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
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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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:
 
    struct SiriusAdapterHit
    {
      OpenMS::String formula;
      OpenMS::String adduct;
      OpenMS::String precursor_formula;
      int rank = 0;
      double rank_score = 0.0;
      double iso_score = 0.0;
      double tree_score = 0.0;
      double sirius_score = 0.0;
      int explainedpeaks = 0;
      double explainedintensity = 0.0;
    };
 
    struct SiriusAdapterIdentification
    {
      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;
    };
 
    struct SiriusAdapterRun
    {
      std::vector<SiriusAdapterIdentification> identifications;
    };
 
    static int extractScanIndex(const String& path);
 
    static int extractScanNumber(const String& path);
 
    static String extractFeatureId(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);
 
    static std::map< String, Size > extract_columnname_to_columnindex(CsvFile& csvfile);
 
  };
 
 
 
}