All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Modules Pages
TargetedSpectraExtractor Member List

This is the complete list of members for TargetedSpectraExtractor, including all inherited members.

annotateSpectra(const std::vector< MSSpectrum > &spectra, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &annotated_spectra, FeatureMap &features, bool compute_features=true) constTargetedSpectraExtractor
annotateSpectra(const std::vector< MSSpectrum > &spectra, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &annotated_spectra) constTargetedSpectraExtractor
annotateSpectra(const std::vector< MSSpectrum > &spectra, const FeatureMap &ms1_features, FeatureMap &ms2_features, std::vector< MSSpectrum > &annotated_spectra) constTargetedSpectraExtractor
check_defaults_DefaultParamHandlerprotected
constructTransitionsList(const OpenMS::FeatureMap &ms1_features, const OpenMS::FeatureMap &ms2_features, TargetedExperiment &t_exp) constTargetedSpectraExtractor
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
deisotopeMS2Spectra_(MSExperiment &experiment) constTargetedSpectraExtractorprotected
deisotoping_annotate_charge_TargetedSpectraExtractorprivate
deisotoping_fragment_tolerance_TargetedSpectraExtractorprivate
deisotoping_fragment_unit_TargetedSpectraExtractorprivate
deisotoping_keep_only_deisotoped_TargetedSpectraExtractorprivate
deisotoping_max_charge_TargetedSpectraExtractorprivate
deisotoping_max_isopeaks_TargetedSpectraExtractorprivate
deisotoping_min_charge_TargetedSpectraExtractorprivate
deisotoping_min_isopeaks_TargetedSpectraExtractorprivate
deisotoping_use_deisotoper_TargetedSpectraExtractorprivate
error_name_DefaultParamHandlerprotected
extractSpectra(const MSExperiment &experiment, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features, bool compute_features=true) constTargetedSpectraExtractor
extractSpectra(const MSExperiment &experiment, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &extracted_spectra) constTargetedSpectraExtractor
extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra) constTargetedSpectraExtractor
extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features) constTargetedSpectraExtractor
extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features, const bool compute_features) constTargetedSpectraExtractorprivate
fwhm_threshold_TargetedSpectraExtractorprivate
fwhm_weight_TargetedSpectraExtractorprivate
getDefaultParameters(Param &params) constTargetedSpectraExtractor
getDefaults() constDefaultParamHandler
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
matchSpectrum(const MSSpectrum &input_spectrum, const Comparator &cmp, std::vector< Match > &matches) constTargetedSpectraExtractor
max_fragment_mz_TargetedSpectraExtractorprivate
max_precursor_mass_threashold_TargetedSpectraExtractorprivate
mergeFeatures(const OpenMS::FeatureMap &fmap_input, OpenMS::FeatureMap &fmap_output) constTargetedSpectraExtractor
min_fragment_mz_TargetedSpectraExtractorprivate
min_match_score_TargetedSpectraExtractorprivate
min_select_score_TargetedSpectraExtractorprivate
mz_tolerance_TargetedSpectraExtractorprivate
mz_unit_is_Da_TargetedSpectraExtractorprivate
operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
organizeMapWithSameIdentifier(const OpenMS::FeatureMap &fmap_input, std::map< OpenMS::String, std::vector< OpenMS::Feature >> &fmapmap) constTargetedSpectraExtractorprotected
param_DefaultParamHandlerprotected
peak_height_max_TargetedSpectraExtractorprivate
peak_height_min_TargetedSpectraExtractorprivate
pickSpectrum(const MSSpectrum &spectrum, MSSpectrum &picked_spectrum) constTargetedSpectraExtractor
relative_allowable_product_mass_TargetedSpectraExtractorprivate
removeMS2SpectraPeaks_(MSExperiment &experiment) constTargetedSpectraExtractorprotected
rt_window_TargetedSpectraExtractorprivate
scoreSpectra(const std::vector< MSSpectrum > &annotated_spectra, const std::vector< MSSpectrum > &picked_spectra, FeatureMap &features, std::vector< MSSpectrum > &scored_spectra, bool compute_features=true) constTargetedSpectraExtractor
scoreSpectra(const std::vector< MSSpectrum > &annotated_spectra, const std::vector< MSSpectrum > &picked_spectra, std::vector< MSSpectrum > &scored_spectra) constTargetedSpectraExtractor
searchSpectrum(OpenMS::FeatureMap &feat_map, OpenMS::FeatureMap &feat_map_output, bool add_unidentified_features=false) constTargetedSpectraExtractor
selectSpectra(const std::vector< MSSpectrum > &scored_spectra, const FeatureMap &features, std::vector< MSSpectrum > &selected_spectra, FeatureMap &selected_features, bool compute_features=true) constTargetedSpectraExtractor
selectSpectra(const std::vector< MSSpectrum > &scored_spectra, std::vector< MSSpectrum > &selected_spectra) constTargetedSpectraExtractor
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
snr_weight_TargetedSpectraExtractorprivate
storeSpectraMSP(const String &filename, MSExperiment &experiment) constTargetedSpectraExtractor
subsections_DefaultParamHandlerprotected
targetedMatching(const std::vector< MSSpectrum > &spectra, const Comparator &cmp, FeatureMap &features)TargetedSpectraExtractor
TargetedSpectraExtractor()TargetedSpectraExtractor
tic_weight_TargetedSpectraExtractorprivate
top_matches_to_report_TargetedSpectraExtractorprivate
untargetedMatching(const std::vector< MSSpectrum > &spectra, const Comparator &cmp, FeatureMap &features)TargetedSpectraExtractor
updateMembers_() overrideTargetedSpectraExtractorprotectedvirtual
use_gauss_TargetedSpectraExtractorprivate
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~TargetedSpectraExtractor() override=defaultTargetedSpectraExtractor