| OpenMS 2.5.0

DIAScoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest, Witold Wolski $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <boost/math/special_functions/fpclassify.hpp> // for isnan
38 #include <OpenMS/CHEMISTRY/AASequence.h>
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40
41 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
42 #include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
43 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
44 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
45
46 namespace OpenMS
47 {
48 class TheoreticalSpectrumGenerator;
49
83 class OPENMS_DLLAPI DIAScoring :
84 public DefaultParamHandler
85 {
87
88 typedef OpenSwath::SpectrumPtr SpectrumPtrType;
91 typedef OpenSwath::LightTransition TransitionType;
93
94 public:
95
97
98 DIAScoring();
100
102 ~DIAScoring() override;
104
106 // DIA / SWATH scoring
107
109
110 void dia_isotope_scores(const std::vector<TransitionType>& transitions,
112 SpectrumPtrType spectrum,
113 OpenSwath::IMRMFeature* mrmfeature,
114 double& isotope_corr,
115 double& isotope_overlap);
116
118 void dia_massdiff_score(const std::vector<TransitionType>& transitions,
119 SpectrumPtrType spectrum,
120 const std::vector<double>& normalized_library_intensity,
121 double& ppm_score,
122 double& ppm_score_weighted,
123 std::vector<double>& diff_ppm);
124
133 bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
134 double& ppm_score);
135
137 void dia_ms1_isotope_scores(double precursor_mz, SpectrumPtrType spectrum, size_t charge_state,
138 double& isotope_corr, double& isotope_overlap, const std::string& sum_formula = "");
139
141 void dia_by_ion_score(SpectrumPtrType spectrum, AASequence& sequence,
142 int charge, double& bseries_score, double& yseries_score);
143
145 void score_with_isotopes(SpectrumPtrType spectrum,
146 const std::vector<TransitionType>& transitions,
147 double& dotprod,
148 double& manhattan);
150
151 private:
152
154 DIAScoring(const DIAScoring& rhs);
155
157 DIAScoring& operator=(const DIAScoring& rhs);
158
160 void updateMembers_() override;
161
163 void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
164 SpectrumPtrType spectrum,
165 std::map<std::string, double>& intensities,
166 double& isotope_corr,
167 double& isotope_overlap);
168
171 void getFirstIsotopeRelativeIntensities_(const std::vector<TransitionType>& transitions,
172 OpenSwath::IMRMFeature* mrmfeature,
173 std::map<std::string, double>& intensities //experimental intensities of transitions
174 );
175
176 private:
177
193 void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio);
194
203 double scoreIsotopePattern_(double product_mz,
204 const std::vector<double>& isotopes_int,
205 int putative_fragment_charge,
206 const std::string& sum_formula = "");
207
208 // Parameters
209 double dia_extract_window_;
210 double dia_centroided_;
211 double dia_byseries_intensity_min_;
212 double dia_byseries_ppm_diff_;
213 double dia_nr_isotopes_;
214 double dia_nr_charges_;
215 double peak_before_mono_max_ppm_diff_;
216 bool dia_extraction_ppm_;
217
218 TheoreticalSpectrumGenerator * generator;
219 };
220 }
221
DataStructures.h
OpenMS::DIAScoring::peak_before_mono_max_ppm_diff_
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:215
OpenMS::DIAScoring::dia_extract_window_
double dia_extract_window_
Definition: DIAScoring.h:209
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenSwath::IMRMFeature
Definition: ITransition.h:56
AASequence.h
OpenMS::DIAScoring::SpectrumPtrType
OpenSwath::SpectrumPtr SpectrumPtrType
Type definitions.
Definition: DIAScoring.h:89
OpenMS::DIAScoring::dia_nr_isotopes_
double dia_nr_isotopes_
Definition: DIAScoring.h:213
OpenMS::DIAScoring
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:83
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DIAScoring::dia_byseries_ppm_diff_
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:212
DefaultParamHandler.h
OpenMS::DIAScoring::TransitionType
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:91
OpenMS::DIAScoring::dia_byseries_intensity_min_
double dia_byseries_intensity_min_
Definition: DIAScoring.h:211
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
OpenMS::DIAScoring::dia_nr_charges_
double dia_nr_charges_
Definition: DIAScoring.h:214
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:67
OpenMS::DIAScoring::dia_extraction_ppm_
bool dia_extraction_ppm_
Definition: DIAScoring.h:216
OpenMS::DIAScoring::generator
TheoreticalSpectrumGenerator * generator
Definition: DIAScoring.h:218
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
TransitionExperiment.h
ISpectrumAccess.h
ITransition.h
OpenMS::DIAScoring::dia_centroided_
double dia_centroided_
Definition: DIAScoring.h:210