OpenMS  3.0.0
CompNovoIdentificationCID.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 #include <map>
44 
45 namespace OpenMS
46 {
54  class OPENMS_DLLAPI CompNovoIdentificationCID :
56  {
57 
58 public:
59 
65 
68 
70  ~CompNovoIdentificationCID() override;
72 
74  CompNovoIdentificationCID & operator=(const CompNovoIdentificationCID & source);
75 
79  void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) override;
81 
83  void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_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, std::map<double, IonScore> & CID_nodes);
95 
97  void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, double prefix, double suffix);
98 
99  void updateMembers_() override;
100 
102  };
103 }
104 
OpenMS::StringUtils::suffix
static String suffix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:156
OpenMS::CompNovoIonScoringBase::IsotopeType
IsotopeType
Definition: CompNovoIonScoringBase.h:60
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::CompNovoIdentificationCID::precursor_mass_tolerance_
double precursor_mass_tolerance_
Definition: CompNovoIdentificationCID.h:101
OpenMS::CompNovoIdentificationBase::Permut
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:67
OpenMS::CompNovoIdentificationCID::Permut
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentificationCID.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
CompNovoIdentificationBase.h
OpenMS::CompNovoIdentificationCID
run with CompNovoIdentificationCID
Definition: CompNovoIdentificationCID.h:54
OpenMS::CompNovoIdentificationCID::IonScore
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationCID.h:88
OpenMS::CompNovoIdentificationBase
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:57
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::CompNovoIdentificationCID::IsotopeType
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentificationCID.h:87
OpenMS::StringUtils::prefix
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66