SiriusMzTabWriter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/MzTabFile.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusMzTabWriter
  {
  public:
 
    struct SiriusAdapterHit
    {
      OpenMS::String formula;
      OpenMS::String adduct;
      int rank = 0;
      double score = 0.;
      double treescore = 0.;
      double isoscore = 0.;
      int explainedpeaks = 0;
      double explainedintensity = 0.;
    };
 
    struct SiriusAdapterIdentification
    {
      double mz = 0.;
      double rt = 0.;
      OpenMS::String native_id;
      int scan_index = -1;
      int scan_number = -1;
      OpenMS::String feature_id;
      std::vector<SiriusAdapterHit> hits;
    };
 
    struct SiriusAdapterRun
    {
      std::vector<SiriusAdapterIdentification> identifications;
    };
 
    static int extract_scan_index(const String& path);
 
    static void read(const std::vector<String>& sirius_output_paths,
                     const String& original_input_mzml,
                     const Size& top_n_hits,
                     MzTab& result);
 
  };
 
}