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 2002-2018.
//
// 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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------

#pragma once

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
    {
      int scan_index;
      int scan_number;
      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);

  };

}