// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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//    may be used to endorse or promote products derived from this software
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_SWATHMAPMASSCORRECTION_H
#define OPENMS_ANALYSIS_OPENSWATH_SWATHMAPMASSCORRECTION_H

#include <vector>

#include <OpenMS/ANALYSIS/OPENSWATH/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(OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map,
                          std::vector< OpenSwath::SwathMap > & swath_maps,
                          std::string corr_type,
                          double mz_extr_window = 0.05, bool ppm = false);

  };
}

#endif // OPENMS_ANALYSIS_OPENSWATH_SWATHMAPMASSCORRECTION_H

