| addModificationsSequences_(std::vector< OpenMS::AASequence > sequences, std::vector< std::vector< size_t > > mods_combs, OpenMS::String modification) | MRMAssay | protected |
| CMD enum value | ProgressLogger | |
| combineDecoyModifications_(OpenMS::AASequence sequence, OpenMS::AASequence decoy_sequence) | MRMAssay | protected |
| combineModifications_(OpenMS::AASequence sequence) | MRMAssay | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) | MRMAssay | |
| endProgress() const | ProgressLogger | |
| generateDecoyAssays_(OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow, PeptideMapT &DecoyPeptideMap, TargetDecoyMapT &TargetDecoyMap, IonMapT DecoyIonMap, IonMapT TargetIonMap) | MRMAssay | protected |
| generateDecoyInSilicoMap_(OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, std::vector< std::pair< double, double > > swathes, int round_decPow, TargetDecoyMapT &TargetDecoyMap, PeptideMapT &TargetPeptideMap, boost::unordered_map< String, String > &DecoySequenceMap, IonMapT &DecoyIonMap, PeptideMapT &DecoyPeptideMap) | MRMAssay | protected |
| generateDecoySequences_(boost::unordered_map< size_t, boost::unordered_map< String, std::set< std::string > > > &TargetSequenceMap, boost::unordered_map< String, String > &DecoySequenceMap, int shuffle_seed) | MRMAssay | protected |
| generateTargetAssays_(OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow, PeptideMapT &TargetPeptideMap, IonMapT &TargetIonMap) | MRMAssay | protected |
| generateTargetInSilicoMap_(OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, std::vector< std::pair< double, double > > swathes, int round_decPow, size_t max_num_alternative_localizations, SequenceMapT &TargetSequenceMap, IonMapT &TargetIonMap, PeptideMapT &TargetPeptideMap) | MRMAssay | protected |
| getLogType() const | ProgressLogger | |
| getMatchingPeptidoforms_(const double fragment_ion, const std::vector< std::pair< double, std::string > > &ions, const double mz_threshold) | MRMAssay | protected |
| getRandomSequence_(size_t sequence_size, boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > pseudoRNG) | MRMAssay | protected |
| getSwath_(const std::vector< std::pair< double, double > > swathes, const double precursor_mz) | MRMAssay | protected |
| GUI enum value | ProgressLogger | |
| IonMapT typedef | MRMAssay | |
| isInSwath_(const std::vector< std::pair< double, double > > swathes, const double precursor_mz, const double product_mz) | 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 | |
| PeptideMapT typedef | MRMAssay | |
| PeptideVectorType typedef | MRMAssay | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProteinVectorType typedef | MRMAssay | |
| reannotateTransitions(OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_reannotation, bool enable_specific_losses, bool enable_unspecific_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 | |
| SequenceMap_T typedef | MRMAssay | |
| SequenceMapT typedef | MRMAssay | |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| TargetDecoyMapT typedef | MRMAssay | |
| TransitionVectorType typedef | MRMAssay | |
| type_ | ProgressLogger | mutableprotected |
| uisTransitions(OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=-1) | MRMAssay | |
| ~MRMAssay() | MRMAssay | |
| ~ProgressLogger() | ProgressLogger | |