AbstractOSequence.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_ABSTRACTOSEQUENCE_H
#define BPP_SEQ_IO_ABSTRACTOSEQUENCE_H
 
 
#include "../Alphabet/Alphabet.h"
#include "../Container/VectorSequenceContainer.h"
#include "../ProbabilisticSequence.h"
#include "OSequence.h"
 
// From the STL:
#include <string>
#include <fstream>
 
namespace bpp
{
class AbstractOSequence :
  public virtual OSequence
{
public:
  AbstractOSequence() {}
  virtual ~AbstractOSequence() {}
 
public:
  void writeSequences(std::ostream& output, const SequenceContainerInterface& sc) const override = 0;
 
  void writeSequences(const std::string& path, const SequenceContainerInterface& sc, bool overwrite = true) const override
  {
    // Open file in specified mode
    std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
    writeSequences(output, sc);
    output.close();
  }
};
 
class AbstractOSequence2 :
  public virtual AbstractOSequence,
  // in case for Diamond inheritance
  public virtual OAlignment
{
public:
  AbstractOSequence2() {}
  virtual ~AbstractOSequence2() {}
 
public:
  void writeAlignment(std::ostream& output, const SiteContainerInterface& sc) const override
  {
    writeSequences(output, sc);
  }
 
  void writeAlignment(const std::string& path, const SiteContainerInterface& sc, bool overwrite = true) const override
  {
    writeSequences(path, sc, overwrite);
  }
};
 
class AbstractOProbabilisticSequence :
  public virtual OProbabilisticSequence
{
public:
  AbstractOProbabilisticSequence() {}
  virtual ~AbstractOProbabilisticSequence() {}
 
public:
  void writeSequences(std::ostream& output, const ProbabilisticSequenceContainerInterface& psc) const override = 0;
 
  void writeSequences(const std::string& path, const ProbabilisticSequenceContainerInterface& psc, bool overwrite = true) const override
  {
    // Open file in specified mode
    std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
    writeSequences(output, psc);
    output.close();
  }
 
};
 
class AbstractOProbabilisticSequence2 :
  public AbstractOProbabilisticSequence,
  public virtual OProbabilisticAlignment
{
public:
  AbstractOProbabilisticSequence2() {}
  virtual ~AbstractOProbabilisticSequence2() {}
 
public:
  void writeAlignment(std::ostream& output, const ProbabilisticSiteContainerInterface& sc) const override
  {
    writeSequences(output, sc);
  }
 
  void writeAlignment(const std::string& path, const ProbabilisticSiteContainerInterface& sc, bool overwrite = true) const override
  {
    writeSequences(path, sc, overwrite);
  }
 
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_ABSTRACTOSEQUENCE_H