XQuestScores.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
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#pragma once

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

namespace OpenMS
{

  class OPENMS_DLLAPI XQuestScores
  {

  public:
    static float preScore(Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta);

    static float preScore(Size matched_alpha, Size ions_alpha);

    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 logOccupancyProb(const PeakSpectrum& theoretical_spec,  const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);


    static double weightedTICScoreXQuest(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);

    static double weightedTICScore(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);

    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);

    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);

    static std::vector< double > xCorrelation(const PeakSpectrum & spec1, const PeakSpectrum & spec2, Int maxshift, double tolerance);

    static double xCorrelationPrescore(const PeakSpectrum & spec1, const PeakSpectrum & spec2, double tolerance);
  };

}