A structure to hold the different scores computed by OpenSWATH. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>

Public Member Functions
	OpenSwath_Scores ()

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_) const

double	calculate_lda_prescore (OpenSwath_Scores scores) const

double	calculate_lda_single_transition (OpenSwath_Scores scores) const

double	calculate_swath_lda_prescore (OpenSwath_Scores scores) const

Public Attributes
double	elution_model_fit_score

double	library_corr

double	library_norm_manhattan

double	library_rootmeansquare

double	library_sangle

double	norm_rt_score

double	isotope_correlation

std::string	ind_isotope_correlation

double	isotope_overlap

std::string	ind_isotope_overlap

double	massdev_score

std::string	ind_massdev_score

double	xcorr_coelution_score

std::string	ind_xcorr_coelution_score

double	xcorr_shape_score

std::string	ind_xcorr_shape_score

double	yseries_score

double	bseries_score

double	log_sn_score

std::string	ind_log_sn_score

int	ind_num_transitions

std::string	ind_transition_names

std::string	ind_area_intensity

std::string	ind_total_area_intensity

std::string	ind_intensity_score

std::string	ind_apex_intensity

std::string	ind_total_mi

std::string	ind_log_intensity

std::string	ind_intensity_ratio

std::string	ind_mi_ratio

double	weighted_coelution_score

double	weighted_xcorr_shape

double	weighted_massdev_score

double	xcorr_ms1_coelution_score

double	xcorr_ms1_shape_score

double	ms1_ppm_score

double	ms1_isotope_correlation

double	ms1_isotope_overlap

double	ms1_mi_score

double	sonar_sn

double	sonar_diff

double	sonar_trend

double	sonar_rsq

double	sonar_shape

double	sonar_lag

double	library_manhattan

double	library_dotprod

double	intensity

double	total_xic

double	nr_peaks

double	sn_ratio

double	mi_score

std::string	ind_mi_score

double	weighted_mi_score

double	rt_difference

double	normalized_experimental_rt

double	raw_rt_score

double	dotprod_score_dia

double	manhatt_score_dia

Detailed Description

A structure to hold the different scores computed by OpenSWATH.

This struct is used to store the individual OpenSWATH (sub-)scores. It also allows to compute some preliminary quality score for a feature by using a predefined combination of the individual scores determined using LDA.

Constructor & Destructor Documentation

◆ OpenSwath_Scores()

OpenSwath_Scores ( )

inline

Member Function Documentation

◆ calculate_lda_prescore()

double calculate_lda_prescore ( OpenSwath_Scores scores ) const

inline

References OpenSwath_Scores::elution_model_fit_score, OpenSwath_Scores::library_corr, OpenSwath_Scores::library_norm_manhattan, OpenSwath_Scores::log_sn_score, OpenSwath_Scores::norm_rt_score, OpenSwath_Scores::xcorr_coelution_score, and OpenSwath_Scores::xcorr_shape_score.

◆ calculate_lda_single_transition()

double calculate_lda_single_transition ( OpenSwath_Scores scores ) const

inline

References OpenSwath_Scores::elution_model_fit_score, OpenSwath_Scores::log_sn_score, and OpenSwath_Scores::norm_rt_score.

◆ calculate_swath_lda_prescore()

double calculate_swath_lda_prescore ( OpenSwath_Scores scores ) const

inline

References OpenSwath_Scores::isotope_correlation, OpenSwath_Scores::isotope_overlap, OpenSwath_Scores::library_corr, OpenSwath_Scores::library_norm_manhattan, OpenSwath_Scores::log_sn_score, OpenSwath_Scores::massdev_score, OpenSwath_Scores::norm_rt_score, OpenSwath_Scores::xcorr_coelution_score, OpenSwath_Scores::xcorr_shape_score, and OpenSwath_Scores::yseries_score.

◆ get_quick_lda_score()

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_
	)		const

inline

Member Data Documentation

◆ bseries_score

double bseries_score

◆ dotprod_score_dia

double dotprod_score_dia

◆ elution_model_fit_score

double elution_model_fit_score

Referenced by OpenSwath_Scores::calculate_lda_prescore(), and OpenSwath_Scores::calculate_lda_single_transition().

◆ ind_apex_intensity

std::string ind_apex_intensity

◆ ind_area_intensity

std::string ind_area_intensity

◆ ind_intensity_ratio

std::string ind_intensity_ratio

◆ ind_intensity_score

std::string ind_intensity_score

◆ ind_isotope_correlation

std::string ind_isotope_correlation

◆ ind_isotope_overlap

std::string ind_isotope_overlap

◆ ind_log_intensity

std::string ind_log_intensity

◆ ind_log_sn_score

std::string ind_log_sn_score

◆ ind_massdev_score

std::string ind_massdev_score

◆ ind_mi_ratio

std::string ind_mi_ratio

◆ ind_mi_score

std::string ind_mi_score

◆ ind_num_transitions

int ind_num_transitions

◆ ind_total_area_intensity

std::string ind_total_area_intensity

◆ ind_total_mi

std::string ind_total_mi

◆ ind_transition_names

std::string ind_transition_names

◆ ind_xcorr_coelution_score

std::string ind_xcorr_coelution_score

◆ ind_xcorr_shape_score

std::string ind_xcorr_shape_score

◆ intensity

double intensity

◆ isotope_correlation

double isotope_correlation

Referenced by OpenSwath_Scores::calculate_swath_lda_prescore().

◆ isotope_overlap

double isotope_overlap

Referenced by OpenSwath_Scores::calculate_swath_lda_prescore().

◆ library_corr

double library_corr

Referenced by OpenSwath_Scores::calculate_lda_prescore(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ library_dotprod

double library_dotprod

◆ library_manhattan

double library_manhattan

◆ library_norm_manhattan

double library_norm_manhattan

Referenced by OpenSwath_Scores::calculate_lda_prescore(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ library_rootmeansquare

double library_rootmeansquare

◆ library_sangle

double library_sangle

◆ log_sn_score

double log_sn_score

Referenced by OpenSwath_Scores::calculate_lda_prescore(), OpenSwath_Scores::calculate_lda_single_transition(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ manhatt_score_dia

double manhatt_score_dia

◆ massdev_score

double massdev_score

Referenced by OpenSwath_Scores::calculate_swath_lda_prescore().

◆ mi_score

double mi_score

◆ ms1_isotope_correlation

double ms1_isotope_correlation

◆ ms1_isotope_overlap

double ms1_isotope_overlap

◆ ms1_mi_score

double ms1_mi_score

◆ ms1_ppm_score

double ms1_ppm_score

◆ norm_rt_score

double norm_rt_score

Referenced by OpenSwath_Scores::calculate_lda_prescore(), OpenSwath_Scores::calculate_lda_single_transition(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ normalized_experimental_rt

double normalized_experimental_rt

◆ nr_peaks

double nr_peaks

◆ raw_rt_score

double raw_rt_score

◆ rt_difference

double rt_difference

◆ sn_ratio

double sn_ratio

◆ sonar_diff

double sonar_diff

◆ sonar_lag

double sonar_lag

◆ sonar_rsq

double sonar_rsq

◆ sonar_shape

double sonar_shape

◆ sonar_sn

double sonar_sn

◆ sonar_trend

double sonar_trend

◆ total_xic

double total_xic

◆ weighted_coelution_score

double weighted_coelution_score

◆ weighted_massdev_score

double weighted_massdev_score

◆ weighted_mi_score

double weighted_mi_score

◆ weighted_xcorr_shape

double weighted_xcorr_shape

◆ xcorr_coelution_score

double xcorr_coelution_score

Referenced by OpenSwath_Scores::calculate_lda_prescore(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ xcorr_ms1_coelution_score

double xcorr_ms1_coelution_score

◆ xcorr_ms1_shape_score

double xcorr_ms1_shape_score

◆ xcorr_shape_score

double xcorr_shape_score

Referenced by OpenSwath_Scores::calculate_lda_prescore(), and OpenSwath_Scores::calculate_swath_lda_prescore().

◆ yseries_score

double yseries_score

Referenced by OpenSwath_Scores::calculate_swath_lda_prescore().

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OpenSwath_Scores()

Member Function Documentation

◆ calculate_lda_prescore()

◆ calculate_lda_single_transition()

◆ calculate_swath_lda_prescore()

◆ get_quick_lda_score()

Member Data Documentation

◆ bseries_score

◆ dotprod_score_dia

◆ elution_model_fit_score

◆ ind_apex_intensity

◆ ind_area_intensity

◆ ind_intensity_ratio

◆ ind_intensity_score

◆ ind_isotope_correlation

◆ ind_isotope_overlap

◆ ind_log_intensity

◆ ind_log_sn_score

◆ ind_massdev_score

◆ ind_mi_ratio

◆ ind_mi_score

◆ ind_num_transitions

◆ ind_total_area_intensity

◆ ind_total_mi

◆ ind_transition_names

◆ ind_xcorr_coelution_score

◆ ind_xcorr_shape_score

◆ intensity

◆ isotope_correlation

◆ isotope_overlap

◆ library_corr

◆ library_dotprod

◆ library_manhattan

◆ library_norm_manhattan

◆ library_rootmeansquare

◆ library_sangle

◆ log_sn_score

◆ manhatt_score_dia

◆ massdev_score

◆ mi_score

◆ ms1_isotope_correlation

◆ ms1_isotope_overlap

◆ ms1_mi_score

◆ ms1_ppm_score

◆ norm_rt_score

◆ normalized_experimental_rt

◆ nr_peaks

◆ raw_rt_score

◆ rt_difference

◆ sn_ratio

◆ sonar_diff

◆ sonar_lag

◆ sonar_rsq

◆ sonar_shape

◆ sonar_sn

◆ sonar_trend

◆ total_xic

◆ weighted_coelution_score

◆ weighted_massdev_score

◆ weighted_mi_score

◆ weighted_xcorr_shape

◆ xcorr_coelution_score

◆ xcorr_ms1_coelution_score

◆ xcorr_ms1_shape_score

◆ xcorr_shape_score

◆ yseries_score