FASTAFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_FASTAFILE_H
#define OPENMS_FORMAT_FASTAFILE_H

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>

#include <functional>
#include <fstream>
#include <memory>
#include <utility>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI FASTAFile
  {
public:
  struct FASTAEntry
  {
      String identifier;
      String description;
      String sequence;

      FASTAEntry() :
        identifier(),
        description(),
        sequence()
      {
      }

      FASTAEntry(String id, String desc, String seq) :
        identifier(id),
        description(desc),
        sequence(seq)
      {
      }
      
      FASTAEntry(const FASTAEntry& rhs)
        :
        identifier(rhs.identifier),
        description(rhs.description),
        sequence(rhs.sequence)
      {
      }

      FASTAEntry(FASTAEntry&& rhs) noexcept
       :
        identifier(::std::move(rhs.identifier)),
        description(::std::move(rhs.description)),
        sequence(::std::move(rhs.sequence)) 
      {
      }

      FASTAEntry& operator=(const FASTAEntry& rhs)
      {
        if (*this == rhs) return *this;
        identifier = rhs.identifier;
        description = rhs.description;
        sequence = rhs.sequence;
        return *this;
      }

      bool operator==(const FASTAEntry& rhs) const
      {
        return identifier == rhs.identifier
               && description == rhs.description
               && sequence == rhs.sequence;
      }
    
      bool headerMatches(const FASTAEntry& rhs) const
      {
        return identifier == rhs.identifier && 
         description == rhs.description;
      }
 
      bool sequenceMatches(const FASTAEntry& rhs) const
      {
        return sequence == rhs.sequence;
      }
    };

    FASTAFile();

    virtual ~FASTAFile();

    void readStart(const String& filename);

    bool readNext(FASTAEntry& protein);


    void writeStart(const String& filename);

    void writeNext(const FASTAEntry& protein);

    void writeEnd();
    

    void static load(const String& filename, std::vector<FASTAEntry>& data);

    void static store(const String& filename, const std::vector<FASTAEntry>& data);

protected:
    std::fstream infile_;   //< filestream for reading; init using FastaFile::readStart()
    std::ofstream outfile_; //< filestream for writing; init using FastaFile::writeStart()
    std::unique_ptr<void, std::function<void(void*) > > reader_; //< filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-constructable; we use void* here, to avoid pulling in seqan includes
    Size entries_read_; //< some internal book-keeping during reading
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_FASTAFILE_H