| AASequenceIdentity(const String &sequence, const String &decoy) | MRMDecoy | |
| begin_ | ProgressLogger | mutableprotected |
| CMD enum value | ProgressLogger | |
| correctMasses(OpenMS::TargetedExperiment &exp, double mz_threshold) | MRMDecoy | |
| dlg_ | ProgressLogger | mutableprotected |
| end_ | ProgressLogger | mutableprotected |
| endProgress() const | ProgressLogger | |
| find_all_tryptic(std::string sequence) | MRMDecoy | |
| generateDecoys(OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, String method, String decoy_tag, double identity_threshold, int max_attempts, double mz_threshold, bool theoretical, double mz_shift, bool exclude_similar, double similarity_threshold, bool remove_CNterm_mods, double precursor_mass_shift) | MRMDecoy | |
| getDecoyIon(String ionid, std::map< String, std::map< String, DoubleReal > > &decoy_ionseries) | MRMDecoy | |
| getIonSeries(AASequence sequence, int precursor_charge, int max_isotopes=2) | MRMDecoy | |
| getLogType() const | ProgressLogger | |
| getTargetIon(double ProductMZ, double mz_threshold, std::map< String, std::map< String, double > > target_ionseries) | MRMDecoy | |
| GUI enum value | ProgressLogger | |
| has_CNterminal_mods(const OpenMS::TargetedExperiment::Peptide &peptide) | MRMDecoy | |
| IonSeries typedef | MRMDecoy | |
| IonSeriesMapType typedef | MRMDecoy | |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| MRMDecoy() | MRMDecoy | inline |
| NONE enum value | ProgressLogger | |
| PeptideTransitionMapType typedef | MRMDecoy | |
| PeptideVectorType typedef | MRMDecoy | |
| ProgressLogger() | ProgressLogger | |
| ProteinVectorType typedef | MRMDecoy | |
| pseudoreversePeptide(OpenMS::TargetedExperiment::Peptide peptide) | MRMDecoy | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| restrictTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) | MRMDecoy | |
| reversePeptide(OpenMS::TargetedExperiment::Peptide peptide) | MRMDecoy | |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| shufflePeptide(OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed=-1, int max_attempts=10) | MRMDecoy | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| stop_watch_ | ProgressLogger | mutableprotected |
| TransitionVectorType typedef | MRMDecoy | |
| type_ | ProgressLogger | mutableprotected |
| value_ | ProgressLogger | mutableprotected |
| ~ProgressLogger() | ProgressLogger | |