35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHSCORING_H
47 #include <boost/shared_ptr.hpp>
48 #include <boost/make_shared.hpp>
72 use_coelution_score_(true),
73 use_shape_score_(true),
75 use_library_score_(true),
76 use_elution_model_score_(true),
77 use_intensity_score_(true),
78 use_total_xic_score_(true),
79 use_nr_peaks_score_(true),
138 elution_model_fit_score(0),
140 library_norm_manhattan(0),
141 library_rootmeansquare(0),
144 isotope_correlation(0),
147 xcorr_coelution_score(0),
148 xcorr_shape_score(0),
152 weighted_coelution_score(0),
153 weighted_xcorr_shape(0),
154 weighted_massdev_score(0),
155 xcorr_ms1_coelution_score(0),
156 xcorr_ms1_shape_score(0),
158 ms1_isotope_correlation(0),
159 ms1_isotope_overlap(0),
160 library_manhattan(0),
166 dotprod_score_dia(0),
172 double get_quick_lda_score(
double library_corr_,
double library_norm_manhattan_,
double norm_rt_score_,
double xcorr_coelution_score_,
173 double xcorr_shape_score_,
double log_sn_score_)
187 double lda_quick_score =
188 library_corr_ * -0.5319046 +
189 library_norm_manhattan_ * 2.1643962 +
190 norm_rt_score_ * 8.0353047 +
191 xcorr_coelution_score_ * 0.1458914 +
192 xcorr_shape_score_ * -1.6901925 +
193 log_sn_score_ * -0.8002824;
194 return lda_quick_score;
429 void initialize(
double rt_normalization_factor,
430 int add_up_spectra,
double spacing_for_spectra_resampling,
450 void calculateChromatographicScores(
452 const std::vector<std::string>& native_ids,
453 const std::vector<double>& normalized_library_intensity,
454 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
472 void calculateLibraryScores(
474 const std::vector<TransitionType> & transitions,
475 const PeptideType& pep,
476 const double normalized_feature_rt,
493 const std::vector<TransitionType> & transitions,
497 const PeptideType& pep,
508 void getNormalized_library_intensities_(
const std::vector<TransitionType> & transitions,
509 std::vector<double>& normalized_library_intensity);
523 double RT,
int nr_spectra_to_add);
double dotprod_score_dia
Definition: OpenSwathScoring.h:134
double isotope_overlap
Definition: OpenSwathScoring.h:105
double xcorr_ms1_coelution_score
Definition: OpenSwathScoring.h:117
double isotope_correlation
Definition: OpenSwathScoring.h:104
OpenSwath::LightPeptide PeptideType
Definition: OpenSwathScoring.h:403
bool use_dia_scores_
Definition: OpenSwathScoring.h:69
bool use_nr_peaks_score_
Definition: OpenSwathScoring.h:67
double weighted_coelution_score
Definition: OpenSwathScoring.h:113
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:90
double rt_normalization_factor_
Definition: OpenSwathScoring.h:406
double spacing_for_spectra_resampling_
Definition: OpenSwathScoring.h:408
bool use_elution_model_score_
Definition: OpenSwathScoring.h:64
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:401
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:172
OpenSwath_Scores_Usage()
Definition: OpenSwathScoring.h:71
double sn_ratio
Definition: OpenSwathScoring.h:128
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:232
double weighted_xcorr_shape
Definition: OpenSwathScoring.h:114
bool use_ms1_fullscan
Definition: OpenSwathScoring.h:85
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
int add_up_spectra_
Definition: OpenSwathScoring.h:407
double total_xic
Definition: OpenSwathScoring.h:126
double xcorr_ms1_shape_score
Definition: OpenSwathScoring.h:118
bool use_library_score_
Definition: OpenSwathScoring.h:63
double raw_rt_score
Definition: OpenSwathScoring.h:132
OpenSwath_Scores()
Definition: OpenSwathScoring.h:137
double library_manhattan
Definition: OpenSwathScoring.h:123
double library_sangle
Definition: OpenSwathScoring.h:102
Definition: TransitionExperiment.h:155
double normalized_experimental_rt
Definition: OpenSwathScoring.h:131
double ms1_isotope_correlation
Definition: OpenSwathScoring.h:120
double ms1_ppm_score
Definition: OpenSwathScoring.h:119
bool use_sn_score_
Definition: OpenSwathScoring.h:68
double log_sn_score
Definition: OpenSwathScoring.h:111
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double massdev_score
Definition: OpenSwathScoring.h:106
double yseries_score
Definition: OpenSwathScoring.h:109
double manhatt_score_dia
Definition: OpenSwathScoring.h:135
double ms1_isotope_overlap
Definition: OpenSwathScoring.h:121
double xcorr_coelution_score
Definition: OpenSwathScoring.h:107
Definition: TransitionExperiment.h:47
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:57
Definition: ITransition.h:56
OpenSwath::LightTransition TransitionType
Definition: OpenSwathScoring.h:404
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScoring.h:96
double library_norm_manhattan
Definition: OpenSwathScoring.h:100
OpenSwath_Scores_Usage su_
Definition: OpenSwathScoring.h:409
double xcorr_shape_score
Definition: OpenSwathScoring.h:108
double calculate_swath_lda_prescore(OpenSwath_Scores scores)
Definition: OpenSwathScoring.h:225
bool use_ms1_correlation
Definition: OpenSwathScoring.h:84
double norm_rt_score
Definition: OpenSwathScoring.h:103
double rt_difference
Definition: OpenSwathScoring.h:130
double library_rootmeansquare
Definition: OpenSwathScoring.h:101
double elution_model_fit_score
Definition: OpenSwathScoring.h:98
double weighted_massdev_score
Definition: OpenSwathScoring.h:115
double intensity
Definition: OpenSwathScoring.h:125
bool use_rt_score_
Definition: OpenSwathScoring.h:62
double bseries_score
Definition: OpenSwathScoring.h:110
double library_dotprod
Definition: OpenSwathScoring.h:124
double library_corr
Definition: OpenSwathScoring.h:99
double nr_peaks
Definition: OpenSwathScoring.h:127
bool use_intensity_score_
Definition: OpenSwathScoring.h:65
bool use_coelution_score_
Definition: OpenSwathScoring.h:60
bool use_total_xic_score_
Definition: OpenSwathScoring.h:66
double calculate_lda_prescore(OpenSwath_Scores scores)
Definition: OpenSwathScoring.h:197
bool use_shape_score_
Definition: OpenSwathScoring.h:61