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OpenMS
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This is the complete list of members for Biosaur2Algorithm, including all inherited members.
| applyRtFiltering_(const std::vector< PatternCandidate > &candidates, const std::vector< Hill > &hills, const std::map< Size, Size > &hill_idx_to_index) const | Biosaur2Algorithm | private |
| Biosaur2Algorithm() | Biosaur2Algorithm | |
| buildFastMzLookup_(const std::vector< Hill > &hills, bool use_im, std::map< int, std::vector< FastHillEntry >> &hills_mz_fast, std::vector< int > &hill_im_bins) const | Biosaur2Algorithm | private |
| calculateMedian_(const std::vector< double > &values) const | Biosaur2Algorithm | private |
| calculatePPM_(double mz1, double mz2) const | Biosaur2Algorithm | private |
| calibrateMass_(const std::vector< double > &mass_errors, double bin_width=0.05) const | Biosaur2Algorithm | private |
| centroidPASEFData_(MSExperiment &exp, double mz_step, double pasef_tolerance) const | Biosaur2Algorithm | private |
| centroidProfileSpectra_(MSExperiment &exp) const | Biosaur2Algorithm | private |
| check_defaults_ | DefaultParamHandler | protected |
| checkingCosCorrelationForCarbon_(const std::vector< double > &theor_full, const std::vector< double > &exp_full, double thresh) const | Biosaur2Algorithm | private |
| checkIsotopeValleySplit_(const std::vector< IsotopeCandidate > &isotopes, const std::vector< Hill > &hills, double ivf) const | Biosaur2Algorithm | private |
| cmax_ | Biosaur2Algorithm | private |
| cmin_ | Biosaur2Algorithm | private |
| computeAveragine_(double neutral_mass, double apex_intensity) const | Biosaur2Algorithm | private |
| computeHillMzStep_(const MSExperiment &exp, double htol_ppm, double min_intensity, double min_mz, double max_mz) const | Biosaur2Algorithm | private |
| convertToFeatureMap_(const std::vector< PeptideFeature > &features, const std::vector< Hill > &hills) const | Biosaur2Algorithm | private |
| convex_hull_mode_ | Biosaur2Algorithm | private |
| cosineCorrelation1D_(const std::vector< double > &v1, const std::vector< double > &v2) const | Biosaur2Algorithm | private |
| cosineCorrelation_(const std::vector< double > &intensities1, const std::vector< Size > &scans1, const std::vector< double > &intensities2, const std::vector< Size > &scans2) const | Biosaur2Algorithm | private |
| debugCheckIsotopeConsistency_(const char *stage_label, double mono_mz_center, double mono_rt_apex, Size mono_hill_idx, int charge, double itol_ppm, const Hill &iso_hill, Size isotope_number) const | Biosaur2Algorithm | private |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| detectHills_(const MSExperiment &exp, double htol_ppm, double min_intensity, double min_mz, double max_mz, bool use_im, std::vector< double > *hill_mass_diffs=nullptr) const | Biosaur2Algorithm | private |
| detectIsotopePatterns_(std::vector< Hill > &hills, double itol_ppm, int min_charge, int max_charge, bool negative_mode, double ivf, int iuse, bool enable_isotope_calib, bool use_im) const | Biosaur2Algorithm | private |
| error_name_ | DefaultParamHandler | protected |
| faims_merge_features_ | Biosaur2Algorithm | private |
| filterByCalibration_(const std::vector< PatternCandidate > &candidates, const std::vector< Hill > &hills, const std::map< Size, Size > &hill_idx_to_index, const std::map< int, std::pair< double, double >> &isotope_calib_map_ready, bool enable_isotope_calib) const | Biosaur2Algorithm | private |
| generateIsotopeCandidates_(const std::vector< Hill > &hills, double itol_ppm, int min_charge, int max_charge, double ivf, double mz_step, const std::map< int, std::vector< FastHillEntry >> &hills_mz_fast, const std::map< Size, Size > &hill_idx_to_index, const std::vector< int > &hill_im_bins, bool use_im) const | Biosaur2Algorithm | private |
| getDefaults() const | DefaultParamHandler | |
| getMSData() | Biosaur2Algorithm | |
| getMSData() const | Biosaur2Algorithm | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| hrttol_ | Biosaur2Algorithm | private |
| htol_ | Biosaur2Algorithm | private |
| hvf_ | Biosaur2Algorithm | private |
| ignore_iso_calib_ | Biosaur2Algorithm | private |
| itol_ | Biosaur2Algorithm | private |
| iuse_ | Biosaur2Algorithm | private |
| ivf_ | Biosaur2Algorithm | private |
| linkScanToHills_(const MSSpectrum &spectrum, Size scan_idx, double htol_ppm, double min_intensity, double min_mz, double max_mz, double mz_step, bool use_im_global, std::vector< Hill > &hills, Size &hill_idx_counter, std::vector< Size > &prev_peak_to_hill, const MSSpectrum *&prev_spectrum_ptr, std::map< int, std::vector< int >> &prev_fast_dict, std::vector< int > &prev_im_bins, std::vector< double > *hill_mass_diffs) const | Biosaur2Algorithm | private |
| maxmz_ | Biosaur2Algorithm | private |
| meanFilter_(const std::vector< double > &data, Size window) const | Biosaur2Algorithm | private |
| mini_ | Biosaur2Algorithm | private |
| minlh_ | Biosaur2Algorithm | private |
| minmz_ | Biosaur2Algorithm | private |
| ms_data_ | Biosaur2Algorithm | private |
| negative_mode_ | Biosaur2Algorithm | private |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| pasefmini_ | Biosaur2Algorithm | private |
| pasefminlh_ | Biosaur2Algorithm | private |
| paseftol_ | Biosaur2Algorithm | private |
| performInitialIsotopeCalibration_(const std::vector< Hill > &hills, double itol_ppm, int min_charge, int max_charge, bool enable_isotope_calib) const | Biosaur2Algorithm | private |
| processFAIMSGroup_(double faims_cv, MSExperiment &group_exp, double original_paseftol, std::vector< Hill > &hills_out, std::vector< PeptideFeature > &features_out) | Biosaur2Algorithm | private |
| processHills_(const std::vector< Hill > &hills, Size min_length) const | Biosaur2Algorithm | private |
| processTOF_(MSExperiment &exp) const | Biosaur2Algorithm | private |
| profile_mode_ | Biosaur2Algorithm | private |
| refineIsotopeCalibration_(const std::vector< PatternCandidate > &candidates, double itol_ppm, bool enable_isotope_calib) const | Biosaur2Algorithm | private |
| run(FeatureMap &feature_map) | Biosaur2Algorithm | |
| run(FeatureMap &feature_map, std::vector< Hill > &hills, std::vector< PeptideFeature > &peptide_features) | Biosaur2Algorithm | |
| selectNonOverlappingPatterns_(const std::vector< PatternCandidate > &filtered_ready, const std::vector< Hill > &hills, bool negative_mode, int iuse, double itol_ppm) const | Biosaur2Algorithm | private |
| setMSData(const MSExperiment &ms_data) | Biosaur2Algorithm | |
| setMSData(MSExperiment &&ms_data) | Biosaur2Algorithm | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| shouldThrowForMissingIM_(const MSSpectrum &spectrum) const | Biosaur2Algorithm | private |
| splitHills_(const std::vector< Hill > &hills, double hvf, Size min_length) const | Biosaur2Algorithm | private |
| subsections_ | DefaultParamHandler | protected |
| tof_mode_ | Biosaur2Algorithm | private |
| updateMembers_() override | Biosaur2Algorithm | protectedvirtual |
| use_hill_calib_ | Biosaur2Algorithm | private |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeHills(const std::vector< Hill > &hills, const String &filename) const | Biosaur2Algorithm | |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| writeTSV(const std::vector< PeptideFeature > &features, const String &filename) const | Biosaur2Algorithm | |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
1.9.1 
