| 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 |  |