39 #include <unordered_map>
83 typedef std::unordered_map<String, double>
IonSeries;
106 std::pair<String, double>
annotateIon(
const IonSeries& ionseries,
const double ProductMZ,
const double mz_threshold);
135 const double precursor_mz_threshold,
136 const double product_mz_threshold,
137 const bool enable_reannotation,
138 const std::vector<String>& fragment_types,
139 const std::vector<size_t>& fragment_charges,
140 const bool enable_specific_losses,
141 const bool enable_unspecific_losses,
142 const int round_decPow = -4);
157 size_t precursor_charge,
158 const std::vector<String>& fragment_types,
159 const std::vector<size_t>& fragment_charges,
160 const bool enable_specific_losses,
161 const bool enable_unspecific_losses,
162 const int round_decPow = -4);
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Definition: MRMIonSeries.h:68
std::unordered_map< String, double > IonSeries
An MRM ion series which maps: "ion_type" -> "fragment m/z".
Definition: MRMIonSeries.h:83
IonSeries getIonSeries(const AASequence &sequence, size_t precursor_charge, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4)
Computed theoretical fragment ion series.
void annotationToCV_(ReactionMonitoringTransition &tr)
std::pair< String, double > getIon(IonSeries &ionseries, const String &ionid)
Selects ion from IonSeries according to annotation string.
TargetedExperiment::Interpretation annotationToCVTermList_(const String &annotation)
void annotateTransitionCV(ReactionMonitoringTransition &tr, const String &annotation)
Annotates transition with CV terms.
~MRMIonSeries()
Destructor.
void annotateTransition(ReactionMonitoringTransition &tr, const TargetedExperiment::Peptide &peptide, const double precursor_mz_threshold, const double product_mz_threshold, const bool enable_reannotation, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4)
Annotates transition.
std::pair< String, double > annotateIon(const IonSeries &ionseries, const double ProductMZ, const double mz_threshold)
Selects ion from IonSeries according to product m/z.
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:58
A more convenient string class.
Definition: String.h:60
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:360
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Product ion interpretation.
Definition: TargetedExperimentHelper.h:505