ISequence.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_ISEQUENCE_H
#define BPP_SEQ_IO_ISEQUENCE_H
 
#include <Bpp/Exceptions.h>
 
#include "../Container/SequenceContainer.h"
#include "../Container/SiteContainer.h"
#include "../Sequence.h"
#include "IoSequence.h"
 
// From the STL:
#include <iostream>
#include <string>
#include <memory>
 
namespace bpp
{
class ISequence :
  public virtual IOSequence
{
public:
  ISequence() {}
  virtual ~ISequence() {}
 
public:
  virtual void readSequences(
      std::istream& input,
      SequenceContainerInterface& container) const = 0;
  virtual void readSequences(
      const std::string& path,
      SequenceContainerInterface& container) const = 0;
 
  virtual std::unique_ptr<SequenceContainerInterface> readSequences(
      std::istream& input,
      std::shared_ptr<const Alphabet> alpha) const = 0;
  virtual std::unique_ptr<SequenceContainerInterface> readSequences(
      const std::string& path,
      std::shared_ptr<const Alphabet> alpha) const = 0;
};
 
class IAlignment :
  public virtual IOSequence
{
public:
  IAlignment() {}
  virtual ~IAlignment() {}
 
public:
  virtual void readAlignment(
      std::istream& input,
      SequenceContainerInterface& container) const = 0;
 
  virtual void readAlignment(
      const std::string& path,
      SequenceContainerInterface& container) const = 0;
 
  virtual std::unique_ptr<SiteContainerInterface> readAlignment(
      std::istream& input,
      std::shared_ptr<const Alphabet> alpha) const = 0;
 
  virtual std::unique_ptr<SiteContainerInterface> readAlignment(
      const std::string& path,
      std::shared_ptr<const Alphabet> alpha) const = 0;
};
 
class IProbabilisticSequence :
  public virtual IOProbabilisticSequence
{
public:
  IProbabilisticSequence() {}
  virtual ~IProbabilisticSequence() {}
 
public:
  virtual void readSequences(
      std::istream& input,
      ProbabilisticSequenceContainerInterface& container) const = 0;
  virtual void readSequences(
      const std::string& path,
      ProbabilisticSequenceContainerInterface& container) const = 0;
 
  virtual std::unique_ptr<ProbabilisticSequenceContainerInterface> readSequences(
      std::istream& input,
      std::shared_ptr<const Alphabet> alpha) const = 0;
 
  virtual std::unique_ptr<ProbabilisticSequenceContainerInterface> readSequences(
      const std::string& path,
      std::shared_ptr<const Alphabet> alpha) const = 0;
};
 
class IProbabilisticAlignment :
  public virtual IOProbabilisticSequence
{
public:
  IProbabilisticAlignment() {}
  virtual ~IProbabilisticAlignment() {}
 
public:
  virtual void readAlignment(
      std::istream& input,
      ProbabilisticSequenceContainerInterface& container) const = 0;
 
  virtual void readAlignment(
      const std::string& path,
      ProbabilisticSequenceContainerInterface& container) const = 0;
 
  virtual std::unique_ptr<ProbabilisticSiteContainerInterface> readAlignment(
      std::istream& input,
      std::shared_ptr<const Alphabet> alpha) const = 0;
 
  virtual std::unique_ptr<ProbabilisticSiteContainerInterface> readAlignment(
      const std::string& path,
      std::shared_ptr<const Alphabet> alpha) const = 0;
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_ISEQUENCE_H