// --------------------------------------------------------------------------
//                   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.
// --------------------------------------------------------------------------
// 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
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// --------------------------------------------------------------------------
// $Maintainer: Dorrestein Lab - University of California San Diego - https://dorresteinlab.ucsd.edu/$
// $Authors: Abinesh Sarvepalli and Louis Felix Nothias$
// $Contributors: Fabian Aicheler and Oliver Alka from Oliver Kohlbacher's group at Tubingen University$

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{
  class OPENMS_DLLAPI GNPSMGFFile : 
    public DefaultParamHandler,
    public ProgressLogger
  {
    public:
      // default c'tor
      GNPSMGFFile();

      // see GNPSExport tool documentation
      /**
      * @brief Create file for GNPS molecular networking.
      * @param consensus_file_path path to consensusXML with spectrum references
      * @param mzml_file_paths path to mzML files referenced in consensusXML. Used to extract spectra as MGF.
      * @param out MGF file with MS2 peak data for molecular networking.
      */
      void store(const String& consensus_file_path, const StringList& mzml_file_paths, const String& out) const;

    private:
      static constexpr double DEF_COSINE_SIMILARITY = 0.9;
      static constexpr double DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES);

//      static constexpr double DEF_PREC_MASS_TOL = 0.5;
//      static constexpr bool DEF_PREC_MASS_TOL_ISPPM = false;

      static constexpr int DEF_PEPT_CUTOFF = 5;
      static constexpr int DEF_MSMAP_CACHE = 50;
  };
}
