| OpenMS 2.5.0

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) | MRMAssay | protected
CMD enum value | ProgressLogger |
CompoundTransitionMapType typedef | MRMAssay |
CompoundVectorType typedef | MRMAssay |
current_logger_ | ProgressLogger | mutable protected
detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) | MRMAssay |
detectingTransitionsCompound(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) | MRMAssay |
endProgress() const | ProgressLogger |
FragmentSeqMap typedef | MRMAssay |
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) | MRMAssay | protected
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) | MRMAssay | protected
generateDecoySequences_(const SequenceMapT &TargetSequenceMap, boost::unordered_map< String, String > &DecoySequenceMap, int shuffle_seed) | MRMAssay | protected
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) | MRMAssay | protected
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) | MRMAssay | protected
generateTheoreticalPeptidoforms_(const OpenMS::AASequence &sequence) | MRMAssay | protected
generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence &sequence, const OpenMS::AASequence &decoy_sequence) | MRMAssay | protected
getLogType() const | ProgressLogger |
getMatchingPeptidoforms_(const double fragment_ion, const FragmentSeqMap &ions, const double mz_threshold) | MRMAssay | protected
getRandomSequence_(size_t sequence_size, boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > pseudoRNG) | MRMAssay | protected
getSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz) | MRMAssay | protected
GUI enum value | ProgressLogger |
IonMapT typedef | MRMAssay |
IonSeries typedef | MRMAssay |
isInSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz, const double product_mz) | MRMAssay | protected
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
ModifiedSequenceMap typedef | MRMAssay |
MRMAssay() | MRMAssay |
nchoosekcombinations_(const std::vector< size_t > &n, size_t k) | MRMAssay | protected
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
operator=(const ProgressLogger &other) | ProgressLogger |
PeptideMapT typedef | MRMAssay |
PeptideTransitionMapType typedef | MRMAssay |
PeptideVectorType typedef | MRMAssay |
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
ProteinVectorType typedef | MRMAssay |
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_ | ProgressLogger | protected static
restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes) | MRMAssay |
SequenceMapT typedef | MRMAssay |
setLogType(LogType type) const | ProgressLogger |
setProgress(SignedSize value) const | ProgressLogger |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |
TargetDecoyMapT typedef | MRMAssay |
TransitionVectorType typedef | MRMAssay |
type_ | ProgressLogger | mutable protected
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() | MRMAssay |
~ProgressLogger() | ProgressLogger |