SiriusMzTabWriter.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/MzTabFile.h>
#include <OpenMS/FORMAT/CsvFile.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusMzTabWriter
  {
  public:
 
    class SiriusAdapterHit
    {
    public:
      OpenMS::String formula;
      OpenMS::String adduct;
      OpenMS::String precursor_formula;
      int rank = 0;
      double iso_score = 0.0;
      double tree_score = 0.0;
      double sirius_score = 0.0;
      int explainedpeaks = 0;
      double explainedintensity = 0.0;
      double median_mass_error_fragment_peaks_ppm = 0.0;
      double median_absolute_mass_error_fragment_peaks_ppm = 0.0;
      double mass_error_precursor_ppm = 0.0;
    };
 
    class SiriusAdapterIdentification
    {
    public:
      double mz = 0.;
      double rt = 0.;
      OpenMS::StringList native_ids;
      int scan_index = -1;
      int scan_number = -1;
      OpenMS::String feature_id;
      std::vector<SiriusAdapterHit> hits;
    };
 
    class SiriusAdapterRun
    {
    public:
      std::vector<SiriusAdapterIdentification> identifications;
    };
 
    class SiriusSpectrumMSInfo
    {
    public:
      StringList ext_n_id; // multiple possible MS2 spectra
      double ext_mz = 0.0;
      double ext_rt = 0.0;
    };
 
    static int extractScanIndex(const String& path);
 
    static int extractScanNumber(const String& path);
 
    static String extractFeatureId(const String& path);
 
    static std::map< std::string, Size > extract_columnname_to_columnindex(CsvFile& csvfile);
 
    static SiriusSpectrumMSInfo extractSpectrumMSInfo(const String& single_sirius_path);
 
    static void read(const std::vector<String>& sirius_output_paths,
                     const String& original_input_mzml,
                     const Size& top_n_hits,
                     MzTab& result);
 
  };
 
  namespace SiriusVersion
  {
    inline const std::string CURRENT_VERSION = "5.6.3";
  }
 
}