OpenMS
MRMAssay Member List

This is the complete list of members for MRMAssay, including all inherited members.

addModificationsSequences_(const std::vector< OpenMS::AASequence > &sequences, const std::vector< std::vector< size_t > > &mods_combs, const OpenMS::String &modification)MRMAssayprotected
CMD enum valueProgressLogger
CompoundTransitionMapType typedefMRMAssay
CompoundVectorType typedefMRMAssay
current_logger_ProgressLoggermutableprotected
detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)MRMAssay
endProgress() constProgressLogger
filterMinMaxTransitionsCompound(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)MRMAssay
filterUnreferencedDecoysCompound(OpenMS::TargetedExperiment &exp)MRMAssay
FragmentSeqMap typedefMRMAssay
generateDecoyAssays_(const OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &DecoyPeptideMap, TargetDecoyMapT &TargetDecoyMap, const IonMapT &DecoyIonMap, const IonMapT &TargetIonMap)MRMAssayprotected
generateDecoyInSilicoMap_(const OpenMS::TargetedExperiment &exp, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, TargetDecoyMapT &TargetDecoyMap, PeptideMapT &TargetPeptideMap, boost::unordered_map< String, String > &DecoySequenceMap, IonMapT &DecoyIonMap, PeptideMapT &DecoyPeptideMap)MRMAssayprotected
generateDecoySequences_(const SequenceMapT &TargetSequenceMap, boost::unordered_map< String, String > &DecoySequenceMap, int shuffle_seed)MRMAssayprotected
generateTargetAssays_(const OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &TargetPeptideMap, const IonMapT &TargetIonMap)MRMAssayprotected
generateTargetInSilicoMap_(const OpenMS::TargetedExperiment &exp, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, size_t max_num_alternative_localizations, SequenceMapT &TargetSequenceMap, IonMapT &TargetIonMap, PeptideMapT &TargetPeptideMap)MRMAssayprotected
generateTheoreticalPeptidoforms_(const OpenMS::AASequence &sequence)MRMAssayprotected
generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence &sequence, const OpenMS::AASequence &decoy_sequence)MRMAssayprotected
getLogType() constProgressLogger
getMatchingPeptidoforms_(const double fragment_ion, const FragmentSeqMap &ions, const double mz_threshold)MRMAssayprotected
getRandomSequence_(size_t sequence_size, boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > pseudoRNG)MRMAssayprotected
getSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz)MRMAssayprotected
GUI enum valueProgressLogger
IonMapT typedefMRMAssay
IonSeries typedefMRMAssay
isInSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz, const double product_mz)MRMAssayprotected
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
ModifiedSequenceMap typedefMRMAssay
MRMAssay()MRMAssay
nchoosekcombinations_(const std::vector< size_t > &n, size_t k)MRMAssayprotected
nextProgress() constProgressLogger
NONE enum valueProgressLogger
operator=(const ProgressLogger &other)ProgressLogger
PeptideMapT typedefMRMAssay
PeptideTransitionMapType typedefMRMAssay
PeptideVectorType typedefMRMAssay
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
ProteinVectorType typedefMRMAssay
reannotateTransitions(OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)MRMAssay
recursion_depth_ProgressLoggerprotectedstatic
restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes)MRMAssay
SequenceMapT typedefMRMAssay
setLogType(LogType type) constProgressLogger
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
TargetDecoyMapT typedefMRMAssay
TransitionVectorType typedefMRMAssay
type_ProgressLoggermutableprotected
uisTransitions(OpenMS::TargetedExperiment &exp, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=-1, bool disable_decoy_transitions=false)MRMAssay
~MRMAssay() overrideMRMAssay
~ProgressLogger()ProgressLoggervirtual