35 #ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H 36 #define OPENMS_SIMULATION_LABELING_ITRAQLABELER_H 82 void preCheck(
Param& param)
const;
104 void addModificationToPeptideHit_(
Feature& feature,
const String& modification,
const Size& pos)
const;
115 Feature mergeFeatures_(
Feature& labeled_channel_feature,
const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index)
const;
118 void updateMembers_();
121 double getRTProfileIntensity_(
const Feature& f,
const double MS2_RT_time)
const;
145 #endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H A more convenient string class.
Definition: String.h:57
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:134
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:137
A container for features.
Definition: FeatureMap.h:94
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:59
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:76
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:61
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:60
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:70
An LC-MS feature.
Definition: Feature.h:70
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:130
Management and storage of parameters / INI files.
Definition: Param.h:75
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:50
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:100
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:140
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:54
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:75
int Int
Signed integer type.
Definition: Types.h:103
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:50