// --------------------------------------------------------------------------
//                   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,
// 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
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.h>
#include <OpenMS/DATASTRUCTURES/ListUtilsIO.h>

#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/Constants.h>

namespace OpenMS
{

/// @brief struct to hold a single report line
struct OPENMS_DLLAPI RNPxlReportRow
{
  bool no_id;
  double rt;
  double original_mz;
  String accessions;
  String RNA;
  String peptide;
  double best_localization_score;
  String localization_scores;
  String best_localization;
  Int charge;
  double score;
  double peptide_weight;
  double RNA_weight;
  double xl_weight;
  double abs_prec_error;
  double rel_prec_error;
  RNPxlMarkerIonExtractor::MarkerIonsType marker_ions;
  double m_H;
  double m_2H;
  double m_3H;
  double m_4H;  
  int rank;
  String getString(const String& separator) const;

};

/// create header line
struct OPENMS_DLLAPI RNPxlReportRowHeader
{
  static String getString(const String& separator);
};

/// create report
struct OPENMS_DLLAPI RNPxlReport
{
  static std::vector<RNPxlReportRow> annotate(const PeakMap& spectra, std::vector<PeptideIdentification>& peptide_ids, double marker_ions_tolerance);
};

}


