35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHSCORING_H 36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHSCORING_H 49 #include <boost/shared_ptr.hpp> 50 #include <boost/make_shared.hpp> 78 use_coelution_score_(true),
79 use_shape_score_(true),
81 use_library_score_(true),
82 use_elution_model_score_(true),
83 use_intensity_score_(true),
84 use_total_xic_score_(true),
85 use_nr_peaks_score_(true),
87 use_dia_scores_(true),
88 use_sonar_scores(true),
89 use_ms1_correlation(true),
90 use_ms1_fullscan(true),
164 elution_model_fit_score(0),
166 library_norm_manhattan(0),
167 library_rootmeansquare(0),
170 isotope_correlation(0),
171 ind_isotope_correlation(
""),
173 ind_isotope_overlap(
""),
175 ind_massdev_score(
""),
176 xcorr_coelution_score(0),
177 ind_xcorr_coelution_score(
""),
178 xcorr_shape_score(0),
179 ind_xcorr_shape_score(
""),
183 ind_log_sn_score(
""),
184 ind_num_transitions(0),
185 ind_transition_names(
""),
186 ind_log_intensity(
""),
187 weighted_coelution_score(0),
188 weighted_xcorr_shape(0),
189 weighted_massdev_score(0),
190 xcorr_ms1_coelution_score(0),
191 xcorr_ms1_shape_score(0),
193 ms1_isotope_correlation(0),
194 ms1_isotope_overlap(0),
201 library_manhattan(0),
207 dotprod_score_dia(0),
213 double get_quick_lda_score(
double library_corr_,
double library_norm_manhattan_,
double norm_rt_score_,
double xcorr_coelution_score_,
214 double xcorr_shape_score_,
double log_sn_score_)
228 double lda_quick_score =
229 library_corr_ * -0.5319046 +
230 library_norm_manhattan_ * 2.1643962 +
231 norm_rt_score_ * 8.0353047 +
232 xcorr_coelution_score_ * 0.1458914 +
233 xcorr_shape_score_ * -1.6901925 +
234 log_sn_score_ * -0.8002824;
235 return lda_quick_score;
470 void initialize(
double rt_normalization_factor,
471 int add_up_spectra,
double spacing_for_spectra_resampling,
491 void calculateChromatographicScores(
493 const std::vector<std::string>& native_ids,
494 const std::string& precursor_chrom_id,
495 const std::vector<double>& normalized_library_intensity,
496 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
517 void calculateChromatographicIdScores(
519 const std::vector<std::string>& native_ids_identification,
520 const std::vector<std::string>& native_ids_detection,
521 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
539 void calculateLibraryScores(
541 const std::vector<TransitionType> & transitions,
542 const CompoundType& compound,
543 const double normalized_feature_rt,
560 const std::vector<TransitionType> & transitions,
561 std::vector<OpenSwath::SwathMap> swath_maps,
564 const CompoundType& compound,
582 const CompoundType& compound,
597 const TransitionType & transition,
598 std::vector<OpenSwath::SwathMap> swath_maps,
610 void getNormalized_library_intensities_(
const std::vector<TransitionType> & transitions,
611 std::vector<double>& normalized_library_intensity);
625 double RT,
int nr_spectra_to_add);
640 double RT,
int nr_spectra_to_add);
double dotprod_score_dia
Definition: OpenSwathScoring.h:160
double isotope_overlap
Definition: OpenSwathScoring.h:114
double xcorr_ms1_coelution_score
Definition: OpenSwathScoring.h:136
double isotope_correlation
Definition: OpenSwathScoring.h:112
bool use_dia_scores_
Definition: OpenSwathScoring.h:71
std::string ind_apex_intensity
Definition: OpenSwathScoring.h:129
bool use_nr_peaks_score_
Definition: OpenSwathScoring.h:69
bool use_uis_scores
Definition: OpenSwathScoring.h:75
std::string ind_log_sn_score
Definition: OpenSwathScoring.h:125
double weighted_coelution_score
Definition: OpenSwathScoring.h:132
double sonar_lag
Definition: OpenSwathScoring.h:147
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:90
double sonar_trend
Definition: OpenSwathScoring.h:144
double rt_normalization_factor_
Definition: OpenSwathScoring.h:447
double spacing_for_spectra_resampling_
Definition: OpenSwathScoring.h:449
bool use_elution_model_score_
Definition: OpenSwathScoring.h:66
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:442
double get_quick_lda_score(double library_corr_, double library_norm_manhattan_, double norm_rt_score_, double xcorr_coelution_score_, double xcorr_shape_score_, double log_sn_score_)
Definition: OpenSwathScoring.h:213
OpenSwath_Scores_Usage()
Definition: OpenSwathScoring.h:77
double sn_ratio
Definition: OpenSwathScoring.h:154
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:244
double weighted_xcorr_shape
Definition: OpenSwathScoring.h:133
bool use_ms1_fullscan
Definition: OpenSwathScoring.h:74
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
int add_up_spectra_
Definition: OpenSwathScoring.h:448
std::string ind_log_intensity
Definition: OpenSwathScoring.h:130
double total_xic
Definition: OpenSwathScoring.h:152
std::string ind_area_intensity
Definition: OpenSwathScoring.h:128
double xcorr_ms1_shape_score
Definition: OpenSwathScoring.h:137
bool use_library_score_
Definition: OpenSwathScoring.h:65
double raw_rt_score
Definition: OpenSwathScoring.h:158
OpenSwath_Scores()
Definition: OpenSwathScoring.h:163
double library_manhattan
Definition: OpenSwathScoring.h:149
double library_sangle
Definition: OpenSwathScoring.h:110
double sonar_sn
Definition: OpenSwathScoring.h:142
double normalized_experimental_rt
Definition: OpenSwathScoring.h:157
std::string ind_isotope_correlation
Definition: OpenSwathScoring.h:113
double ms1_isotope_correlation
Definition: OpenSwathScoring.h:139
double ms1_ppm_score
Definition: OpenSwathScoring.h:138
std::string ind_xcorr_coelution_score
Definition: OpenSwathScoring.h:119
bool use_sn_score_
Definition: OpenSwathScoring.h:70
double log_sn_score
Definition: OpenSwathScoring.h:124
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double massdev_score
Definition: OpenSwathScoring.h:116
double yseries_score
Definition: OpenSwathScoring.h:122
std::string ind_massdev_score
Definition: OpenSwathScoring.h:117
double sonar_diff
Definition: OpenSwathScoring.h:143
Definition: TransitionExperiment.h:150
double manhatt_score_dia
Definition: OpenSwathScoring.h:161
double ms1_isotope_overlap
Definition: OpenSwathScoring.h:140
double xcorr_coelution_score
Definition: OpenSwathScoring.h:118
bool use_sonar_scores
Definition: OpenSwathScoring.h:72
Definition: TransitionExperiment.h:47
std::string ind_xcorr_shape_score
Definition: OpenSwathScoring.h:121
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:59
Definition: ITransition.h:56
std::string ind_isotope_overlap
Definition: OpenSwathScoring.h:115
OpenSwath::LightTransition TransitionType
Definition: OpenSwathScoring.h:445
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScoring.h:104
double library_norm_manhattan
Definition: OpenSwathScoring.h:108
double sonar_shape
Definition: OpenSwathScoring.h:146
OpenSwath_Scores_Usage su_
Definition: OpenSwathScoring.h:450
double xcorr_shape_score
Definition: OpenSwathScoring.h:120
double calculate_swath_lda_prescore(OpenSwath_Scores scores)
Definition: OpenSwathScoring.h:266
bool use_ms1_correlation
Definition: OpenSwathScoring.h:73
double norm_rt_score
Definition: OpenSwathScoring.h:111
OpenSwath::LightCompound CompoundType
Definition: OpenSwathScoring.h:444
double rt_difference
Definition: OpenSwathScoring.h:156
std::string ind_transition_names
Definition: OpenSwathScoring.h:127
double library_rootmeansquare
Definition: OpenSwathScoring.h:109
double elution_model_fit_score
Definition: OpenSwathScoring.h:106
double weighted_massdev_score
Definition: OpenSwathScoring.h:134
double intensity
Definition: OpenSwathScoring.h:151
double sonar_rsq
Definition: OpenSwathScoring.h:145
int ind_num_transitions
Definition: OpenSwathScoring.h:126
bool use_rt_score_
Definition: OpenSwathScoring.h:64
double bseries_score
Definition: OpenSwathScoring.h:123
double library_dotprod
Definition: OpenSwathScoring.h:150
double library_corr
Definition: OpenSwathScoring.h:107
double nr_peaks
Definition: OpenSwathScoring.h:153
bool use_intensity_score_
Definition: OpenSwathScoring.h:67
bool use_coelution_score_
Definition: OpenSwathScoring.h:62
bool use_total_xic_score_
Definition: OpenSwathScoring.h:68
double calculate_lda_prescore(OpenSwath_Scores scores)
Definition: OpenSwathScoring.h:238
bool use_shape_score_
Definition: OpenSwathScoring.h:63