OpenMS  2.5.0
ITRAQLabeler.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
41 
42 namespace OpenMS
43 {
44 
53  class OPENMS_DLLAPI ITRAQLabeler :
54  public BaseLabeler
55  {
56 public:
57 
61 
63  ITRAQLabeler();
64 
66  ~ITRAQLabeler() override;
67 
69  static BaseLabeler* create()
70  {
71  return new ITRAQLabeler();
72  }
73 
75  static const String getProductName()
76  {
77  return "itraq";
78  }
79 
80  // redeclaration of virtual methods
81  void preCheck(Param& param) const override;
82 
83  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
84 
85  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86 
87  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
88 
89  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
90 
91  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
92 
93  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
94 
95  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
96 
97 protected:
98 
103  void addModificationToPeptideHit_(Feature& feature, const String& modification, const Size& pos) const;
104 
112  void labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const;
113 
114  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
115 
117  void updateMembers_() override;
118 
119  // get the closest RT profile factor of a feature for a given RT
120  double getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const;
121 
123  EigenMatrixXdPtr getItraqIntensity_(const Feature& f, const double MS2_RT_time) const;
124 
125 
126  // Members:
127 
130 
134 
137 
140 
141  };
142 } // namespace OpenMS
143 
SimTypes.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ITRAQLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:75
BaseLabeler.h
MatrixUtils.h
OpenMS::ITRAQLabeler::y_labeling_efficiency_
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:139
OpenMS::ITRAQLabeler::itraq_type_
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:129
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ItraqConstants::ChannelInfo
stores information on an iTRAQ channel
Definition: ItraqConstants.h:61
OpenMS::ItraqConstants::IsotopeMatrices
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:74
OpenMS::ITRAQLabeler::ChannelInfo
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:58
OpenMS::ITRAQLabeler::IsotopeMatrices
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:60
OpenMS::EigenMatrixXdPtr
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:49
int
OpenMS::ITRAQLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:69
ItraqConstants.h
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::ITRAQLabeler::isotope_corrections_
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:136
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::ITRAQLabeler::ChannelMapType
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:59
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::ITRAQLabeler
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:53
OpenMS::ITRAQLabeler::channel_map_
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:133