| addModification_(std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, ResidueModification &rmod, const String &name) | MRMAssay | protected |
| addModificationsSequences_(std::vector< OpenMS::AASequence > sequences, std::vector< std::vector< size_t > > mods_combs, OpenMS::String modification) | MRMAssay | protected |
| CMD enum value | ProgressLogger | |
| combineModifications_(OpenMS::AASequence sequence) | MRMAssay | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) | MRMAssay | |
| endProgress() const | ProgressLogger | |
| getLogType() const | ProgressLogger | |
| getSwath_(const std::vector< std::pair< double, double > > swathes, const double precursor_mz) | MRMAssay | protected |
| GUI enum value | ProgressLogger | |
| insilicoTransitions(OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4) | MRMAssay | |
| isInSwath_(const std::vector< std::pair< double, double > > swathes, const double precursor_mz, const double product_mz) | MRMAssay | protected |
| isSiteUIS_(const AASequence sequence, ReactionMonitoringTransition &tr) | MRMAssay | protected |
| isUIS_(const double fragment_ion, std::vector< double > ions, const double mz_threshold) | MRMAssay | protected |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| MRMAssay() | MRMAssay | |
| nchoosekcombinations_(std::vector< size_t > n, size_t k) | MRMAssay | protected |
| NONE enum value | ProgressLogger | |
| operator=(const ProgressLogger &other) | ProgressLogger | |
| PeptideVectorType typedef | MRMAssay | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProteinVectorType typedef | MRMAssay | |
| reannotateTransitions(OpenMS::TargetedExperiment &exp, double mz_threshold, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_alternative_localizations, bool enable_reannotation, bool enable_losses, int round_decPow=-4) | MRMAssay | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, std::vector< std::pair< double, double > > swathes) | MRMAssay | |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| TransitionVectorType typedef | MRMAssay | |
| type_ | ProgressLogger | mutableprotected |
| uisTransitions(OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, bool enable_uis_scoring, bool enable_site_scoring, double mz_threshold, std::vector< std::pair< double, double > > swathes) | MRMAssay | |
| ~MRMAssay() | MRMAssay | |
| ~ProgressLogger() | ProgressLogger | |