text: // --------------------------------------------------------------------------
  //                   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
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Hannes Roest$
  // $Authors: Hannes Roest$
  // --------------------------------------------------------------------------
  
  #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"
       * @param mz_extraction_window Extraction window for calibration in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
       * @param ppm Whether the extraction window is given in ppm or Da
       *
       */
      static void correctMZ(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *>& 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);
  
    };
  }
  
  