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OpenMS
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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) const | TargetedSpectraExtractor | |
| annotateSpectra(const std::vector< MSSpectrum > &spectra, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &annotated_spectra) const | TargetedSpectraExtractor | |
| annotateSpectra(const std::vector< MSSpectrum > &spectra, const FeatureMap &ms1_features, FeatureMap &ms2_features, std::vector< MSSpectrum > &annotated_spectra) const | TargetedSpectraExtractor | |
| check_defaults_ | DefaultParamHandler | protected |
| constructTransitionsList(const OpenMS::FeatureMap &ms1_features, const OpenMS::FeatureMap &ms2_features, TargetedExperiment &t_exp) const | TargetedSpectraExtractor | |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| deisotopeMS2Spectra_(MSExperiment &experiment) const | TargetedSpectraExtractor | protected |
| deisotoping_annotate_charge_ | TargetedSpectraExtractor | private |
| deisotoping_fragment_tolerance_ | TargetedSpectraExtractor | private |
| deisotoping_fragment_unit_ | TargetedSpectraExtractor | private |
| deisotoping_keep_only_deisotoped_ | TargetedSpectraExtractor | private |
| deisotoping_max_charge_ | TargetedSpectraExtractor | private |
| deisotoping_max_isopeaks_ | TargetedSpectraExtractor | private |
| deisotoping_min_charge_ | TargetedSpectraExtractor | private |
| deisotoping_min_isopeaks_ | TargetedSpectraExtractor | private |
| deisotoping_use_deisotoper_ | TargetedSpectraExtractor | private |
| error_name_ | DefaultParamHandler | protected |
| extractSpectra(const MSExperiment &experiment, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features, bool compute_features=true) const | TargetedSpectraExtractor | |
| extractSpectra(const MSExperiment &experiment, const TargetedExperiment &targeted_exp, std::vector< MSSpectrum > &extracted_spectra) const | TargetedSpectraExtractor | |
| extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra) const | TargetedSpectraExtractor | |
| extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features) const | TargetedSpectraExtractor | |
| extractSpectra(const MSExperiment &experiment, const FeatureMap &ms1_features, std::vector< MSSpectrum > &extracted_spectra, FeatureMap &extracted_features, const bool compute_features) const | TargetedSpectraExtractor | private |
| fwhm_threshold_ | TargetedSpectraExtractor | private |
| fwhm_weight_ | TargetedSpectraExtractor | private |
| getDefaultParameters(Param ¶ms) const | TargetedSpectraExtractor | |
| getDefaults() const | DefaultParamHandler | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| matchSpectrum(const MSSpectrum &input_spectrum, const Comparator &cmp, std::vector< Match > &matches) const | TargetedSpectraExtractor | |
| max_fragment_mz_ | TargetedSpectraExtractor | private |
| max_precursor_mass_threashold_ | TargetedSpectraExtractor | private |
| mergeFeatures(const OpenMS::FeatureMap &fmap_input, OpenMS::FeatureMap &fmap_output) const | TargetedSpectraExtractor | |
| min_fragment_mz_ | TargetedSpectraExtractor | private |
| min_match_score_ | TargetedSpectraExtractor | private |
| min_select_score_ | TargetedSpectraExtractor | private |
| mz_tolerance_ | TargetedSpectraExtractor | private |
| mz_unit_is_Da_ | TargetedSpectraExtractor | private |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| organizeMapWithSameIdentifier(const OpenMS::FeatureMap &fmap_input, std::map< OpenMS::String, std::vector< OpenMS::Feature >> &fmapmap) const | TargetedSpectraExtractor | protected |
| param_ | DefaultParamHandler | protected |
| peak_height_max_ | TargetedSpectraExtractor | private |
| peak_height_min_ | TargetedSpectraExtractor | private |
| pickSpectrum(const MSSpectrum &spectrum, MSSpectrum &picked_spectrum) const | TargetedSpectraExtractor | |
| relative_allowable_product_mass_ | TargetedSpectraExtractor | private |
| removeMS2SpectraPeaks_(MSExperiment &experiment) const | TargetedSpectraExtractor | protected |
| rt_window_ | TargetedSpectraExtractor | private |
| scoreSpectra(const std::vector< MSSpectrum > &annotated_spectra, const std::vector< MSSpectrum > &picked_spectra, FeatureMap &features, std::vector< MSSpectrum > &scored_spectra, bool compute_features=true) const | TargetedSpectraExtractor | |
| scoreSpectra(const std::vector< MSSpectrum > &annotated_spectra, const std::vector< MSSpectrum > &picked_spectra, std::vector< MSSpectrum > &scored_spectra) const | TargetedSpectraExtractor | |
| searchSpectrum(OpenMS::FeatureMap &feat_map, OpenMS::FeatureMap &feat_map_output, bool add_unidentified_features=false) const | TargetedSpectraExtractor | |
| selectSpectra(const std::vector< MSSpectrum > &scored_spectra, const FeatureMap &features, std::vector< MSSpectrum > &selected_spectra, FeatureMap &selected_features, bool compute_features=true) const | TargetedSpectraExtractor | |
| selectSpectra(const std::vector< MSSpectrum > &scored_spectra, std::vector< MSSpectrum > &selected_spectra) const | TargetedSpectraExtractor | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| snr_weight_ | TargetedSpectraExtractor | private |
| storeSpectraMSP(const String &filename, MSExperiment &experiment) const | TargetedSpectraExtractor | |
| subsections_ | DefaultParamHandler | protected |
| targetedMatching(const std::vector< MSSpectrum > &spectra, const Comparator &cmp, FeatureMap &features) | TargetedSpectraExtractor | |
| TargetedSpectraExtractor() | TargetedSpectraExtractor | |
| tic_weight_ | TargetedSpectraExtractor | private |
| top_matches_to_report_ | TargetedSpectraExtractor | private |
| untargetedMatching(const std::vector< MSSpectrum > &spectra, const Comparator &cmp, FeatureMap &features) | TargetedSpectraExtractor | |
| updateMembers_() override | TargetedSpectraExtractor | protectedvirtual |
| use_gauss_ | TargetedSpectraExtractor | private |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~TargetedSpectraExtractor() override=default | TargetedSpectraExtractor |
1.9.1 
