OpenMS  2.7.0
MRMIonSeries.h
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34 
35 #pragma once
36 
39 #include <boost/unordered_map.hpp>
40 #include <boost/assign.hpp>
41 #include <boost/lexical_cast.hpp>
42 
43 // #define DEBUG_MRMIONSERIES
44 
45 namespace OpenMS
46 {
47 
69  class OPENMS_DLLAPI MRMIonSeries
70  {
71 private:
73 
75 
76 public:
78  MRMIonSeries();
80 
84 
85  typedef boost::unordered_map<String, double> IonSeries;
86 
96  std::pair<String, double> getIon(IonSeries& ionseries, const String& ionid);
97 
108  std::pair<String, double> annotateIon(const IonSeries& ionseries, const double ProductMZ, const double mz_threshold);
109 
118 
136  const TargetedExperiment::Peptide& peptide,
137  const double precursor_mz_threshold,
138  const double product_mz_threshold,
139  const bool enable_reannotation,
140  const std::vector<String>& fragment_types,
141  const std::vector<size_t>& fragment_charges,
142  const bool enable_specific_losses,
143  const bool enable_unspecific_losses,
144  const int round_decPow = -4);
145 
159  size_t precursor_charge,
160  const std::vector<String>& fragment_types,
161  const std::vector<size_t>& fragment_charges,
162  const bool enable_specific_losses,
163  const bool enable_unspecific_losses,
164  const int round_decPow = -4);
165  };
166 }
167 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Definition: MRMIonSeries.h:70
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)
boost::unordered_map< String, double > IonSeries
An MRM ion series which maps: "ion_type" -> "fragment m/z".
Definition: MRMIonSeries.h:85
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:61
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:360
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Product ion interpretation.
Definition: TargetedExperimentHelper.h:505