| OpenMS 2.5.0

CompNovoIonScoringCID.h
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1 // --------------------------------------------------------------------------
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.
6 //
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 // OpenMS includes
39 #include <OpenMS/METADATA/PeptideIdentification.h>
40 #include <OpenMS/KERNEL/StandardTypes.h>
41 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
42 #include <OpenMS/DATASTRUCTURES/Map.h>
43 #include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
44 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
45 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
46 #include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringBase.h>
47
48 // stl includes
49 #include <vector>
50
51 namespace OpenMS
52 {
60 class OPENMS_DLLAPI CompNovoIonScoringCID :
61 public CompNovoIonScoringBase
62 {
63
64 public:
65
66 typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
67 typedef CompNovoIonScoringBase::IonScore IonScore;
68
69
73 CompNovoIonScoringCID();
75
77 CompNovoIonScoringCID(const CompNovoIonScoringCID & source);
78
80 ~CompNovoIonScoringCID() override;
82
84 CompNovoIonScoringCID & operator=(const CompNovoIonScoringCID & source);
85
89 void scoreSpectrum(Map<double, IonScore> & CID_ion_scores, PeakSpectrum & CID_spec, double precursor_weight, Size charge);
91
92 protected:
93
94 void scoreWitnessSet_(Size charge, double precursor_weight, Map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec) override;
95 };
96
97 }
98
CompNovoIonScoringBase.h
OpenMS::CompNovoIonScoringBase::IsotopeType
IsotopeType
Definition: CompNovoIonScoringBase.h:59
OpenMS::CompNovoIonScoringBase
run with CompNovoIonScoringBase
Definition: CompNovoIonScoringBase.h:53
StandardTypes.h
ZhangSimilarityScore.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::CompNovoIonScoringCID
run with CompNovoIonScoringCID
Definition: CompNovoIonScoringCID.h:60
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:66
MassDecomposition.h
DefaultParamHandler.h
Map.h
MassDecompositionAlgorithm.h
OpenMS::CompNovoIonScoringCID::IonScore
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIonScoringCID.h:67
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::CompNovoIonScoringCID::IsotopeType
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIonScoringCID.h:66