OpenMS  2.7.0
CompNovoIdentification.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 
36 #pragma once
37 
38 // OpenMS includes
40 
41 // stl includes
42 #include <vector>
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI CompNovoIdentification :
55  {
56 
57 public:
58 
64 
67 
71 
74 
79  void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) override;
80 
82  void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec, const PeakSpectrum & ETD_spec);
84 
85 
89 
90 protected:
91 
93  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);
94 
96  void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, double prefix, double suffix);
97 
99  double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);
100 
101  };
102 }
103 
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:187
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:59
run with CompNovoIdentification
Definition: CompNovoIdentification.h:55
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)
call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with can...
void reducePermuts_(std::set< String > &permuts, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_orig_spec, double prefix, double suffix)
reduces the given number of permuts by scoring the permutations to the CID and ETD spec
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentification.h:88
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentification.h:87
CompNovoIdentification()
default constructor
~CompNovoIdentification() override
destructor
void getIdentification(PeptideIdentification &id, const PeakSpectrum &CID_spec, const PeakSpectrum &ETD_spec)
performs an ProteinIdentification run on a PeakSpectrum
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentification.h:86
void getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp) override
performs an ProteinIdentification run on a PeakMap
CompNovoIdentification(const CompNovoIdentification &source)
copy constructor
double estimatePrecursorWeight_(const PeakSpectrum &ETD_spec, Size &charge)
estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor i...
CompNovoIdentification & operator=(const CompNovoIdentification &source)
IsotopeType
Definition: CompNovoIonScoringBase.h:60
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:80
The representation of a 1D spectrum.
Definition: MSSpectrum.h:71
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: CompNovoIonScoringBase.h:67