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 | |