HyperScore.h

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

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Macros.h>
#include <vector>

namespace OpenMS
{

struct OPENMS_DLLAPI HyperScore
{
  typedef std::pair<Size, double> IndexScorePair; 

  /* @brief compute the (ln transformed) X!Tandem HyperScore 
   *  1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated
   *  2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions
   * @note Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities
   * @param fragment_mass_tolerance mass tolerance applied left and right of the theoretical spectrum peak position
   * @param fragment_mass_tolerance_unit_ppm Unit of the mass tolerance is: Thomson if false, ppm if true
   * @param exp_spectrum measured spectrum
   * @param theo_spectrum theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator.
   */
//  static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const RichPeakSpectrum& theo_spectrum);

  static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum);

  private:
    // helper to compute the log factorial
    static double logfactorial_(UInt x);
};

}

#endif