text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
  //
  // 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: Eugen Netz $
  // $Authors: Eugen Netz $
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/KERNEL/MSSpectrum.h>
  #include <OpenMS/KERNEL/StandardTypes.h>
  #include <OpenMS/CONCEPT/Types.h>
  #include <OpenMS/CHEMISTRY/SimpleTSGXLMS.h>
  #include <vector>
  
  namespace OpenMS
  {
  
  /**
   *  @brief An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")
   */
  
    class OPENMS_DLLAPI XQuestScores
    {
  
    public:
     /**
      * @brief compute a simple and fast to compute pre-score for a cross-link spectrum match
      * @param number of experimental peaks matched to theoretical linear ions from the alpha peptide
      * @param number of theoretical ions from the alpha peptide
      * @param number of experimental peaks matched to theoretical linear ions from the beta peptide
      * @param number of theoretical ions from the beta peptide
      */
      static float preScore(Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta);
  
     /**
      * @brief compute a simple and fast to compute pre-score for a mono-link spectrum match
      * @param number of experimental peaks matched to theoretical linear ions from the alpha peptide
      * @param number of theoretical ions from the alpha peptide
      */
      static float preScore(Size matched_alpha, Size ions_alpha);
  
     /**
      * @brief compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance
      * @param theoretical spectrum, sorted by position
      * @param alignment between the theoretical and the experimental spectra
      * @param fragment mass tolerance of the alignment
      * @param fragment mass tolerance unit of the alignment, true = ppm, false = Da
      * @param type of cross-link, true = cross-link, false = mono-link
      * @param number of considered charges in the theoretical spectrum
      */
      static double matchOddsScore(const PeakSpectrum& theoretical_spec,  const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum = false, Size n_charges = 1);
  
      static double matchOddsScoreSimpleSpec(const std::vector< SimpleTSGXLMS::SimplePeak >& theoretical_spec,  const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum = false, Size n_charges = 1);
  
  
      /**
       * @brief compute the logOccupancyProb score, similar to the match_odds, a score based on the probability of getting the given number of matched peaks by chance
       * @param theoretical_spec theoretical spectrum, sorted by position
       * @param matched_size number of matched peaks between experimental and theoretical spectra
       * @param fragment_mass_tolerance the tolerance of the alignment
       * @param fragment_mass_tolerance_unit the tolerance unit of the alignment, true = ppm, false = Da
       */
      static double logOccupancyProb(const PeakSpectrum& theoretical_spec,  const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
  
     /**
      * @brief compute the weighted total ion current score for a cross-link. Reimplementation from xQuest.
      * @param sequence length of alpha peptide
      * @param sequence length of beta peptide
      * @param intensity sum of matched peaks from alpha peptide
      * @param intensity sum of matched peaks from beta peptide
      * @param type of cross-link, true = cross-link, false = mono-link
      * @param sum of peak intensities of the experimental spectrum
      * @param true = cross-link, false = mono-link. in case of a mono-link, beta_size and intsum_beta should be 0
      */
      static double weightedTICScoreXQuest(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
  
     /**
      * @brief compute the weighted total ion current score for a cross-link. Scaling changed from original xQuest.
      * @param sequence length of alpha peptide
      * @param sequence length of beta peptide
      * @param intensity sum of matched peaks from alpha peptide
      * @param intensity sum of matched peaks from beta peptide
      * @param type of cross-link, true = cross-link, false = mono-link
      * @param sum of peak intensities of the experimental spectrum
      * @param true = cross-link, false = mono-link. in case of a mono-link, beta_size and intsum_beta should be 0
      */
      static double weightedTICScore(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
  
     /**
      * @brief computes sum of peak intensities of matched peaks for either the alpha or the beta peptide
      * @param alignment between linear alpha or beta ions and linear experimental peaks
      * @param alignment between xlink alpha or beta ions and xlink experimental peaks
      * @param experimental linear ion spectrum
      * @param experimental xlink spectrum
      */
      static double matchedCurrentChain(const std::vector< std::pair< Size, Size > >& matched_spec_linear, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks, const PeakSpectrum& spectrum_linear_peaks, const PeakSpectrum& spectrum_xlink_peaks);
  
     /**
      * @brief computes sum of peak intensities of all matched peaks
      * @param alignment between linear alpha ions and linear experimental peaks
      * @param alignment between linear beta ions and linear experimental peaks
      * @param alignment between xlink alpha ions and xlink experimental peaks
      * @param alignment between xlink beta ions and xlink experimental peaks
      * @param experimental linear ion spectrum
      * @param experimental xlink spectrum
      */
      static double totalMatchedCurrent(const std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha, const std::vector< std::pair< Size, Size > >& matched_spec_linear_beta, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta, const PeakSpectrum& spectrum_linear_peaks, const PeakSpectrum& spectrum_xlink_peaks);
  
     /**
      * @brief computes a crude cross-correlation between two spectra. Crude, because it uses a static binsize based on a tolerance in Da and it uses equal intensities for all peaks
      * @param first spectrum
      * @param second spectrum
      * @param number of bins, that should be considered for shifting the second spectrum. the second spectrum is shifted from -maxshift to +maxshift of tolerance bins and a correlation is computed for each position.
      * @param tolerance or binsize in Da
      */
      static std::vector< double > xCorrelation(const PeakSpectrum & spec1, const PeakSpectrum & spec2, Int maxshift, double tolerance);
  
      /**
       * @brief computes a crude dot product between two spectra. Crude, because it uses a static binsize based on a tolerance in Da and it uses equal intensities for all peaks
       * @param spec1 first spectrum
       * @param spec2 second spectrum
       * @param tolerance tolerance or binsize in Da
       */
      static double xCorrelationPrescore(const PeakSpectrum & spec1, const PeakSpectrum & spec2, double tolerance);
    };
  
  }
  