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 2002-2021.
//
// 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
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $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 = "4.9.0";
  }
 
}