OpenMS  2.8.0
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
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
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)DefaultParamHandlervirtual
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
organizeMapWithSameIdentifier(const OpenMS::FeatureMap &fmap_input, std::map< std::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) 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
storeSpectraTraML(const String &filename, const OpenMS::FeatureMap &ms1_features, const OpenMS::FeatureMap &ms2_features) 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
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