// --------------------------------------------------------------------------
//                   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,
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
// --------------------------------------------------------------------------

#pragma once

#include <vector>

#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>

namespace OpenMS
{

  /**
   * @brief A class containing correction functions for Swath MS maps
   *
   * This class can use a set of pre-determined points in a Swath-MS map to
   * correct all maps according to the m/z shift found in those fixed points.
   *
   */
  class OPENMS_DLLAPI SwathMapMassCorrection
  {

public:

    /**
     * @brief Correct the m/z values of a SWATH map based on the RT-normalization peptides
     *
     * This extracts the full spectra at the most likely elution time of the
     * calibrant masses and fits a regression curve to correct for a possible
     * mass shift of the empirical masses vs the theoretically expected masses.
     * Several types of regressions are available (see below corr_type parameter).
     *
     * The function will replace the pointers stored in swath_maps with a
     * transforming map that will contain corrected m/z values.
     *
     * @param transition_group_map A MRMFeatureFinderScoring result map
     * @param swath_maps The raw swath maps from the current run
     * @param corr_type Regression type, one of "none", "unweighted_regression", "weighted_regression", "quadratic_regression", "quadratic_regression_delta_ppm"
     *
     *
     */
    static void correctMZ(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map,
                          std::vector< OpenSwath::SwathMap > & swath_maps,
                          const std::string& corr_type,
                          const double mz_extr_window = 0.05,
                          const bool ppm = false);

  };
}

