| OpenMS 2.5.0

CompNovoIdentification.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 // OpenMS includes
39 #include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>
40
41 // stl includes
42 #include <vector>
43
44 namespace OpenMS
45 {
53 class OPENMS_DLLAPI CompNovoIdentification :
54 public CompNovoIdentificationBase
55 {
56
57 public:
58
62 CompNovoIdentification();
64
66 CompNovoIdentification(const CompNovoIdentification & source);
67
69 ~CompNovoIdentification() override;
71
73 CompNovoIdentification & operator=(const CompNovoIdentification & source);
74
78 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
86 typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
87 typedef CompNovoIonScoringBase::IonScore IonScore;
88 typedef CompNovoIdentificationBase::Permut Permut;
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
OpenMS::CompNovoIdentification::IonScore
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentification.h:87
OpenMS::CompNovoIdentification
run with CompNovoIdentification
Definition: CompNovoIdentification.h:53
OpenMS::CompNovoIonScoringBase::IsotopeType
IsotopeType
Definition: CompNovoIonScoringBase.h:59
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
CompNovoIdentificationBase.h
OpenMS::CompNovoIdentification::IsotopeType
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentification.h:86
OpenMS::CompNovoIdentificationBase::Permut
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::CompNovoIdentification::Permut
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentification.h:88
OpenMS::CompNovoIdentificationBase
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:57
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:66
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127