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CompNovoIdentification.h
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34 
35 
36 #ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H
37 #define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H
38 
39 // OpenMS includes
41 
42 // stl includes
43 #include <vector>
44 
45 namespace OpenMS
46 {
54  class OPENMS_DLLAPI CompNovoIdentification :
56  {
57 
58 public:
59 
65 
68 
70  virtual ~CompNovoIdentification();
72 
74  CompNovoIdentification & operator=(const CompNovoIdentification & source);
75 
79  void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp);
81 
83  void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec, const PeakSpectrum & ETD_spec);
85 
86 
90 
91 protected:
92 
94  void getDecompositionsDAC_(std::set<String> & sequences, Size left, Size right, double peptide_weight, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, Map<double, IonScore> & CID_nodes);
95 
97  void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, double prefix, double suffix);
98 
100  void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);
101 
103  double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);
104 
105  };
106 }
107 
108 #endif
A more convenient string class.
Definition: String.h:57
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentification.h:89
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentification.h:87
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
IsotopeType
Definition: CompNovoIonScoringBase.h:60
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentification.h:88
run with CompNovoIdentification
Definition: CompNovoIdentification.h:54
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
Definition: CompNovoIonScoringBase.h:67
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:21:59 using doxygen 1.8.13