// --------------------------------------------------------------------------
//                   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
//    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,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>

namespace OpenMS
{

  class OPENMS_DLLAPI SiriusMSFile
  {
public:

  /**
    @brief Internal structure used in @ref SiriusAdapter that is used
    for the conversion of a MzMlFile to an internal format.

    @ingroup ID

    Store .ms file.
    Adducts are written to SIRIUS .ms file. If adduct information for a spectrum is missing, 
    no adduct information is written. In this case, SIRIUS assumes default adducts for the respective spectrum.
    
    @return string (full path to file)
    
    @param spectra: Peakmap from input mzml
    @param msfile: (internal) written .ms file from sirius 
    @param map_precursor_to_adducts: adducts of a spectrum (index). 
    */

    // preprocessing e.g. feature information
    static void store(const PeakMap& spectra,
                      const OpenMS::String& msfile,
                      const FeatureMapping::FeatureToMs2Indices& feature_mapping,
                      const bool& feature_only,
                      const int& isotope_pattern_iterations,
                      const bool no_mt_info);

  };

}

