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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
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#ifndef OPENMS_ANALYSIS_RNPXL_PSCORE_H
#define OPENMS_ANALYSIS_RNPXL_PSCORE_H

#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/CONCEPT/Types.h>
#include <vector>
#include <map>

namespace OpenMS
{
  /**
    @brief Implementation of the PScore PSM scoring algorithm
  */

struct OPENMS_DLLAPI PScore
{
  /* @brief calculate local (windowed) peak ranks.
   * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity 
   * The result can be used to efficiently filter spectra for top 1..n peaks in mass windows 
   * @note: ranks are zero based (highest intensity peak in window has rank 0)
   * @param mz m/z positions of the peaks
   * @param intensities of the peaks
   * @param mz_window window in Thomson centered at each peak
   */  
  static std::vector<Size> calculateIntensityRankInMZWindow(const std::vector<double>& mz, const std::vector<double>& intensities, double mz_window);

  /* @brief precalculated, windowed peak ranks for a whole experiment. 
   * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity 
   * 1. Each spectrum is subdivided into windows of size @param mz_window.
   * 2. For each window, peak ranks are assigned using calculateIntensityRankInMZWindow.
   * 3. A rank map is returned
   * @note: ranks are zero based (top element has rank 0)
   * @param peak_map Fragment spectra used for rank calculation. Typically a peak map after removal of all MS1 spectra.
   * @param mz_window window in Thomson centered at each peak
   */
  static std::vector<std::vector<Size> > calculateRankMap(const PeakMap& peak_map, double mz_window = 100);

  /* @brief Calculates spectra for peak level between min_level to max_level and stores them in the map
   * A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak.
   * @note: levels are zero based (level 0 has only the top intensity peaks for each window, level 1 the top and second most intensive one)
   * @note: min and max level are taken from the Andromeda publication but are similar to the AScore publication
   */ 
  static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra(const PeakSpectrum& spec, const std::vector<Size>& ranks, Size min_level = 1, Size max_level = 9);

  /* @brief Computes the PScore for a vector of theoretical spectra
   * Similar to Andromeda, a vector of theoretical spectra can be provided that e.g. contain loss spectra or higher charge spectra depending on the sequence.
   * The best score obtained by scoring all those theoretical spectra against the experimental ones is returned.
   * @param fragment_mass_tolerance mass tolerance for matching peaks
   * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used
   * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank).
   * @param theo_spectra theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator
   * @param mz_window window in Thomson centered at each peak
   */ 
  static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map<Size, PeakSpectrum>& peak_level_spectra, const std::vector<PeakSpectrum>& theo_spectra, double mz_window = 100.0);

  /* @brief Computes the PScore for a single theoretical spectrum
   * @param fragment_mass_tolerance mass tolerance for matching peaks
   * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used
   * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank).
   * @param theo_spectra theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator
   * @param mz_window window in Thomson centered at each peak
   */ 
  static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map<Size, PeakSpectrum>& peak_level_spectra, const PeakSpectrum& theo_spectrum, double mz_window = 100.0);

  /// additive correction terms used by Andromeda (pscore + massC + cleaveC + modC - 100). For reference see the Andromeda source code.
  /// @note: constants used in the correction term might be instrument dependent
  static double massCorrectionTerm(double mass);

  /// correction term for type of cleavage. For reference see the Andromeda source code.
  /// @note: constants used in the correction term might be instrument dependent
  static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage);

  /// correction term for modification. For reference see the Andromeda source code.
  /// @note: constants used in the correction term might be instrument dependent
  static double modificationCorrectionTerm(Size modifications);
};

}
#endif

