| OpenMS 2.5.0

XQuestScores.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/MSSpectrum.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/CONCEPT/Types.h>
40 #include <OpenMS/CHEMISTRY/SimpleTSGXLMS.h>
41 #include <vector>
42
43 namespace OpenMS
44 {
45
50 class OPENMS_DLLAPI XQuestScores
51 {
52
53 public:
61 static float preScore(Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta);
62
68 static float preScore(Size matched_alpha, Size ions_alpha);
69
79 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);
80
81 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);
82
83
91 static double logOccupancyProb(const PeakSpectrum& theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
92
103 static double weightedTICScoreXQuest(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
104
115 static double weightedTICScore(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
116
124 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);
125
135 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);
136
144 static std::vector< double > xCorrelation(const PeakSpectrum & spec1, const PeakSpectrum & spec2, Int maxshift, double tolerance);
145
152 static double xCorrelationPrescore(const PeakSpectrum & spec1, const PeakSpectrum & spec2, double tolerance);
153 };
154
155 }
SimpleTSGXLMS.h
StandardTypes.h
Types.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::XQuestScores
An implementation of the scores for cross-link identification from the xQuest algorithm (O...
Definition: XQuestScores.h:50
MSSpectrum.h
int
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127