| annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool mapMS1=false) | IDMapper | inline |
| annotate(PeakMap &map, FeatureMap fmap, const bool clear_ids=false, const bool mapMS1=false) | IDMapper | inline |
| annotate(FeatureMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false, const PeakMap &spectra=PeakMap()) | IDMapper | |
| annotate(ConsensusMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool measure_from_subelements=false, bool annotate_ids_with_subelements=false, const PeakMap &spectra=PeakMap()) | IDMapper | |
| check_defaults_ | DefaultParamHandler | protected |
| checkHits_(const std::vector< PeptideIdentification > &ids) const | IDMapper | protected |
| checkMassType_(const std::vector< DataProcessing > &processing) const | IDMapper | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| error_name_ | DefaultParamHandler | protected |
| getAbsoluteMZTolerance_(const double mz) const | IDMapper | protected |
| getDefaults() const | DefaultParamHandler | |
| getIDDetails_(const PeptideIdentification &id, double &rt_pep, DoubleList &mz_values, IntList &charges, bool use_avg_mass=false) const | IDMapper | protected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| IDMapper() | IDMapper | |
| IDMapper(const IDMapper &cp) | IDMapper | |
| ignore_charge_ | IDMapper | protected |
| increaseBoundingBox_(DBoundingBox< 2 > &box) | IDMapper | protected |
| isMatch_(const double rt_distance, const double mz_theoretical, const double mz_observed) const | IDMapper | protected |
| mapPrecursorsToIdentifications(const PeakMap &spectra, const std::vector< PeptideIdentification > &ids, double mz_tol=0.001, double rt_tol=0.001) | IDMapper | inlinestatic |
| Measure enum name | IDMapper | |
| measure_ | IDMapper | protected |
| MEASURE_DA enum value | IDMapper | |
| MEASURE_PPM enum value | IDMapper | |
| mz_tolerance_ | IDMapper | protected |
| operator=(const IDMapper &rhs) | IDMapper | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| rt_tolerance_ | IDMapper | protected |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| subsections_ | DefaultParamHandler | protected |
| updateMembers_() | IDMapper | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |