XQuestScores.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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
{
 
  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 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);
 
 
    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);
  };
 
}