SequencedValuesContainer.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CONTAINER_SEQUENCEDVALUESCONTAINER_H
#define BPP_SEQ_CONTAINER_SEQUENCEDVALUESCONTAINER_H
 
#include <Bpp/Clonable.h>
 
#include "../Alphabet/Alphabet.h"
#include "../Commentable.h"
#include "SequenceContainerExceptions.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
class Sequence;
 
class SequencedValuesContainer :
  public virtual Clonable
{
// public:
//   SequencedValuesContainer() {}
//   virtual ~SequencedValuesContainer() {}
 
public:
  virtual const Alphabet* getAlphabet() const = 0;
 
  virtual std::string toString(const std::string& name) const = 0;
 
  virtual bool hasSequence(const std::string& name) const = 0;
 
  virtual size_t getNumberOfSequences() const = 0;
 
  virtual std::vector<std::string> getSequenceNames() const = 0;
 
  virtual void setSequenceNames(const std::vector<std::string>& names, bool checkNames) = 0;
 
  virtual double getStateValueAt(size_t siteIndex, const std::string& sequenceName, int state) const = 0;
 
  virtual double operator()(size_t siteIndex, const std::string& sequenceName, int state) const = 0;
 
  virtual const Comments& getComments(const std::string& name) const = 0;
 
  virtual void setComments(const std::string& name, const Comments& comments) = 0;
 
  virtual const Comments& getGeneralComments() const = 0;
 
  virtual void setGeneralComments(const Comments& comments) = 0;
 
  virtual void deleteGeneralComments() = 0;
 
  virtual void clear() = 0;
 
  virtual SequencedValuesContainer* createEmptyContainer() const = 0;
};
} // end of namespace bpp.
#endif // BPP_SEQ_CONTAINER_SEQUENCEDVALUESCONTAINER_H