OpenMS  3.0.0
ITRAQLabeler.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
40 
41 // forward decl
42 namespace Eigen
43 {
44  template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
45  class Matrix;
46  using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
47  using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
48 }
49 typedef boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr;
50 
51 namespace OpenMS
52 {
53 
62  class OPENMS_DLLAPI ITRAQLabeler :
63  public BaseLabeler
64  {
65 public:
66 
70 
72  ITRAQLabeler();
73 
75  ~ITRAQLabeler() override;
76 
78  static BaseLabeler* create()
79  {
80  return new ITRAQLabeler();
81  }
82 
84  static const String getProductName()
85  {
86  return "itraq";
87  }
88 
89  // redeclaration of virtual methods
90  void preCheck(Param& param) const override;
91 
92  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
93 
94  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
95 
96  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
97 
98  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
99 
100  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
101 
102  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
103 
104  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
105 
106 protected:
107 
112  void addModificationToPeptideHit_(Feature& feature, const String& modification, const Size& pos) const;
113 
121  void labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const;
122 
123  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
124 
126  void updateMembers_() override;
127 
128  // get the closest RT profile factor of a feature for a given RT
129  double getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const;
130 
132  EigenMatrixXdPtr getItraqIntensity_(const Feature& f, const double MS2_RT_time) const;
133 
134 
135  // Members:
136 
139 
143 
146 
149 
150  };
151 } // namespace OpenMS
152 
SimTypes.h
Eigen
Definition: IsobaricIsotopeCorrector.h:40
double
OpenMS::ItraqConstants::ChannelMapType
std::map< Int, ChannelInfo > ChannelMapType
maps iTRAQ channel (e.g. 117) to more information
Definition: ItraqConstants.h:72
EigenMatrixXdPtr
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: ITRAQLabeler.h:49
Eigen::MatrixXd
Matrix< double, -1, -1, 0, -1, -1 > MatrixXd
Definition: IsobaricIsotopeCorrector.h:44
OpenMS::String
A more convenient string class.
Definition: String.h:58
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::ITRAQLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:84
BaseLabeler.h
OpenMS::ITRAQLabeler::y_labeling_efficiency_
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:148
OpenMS::ITRAQLabeler::itraq_type_
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:138
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ItraqConstants::ChannelInfo
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
OpenMS::ItraqConstants::IsotopeMatrices
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:75
OpenMS::ITRAQLabeler::ChannelInfo
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:67
OpenMS::ITRAQLabeler::IsotopeMatrices
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:69
OpenMS::EigenMatrixXdPtr
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:49
OpenMS::ITRAQLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:78
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:98
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:145
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::ITRAQLabeler::ChannelMapType
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:68
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::ITRAQLabeler
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:62
Eigen::VectorXd
Matrix< double, -1, 1, 0, -1, 1 > VectorXd
Definition: IsobaricIsotopeCorrector.h:45
OpenMS::ITRAQLabeler::channel_map_
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:142