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OpenSwathScores.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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/OpenMSConfig.h>
38 #include <OpenMS/CONCEPT/Types.h>
39
40 #include <OpenMS/DATASTRUCTURES/String.h>
41 #include <vector>
42
43 namespace OpenMS
44 {
45
50 struct OPENMS_DLLAPI OpenSwath_Scores_Usage
51 {
52 bool use_coelution_score_ = true;
53 bool use_shape_score_ = true;
54 bool use_rt_score_ = true;
55 bool use_library_score_ = true;
56 bool use_elution_model_score_ = true;
57 bool use_intensity_score_ = true;
58 bool use_total_xic_score_ = true;
59 bool use_total_mi_score_ = true;
60 bool use_nr_peaks_score_ = true;
61 bool use_sn_score_ = true;
62 bool use_mi_score_ = true;
63 bool use_dia_scores_ = true;
64 bool use_sonar_scores = true;
65 bool use_im_scores = true;
66 bool use_ms1_correlation = true;
67 bool use_ms1_fullscan = true;
68 bool use_ms1_mi = true;
69 bool use_uis_scores = true;
70 };
71
80 struct OPENMS_DLLAPI OpenSwath_Scores
81 {
82 double elution_model_fit_score = 0;
83 double library_corr = 0;
84 double library_norm_manhattan = 0;
85 double library_rootmeansquare = 0;
86 double library_sangle = 0;
87 double norm_rt_score = 0;
88
89 double isotope_correlation = 0;
90 double isotope_overlap = 0;
91 double massdev_score = 0;
92 double xcorr_coelution_score = 0;
93 double xcorr_shape_score = 0;
94
95 double yseries_score = 0;
96 double bseries_score = 0;
97 double log_sn_score = 0;
98
99 double weighted_coelution_score = 0;
100 double weighted_xcorr_shape = 0;
101 double weighted_massdev_score = 0;
102
103 double ms1_xcorr_coelution_score = -1;
104 double ms1_xcorr_coelution_contrast_score = 0;
105 double ms1_xcorr_coelution_combined_score = 0;
106 double ms1_xcorr_shape_score = -1;
107 double ms1_xcorr_shape_contrast_score = 0;
108 double ms1_xcorr_shape_combined_score = 0;
109 double ms1_ppm_score = 0;
110 double ms1_isotope_correlation = 0;
111 double ms1_isotope_overlap = 0;
112 double ms1_mi_score = -1;
113 double ms1_mi_contrast_score = 0;
114 double ms1_mi_combined_score = 0;
115
116 double sonar_sn = 0;
117 double sonar_diff = 0;
118 double sonar_trend = 0;
119 double sonar_rsq = 0;
120 double sonar_shape = 0;
121 double sonar_lag = 0;
122
123 double im_xcorr_coelution_score = 0;
124 double im_xcorr_shape_score = 0;
125 double im_delta_score = 0;
126 double im_ms1_delta_score = 0;
127 double im_drift = 0;
128 double im_drift_weighted = 0;
129 double im_ms1_contrast_coelution = 0;
130 double im_ms1_contrast_shape = 0;
131 double im_ms1_sum_contrast_coelution = 0;
132 double im_ms1_sum_contrast_shape = 0;
133
134 double library_manhattan = 0;
135 double library_dotprod = 0;
136 double intensity = 0;
137 double total_xic = 0;
138 double nr_peaks = 0;
139 double sn_ratio = 0;
140 double mi_score = 0;
141 double weighted_mi_score = 0;
142
143 double rt_difference = 0;
144 double normalized_experimental_rt = 0;
145 double raw_rt_score = 0;
146
147 double dotprod_score_dia = 0;
148 double manhatt_score_dia = 0;
149
150 OpenSwath_Scores() = default;
151
152 double get_quick_lda_score(double library_corr_,
153 double library_norm_manhattan_,
154 double norm_rt_score_,
155 double xcorr_coelution_score_,
156 double xcorr_shape_score_,
157 double log_sn_score_) const;
158
169 double calculate_lda_prescore(const OpenSwath_Scores& scores) const;
170
179 double calculate_lda_single_transition(const OpenSwath_Scores& scores) const;
180
188 double calculate_swath_lda_prescore(const OpenSwath_Scores& scores) const;
189
190 };
191
192 struct OPENMS_DLLAPI OpenSwath_Ind_Scores
193 {
194 int ind_num_transitions = 0;
195 std::vector<OpenMS::String> ind_transition_names;
196 std::vector<double> ind_isotope_correlation;
197 std::vector<double> ind_isotope_overlap;
198 std::vector<double> ind_massdev_score;
199 std::vector<double> ind_xcorr_coelution_score;
200 std::vector<double> ind_xcorr_shape_score;
201 std::vector<double> ind_log_sn_score;
202 std::vector<double> ind_area_intensity;
203 std::vector<double> ind_total_area_intensity;
204 std::vector<double> ind_intensity_score;
205 std::vector<double> ind_apex_intensity;
206 std::vector<double> ind_total_mi;
207 std::vector<double> ind_log_intensity;
208 std::vector<double> ind_intensity_ratio;
209 std::vector<double> ind_mi_ratio;
210 std::vector<double> ind_mi_score;
211
212 OpenSwath_Ind_Scores() = default;
213
214 };
215
216 }
217
218
OpenMS::OpenSwath_Ind_Scores::ind_transition_names
std::vector< OpenMS::String > ind_transition_names
Definition: OpenSwathScores.h:195
OpenMS::OpenSwath_Ind_Scores::ind_intensity_score
std::vector< double > ind_intensity_score
Definition: OpenSwathScores.h:204
OpenMS::OpenSwath_Ind_Scores::ind_isotope_overlap
std::vector< double > ind_isotope_overlap
Definition: OpenSwathScores.h:197
OpenMS::OpenSwath_Ind_Scores::ind_log_intensity
std::vector< double > ind_log_intensity
Definition: OpenSwathScores.h:207
OpenMS::OpenSwath_Scores_Usage
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:50
OpenMS::OpenSwath_Ind_Scores::ind_log_sn_score
std::vector< double > ind_log_sn_score
Definition: OpenSwathScores.h:201
OpenMS::OpenSwath_Ind_Scores::ind_massdev_score
std::vector< double > ind_massdev_score
Definition: OpenSwathScores.h:198
Types.h
OpenMS::OpenSwath_Ind_Scores::ind_intensity_ratio
std::vector< double > ind_intensity_ratio
Definition: OpenSwathScores.h:208
OpenMS::OpenSwath_Ind_Scores::ind_mi_score
std::vector< double > ind_mi_score
Definition: OpenSwathScores.h:210
OpenMS::OpenSwath_Ind_Scores
Definition: OpenSwathScores.h:192
String.h
OpenMS::OpenSwath_Ind_Scores::ind_xcorr_shape_score
std::vector< double > ind_xcorr_shape_score
Definition: OpenSwathScores.h:200
OpenMS::OpenSwath_Ind_Scores::ind_total_area_intensity
std::vector< double > ind_total_area_intensity
Definition: OpenSwathScores.h:203
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenSwath_Ind_Scores::ind_area_intensity
std::vector< double > ind_area_intensity
Definition: OpenSwathScores.h:202
OpenMS::OpenSwath_Scores
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScores.h:80
OpenMS::OpenSwath_Ind_Scores::ind_xcorr_coelution_score
std::vector< double > ind_xcorr_coelution_score
Definition: OpenSwathScores.h:199
OpenMS::OpenSwath_Ind_Scores::ind_apex_intensity
std::vector< double > ind_apex_intensity
Definition: OpenSwathScores.h:205
OpenMS::OpenSwath_Ind_Scores::ind_isotope_correlation
std::vector< double > ind_isotope_correlation
Definition: OpenSwathScores.h:196
OpenMS::OpenSwath_Ind_Scores::ind_mi_ratio
std::vector< double > ind_mi_ratio
Definition: OpenSwathScores.h:209
OpenMS::OpenSwath_Ind_Scores::ind_total_mi
std::vector< double > ind_total_mi
Definition: OpenSwathScores.h:206