OpenMS
PScore.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
38 
39 #include <OpenMS/CONCEPT/Types.h>
40 #include <vector>
41 #include <map>
42 
43 namespace OpenMS
44 {
49 struct OPENMS_DLLAPI PScore
50 {
62  static std::vector<Size> calculateIntensityRankInMZWindow(const std::vector<double>& mz, const std::vector<double>& intensities, double mz_window);
63 
77  static std::vector<std::vector<Size> > calculateRankMap(const PeakMap& peak_map, double mz_window = 100);
78 
86  static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra(const PeakSpectrum& spec, const std::vector<Size>& ranks, Size min_level = 1, Size max_level = 9);
87 
99  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);
100 
109  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);
110 
113  static double massCorrectionTerm(double mass);
114 
117  static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage);
118 
121  static double modificationCorrectionTerm(Size modifications);
122 };
123 
124 }
125 
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Implementation of the PScore PSM scoring algorithm.
Definition: PScore.h:50
static std::vector< Size > calculateIntensityRankInMZWindow(const std::vector< double > &mz, const std::vector< double > &intensities, double mz_window)
calculate local (windowed) peak ranks.
static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage)
static double modificationCorrectionTerm(Size modifications)
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)
Computes the PScore for a vector of theoretical spectra.
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)
Computes the PScore for a single theoretical spectrum.
static double massCorrectionTerm(double mass)
static std::map< Size, PeakSpectrum > calculatePeakLevelSpectra(const PeakSpectrum &spec, const std::vector< Size > &ranks, Size min_level=1, Size max_level=9)
Calculates spectra for peak level between min_level to max_level and stores them in the map A spectru...
static std::vector< std::vector< Size > > calculateRankMap(const PeakMap &peak_map, double mz_window=100)
precalculated, windowed peak ranks for a whole experiment.