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MRMAssay.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H
37 
44 
45 #include <boost/bind.hpp>
46 
47 // #define DEBUG_MRMASSAY
48 
49 namespace OpenMS
50 {
65  class OPENMS_DLLAPI MRMAssay :
66  public ProgressLogger
67  {
68 
69 public:
71  MRMAssay(); // empty, no members
73 
75  ~MRMAssay();
77 
78  typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
79  typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
80  typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;
81 
98  void reannotateTransitions(OpenMS::TargetedExperiment& exp, double mz_threshold, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_alternative_localizations, bool enable_reannotation, bool enable_losses, int round_decPow = -4);
99 
110  void restrictTransitions(OpenMS::TargetedExperiment& exp, double lower_mz_limit, double upper_mz_limit, std::vector<std::pair<double, double> > swathes);
111 
120  void detectingTransitions(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);
121 
137  void uisTransitions(OpenMS::TargetedExperiment& exp, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_losses, bool enable_uis_scoring, bool enable_site_scoring, double mz_threshold, std::vector<std::pair<double, double> > swathes);
138 
150  void insilicoTransitions(OpenMS::TargetedExperiment& exp, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_losses, int round_decPow = -4);
151 
152 protected:
160  bool isUIS_(const double fragment_ion, std::vector<double> ions, const double mz_threshold);
161 
168  void isSiteUIS_(const AASequence sequence, ReactionMonitoringTransition& tr);
169 
176  int getSwath_(const std::vector<std::pair<double, double> > swathes, const double precursor_mz);
177 
185  bool isInSwath_(const std::vector<std::pair<double, double> > swathes, const double precursor_mz, const double product_mz);
186 
195  std::vector<std::vector<size_t> > nchoosekcombinations_(std::vector<size_t> n, size_t k);
196 
204  std::vector<OpenMS::AASequence> combineModifications_(OpenMS::AASequence sequence);
205 
213  std::vector<OpenMS::AASequence> addModificationsSequences_(std::vector<OpenMS::AASequence> sequences, std::vector<std::vector<size_t> > mods_combs, OpenMS::String modification);
214 
224  void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods, int location, ResidueModification& rmod, const String& name);
225 
226  };
227 }
228 
229 #endif
const double k
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:65
A more convenient string class.
Definition: String.h:57
Representation of a modification.
Definition: ResidueModification.h:65
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMAssay.h:79
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMAssay.h:78
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMAssay.h:80
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