SiriusMzTabWriter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
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#ifndef OPENMS_FORMAT_DATAACCESS_SIRIUSMZTABWRITER_H
#define OPENMS_FORMAT_DATAACCESS_SIRIUSMZTABWRITER_H

namespace OpenMS
{
  class OPENMS_DLLAPI SiriusMzTabWriter
  {
  public:


    struct SiriusAdapterHit
    {
      OpenMS::String formula;
      OpenMS::String adduct;
      int rank;
      double score;
      double treescore;
      double isoscore;
      int explainedpeaks;
      double explainedintensity;
    };

    struct SiriusAdapterIdentification
    {
      OpenMS::String scan_index;
      std::vector<SiriusAdapterHit> hits;
    };

    struct SiriusAdapterRun
    {
      std::vector<SiriusAdapterIdentification> identifications;
    };

    // extract scan_index from filepath
    static String extract_scan_index(const String & path);

    //Output of Sirius is one directory per spectrum/compound
    //paths: Path to output directories of sirius
    //number: Amount of entries for each file/compound should be written to the mztab file
    static void read(const std::vector<String> & paths, Size number, MzTab & result);

  };

}

#endif //OPENMS_FORMAT_DATAACCESS_SIRIUSMZTABWRITER_H