstractTemplateSequenceContainer(std::shared_ptr<const Alphabet> alphabet, const Comments& comments) :
    SimpleCommentable(comments),
    alphabet_(alphabet)
  {}
 
  AbstractTemplateSequenceContainer(const AbstractTemplateSequenceContainer<SequenceType, HashType>& sc) :
    SimpleCommentable(sc), alphabet_(sc.alphabet_)
  {}
 
  AbstractTemplateSequenceContainer& operator=(const AbstractTemplateSequenceContainer<SequenceType, HashType>& sc)
  {
    SimpleCommentable::operator=(sc);
    alphabet_ = sc.alphabet_;
    return *this;
  }
 
  AbstractTemplateSequenceContainer(const TemplateSequenceContainerInterface<SequenceType, HashType>& sc) :
    SimpleCommentable(sc.getComments()),
    alphabet_(sc.getAlphabet())
  {}
 
  AbstractTemplateSequenceContainer& operator=(const TemplateSequenceContainerInterface<SequenceType, HashType>& sc)
  {
    alphabet_ = sc.getAlphabet();
    setComments(sc.getComments());
 
    return *this;
  }
 
  virtual ~AbstractTemplateSequenceContainer() {}
 
public:
  const Alphabet& alphabet() const override
  {
    if (!alphabet_) throw Exception("AbstractSequenceContainer::alphabet() : no associated alphabet.");
    return *alphabet_;
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override { return alphabet_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_ABSTRACTSEQUENCECONTAINER_H