FASTAFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Sandro Andreotti $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_FASTAFILE_H
#define OPENMS_FORMAT_FASTAFILE_H

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

#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)
      {
      }

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

    };

    FASTAFile();

    virtual ~FASTAFile();

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

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

  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_FASTAFILE_H