CsiFingerIdMzTabWriter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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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>
 
namespace OpenMS
{
  class OPENMS_DLLAPI CsiFingerIdMzTabWriter
      {
          public:
 
          class CsiAdapterHit
          {
          public:
            OpenMS::String inchikey2D;
            OpenMS::String inchi;
            unsigned int rank = 0;
            unsigned int formula_rank = 0;
            OpenMS::String adduct;
            OpenMS::String molecular_formula;
            double score = 0.;
            OpenMS::String name;
            OpenMS::String smiles;
            OpenMS::String xlogp;
            OpenMS::String dbflags;
            std::vector<String> pubchemids;
            std::vector<String> links;
 
          };
 
          class CsiAdapterIdentification
          {
          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<CsiAdapterHit> hits;
          };
 
          class CsiAdapterRun
          {
          public:
            std::vector <CsiAdapterIdentification> identifications;
          };
 
          static void read(const std::vector<String>& sirius_output_paths,
                           const String& original_input_mzml,
                           const Size& top_n_hits,
                           MzTab& result);
 
      };
}