PScore.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <OpenMS/CONCEPT/Types.h>
#include <vector>
#include <map>
 
namespace OpenMS
{
struct OPENMS_DLLAPI PScore
{
  static std::vector<Size> calculateIntensityRankInMZWindow(const std::vector<double>& mz, const std::vector<double>& intensities, double mz_window);
 
  static std::vector<std::vector<Size> > calculateRankMap(const PeakMap& peak_map, double mz_window = 100);
 
  static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra(const PeakSpectrum& spec, const std::vector<Size>& ranks, Size min_level = 1, Size max_level = 9);
 
  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);
 
  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);
 
  static double massCorrectionTerm(double mass);
 
  static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage);
 
  static double modificationCorrectionTerm(Size modifications);
};
 
}