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MRMIonSeries.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMIONSERIES_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMIONSERIES_H
37 
40 #include <boost/unordered_map.hpp>
41 #include <boost/assign.hpp>
42 
43 // #define DEBUG_MRMIONSERIES
44 
45 namespace OpenMS
46 {
56  class OPENMS_DLLAPI MRMIonSeries
57  {
58 private:
59  CVTermList annotationToCVTermList_(String annotation);
60 
61  void annotationToCV_(ReactionMonitoringTransition& tr);
62 
63 public:
65  MRMIonSeries();
67 
69  ~MRMIonSeries();
71 
72  typedef boost::unordered_map<String, double> IonSeries;
73 
83  std::pair<String, double> getIon(IonSeries ionseries, String ionid);
84 
95  std::pair<String, double> annotateIon(IonSeries ionseries, double ProductMZ, double mz_threshold);
96 
104  void annotateTransitionCV(ReactionMonitoringTransition& tr, String annotation);
105 
120  void annotateTransition(ReactionMonitoringTransition& tr, const TargetedExperiment::Peptide peptide, const double mz_threshold, bool enable_reannotation, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_losses, int round_decPow = -4);
121 
133  IonSeries getIonSeries(AASequence sequence, size_t precursor_charge, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_losses, int round_decPow = -4);
134  };
135 }
136 
137 #endif
A more convenient string class.
Definition: String.h:57
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
boost::unordered_map< String, double > IonSeries
Definition: MRMIonSeries.h:72
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Definition: MRMIonSeries.h:56
Definition: TargetedExperimentHelper.h:211
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:55

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:25 using doxygen 1.8.9.1