| OpenMS 2.5.0

O18Labeler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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 // $Authors: Stephan Aiche$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
38
39 namespace OpenMS
40 {
41
49 class OPENMS_DLLAPI O18Labeler :
50 public BaseLabeler
51 {
52 public:
53
55 O18Labeler();
56
58 ~O18Labeler() override;
59
61 static BaseLabeler* create()
62 {
63 return new O18Labeler();
64 }
65
67 static const String getProductName()
68 {
69 return "o18";
70 }
71
72 // redeclaration of virtual methods
73 void preCheck(Param& param) const override;
74
75 void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
76
77 void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
78
79 void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
80
81 void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
82
83 void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
84
85 void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86
87 void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
88
89 protected:
90 void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
91
92 Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
93
94 private:
96 static const int LIGHT_CHANNEL_ID_;
98 static const int MEDIUM_CHANNEL_ID_;
100 static const int HEAVY_CHANNEL_ID_;
101 };
102 } // namespace OpenMS
103
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::O18Labeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: O18Labeler.h:67
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::O18Labeler::LIGHT_CHANNEL_ID_
static const int LIGHT_CHANNEL_ID_
Map ID for the light/unlabeled channel.
Definition: O18Labeler.h:96
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::O18Labeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: O18Labeler.h:61
OpenMS::O18Labeler::MEDIUM_CHANNEL_ID_
static const int MEDIUM_CHANNEL_ID_
Map ID for the medium/mono-labeled channel.
Definition: O18Labeler.h:98
OpenMS::O18Labeler
Simulate O-18 experiments.
Definition: O18Labeler.h:49
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::O18Labeler::HEAVY_CHANNEL_ID_
static const int HEAVY_CHANNEL_ID_
Map ID for the heavy/bi-labeled channel.
Definition: O18Labeler.h:100
BaseLabeler.h