| AASequenceIdentity(const String &sequence, const String &decoy) | MRMDecoy | |
| CMD enum value | ProgressLogger | |
| current_logger_ | 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, double mz_shift, bool exclude_similar, double similarity_threshold, bool remove_CNterm_mods, double precursor_mass_shift, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool remove_unannotated, int round_decPow=-4) | MRMDecoy | |
| getLogType() const | ProgressLogger | |
| GUI enum value | ProgressLogger | |
| has_CNterminal_mods(const OpenMS::TargetedExperiment::Peptide &peptide) | MRMDecoy | |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| MRMDecoy() | MRMDecoy | inline |
| NONE enum value | ProgressLogger | |
| operator=(const ProgressLogger &other) | ProgressLogger | |
| PeptideTransitionMapType typedef | MRMDecoy | |
| PeptideVectorType typedef | MRMDecoy | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProteinVectorType typedef | MRMDecoy | |
| pseudoreversePeptide(OpenMS::TargetedExperiment::Peptide peptide) | MRMDecoy | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| 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, bool replace_aa_instead_append=false) | MRMDecoy | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| TransitionVectorType typedef | MRMDecoy | |
| type_ | ProgressLogger | mutableprotected |
| ~ProgressLogger() | ProgressLogger | |