 |
OpenMS
|
This is the complete list of members for PeptDeepRescoring, including all inherited members.
| annotate(const PeakMap &spectra, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) | PeptDeepRescoring | |
| annotateRun_(const std::string &run_id, const std::map< std::string, double > &collision_energies, PeptideIdentificationList &peptide_ids, const PSMRows &psms, const std::vector< Size > &run_rows, bool higher_better, PeptDeepMS2Inference &ms2_inference, PeptDeepRTInference &rt_inference) | PeptDeepRescoring | protected |
| batch_size_ | PeptDeepRescoring | protected |
| calibration_quantile_ | PeptDeepRescoring | protected |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| collisionEnergies_(const PeakMap &spectra) | PeptDeepRescoring | protectedstatic |
| confidentRows_(const std::vector< Row > &rows, const std::vector< Size > &run_rows, bool higher_better) const | PeptDeepRescoring | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| DefaultParamHandler(const std::string &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| error_name_ | DefaultParamHandler | protected |
| featureNames() | PeptDeepRescoring | static |
| gatherPSMs_(const PeptideIdentificationList &peptide_ids) | PeptDeepRescoring | protectedstatic |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getNumPredictedPSMs() const | PeptDeepRescoring | |
| getNumPSMs() const | PeptDeepRescoring | |
| getParameters() const | DefaultParamHandler | |
| getRTCalibrationError() const | PeptDeepRescoring | |
| getSubsections() const | DefaultParamHandler | |
| getUsedNCE() const | PeptDeepRescoring | |
| GUI enum value | ProgressLogger | |
| instrument_ | PeptDeepRescoring | protected |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| ms2_min_ordinal_ | PeptDeepRescoring | protected |
| ms2_model_ | PeptDeepRescoring | protected |
| ms2_strong_fraction_ | PeptDeepRescoring | protected |
| nce_ | PeptDeepRescoring | protected |
| nce_fallback_ | PeptDeepRescoring | protected |
| nce_grid_halfwidth_ | PeptDeepRescoring | protected |
| nce_grid_step_ | PeptDeepRescoring | protected |
| NCE_META_VALUE | PeptDeepRescoring | static |
| nce_sample_size_ | PeptDeepRescoring | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| num_predicted_psms_ | PeptDeepRescoring | protected |
| num_psms_ | PeptDeepRescoring | protected |
| OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| PeptDeepRescoring() | PeptDeepRescoring | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| rt_calibration_error_ | PeptDeepRescoring | protected |
| rt_model_ | PeptDeepRescoring | protected |
| rt_model_type_ | PeptDeepRescoring | protected |
| rt_num_nodes_ | PeptDeepRescoring | protected |
| selectNCE(const PeakMap &spectra, std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids) | PeptDeepRescoring | |
| selectNCE(const PeakMap &spectra, std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids, PeptDeepMS2Inference &ms2_inference) | PeptDeepRescoring | |
| selectNCE_(const PeakMap &spectra, std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids, PeptDeepMS2Inference &ms2_inference) | PeptDeepRescoring | protected |
| selectRunNCE_(const std::map< std::string, double > &collision_energies, const PeptideIdentificationList &peptide_ids, const PSMRows &psms, const std::vector< Size > &run_rows, const std::vector< Size > &confident, PeptDeepMS2Inference &ms2_inference, double ¢re, double &median_cosine) | PeptDeepRescoring | protected |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const std::string &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startCall_(const PeptideIdentificationList &peptide_ids, const StringList &models, const std::string &what) | PeptDeepRescoring | protected |
| startProgress(SignedSize begin, SignedSize end, const std::string &label) const | ProgressLogger | |
| storeNCE_(std::vector< ProteinIdentification > &protein_ids, const std::map< std::string, double > &nce_by_run) | PeptDeepRescoring | protectedstatic |
| subsections_ | DefaultParamHandler | protected |
| threads_ | PeptDeepRescoring | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | PeptDeepRescoring | protectedvirtual |
| used_nce_ | PeptDeepRescoring | protected |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~PeptDeepRescoring() override | PeptDeepRescoring | |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.8 