35 #ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
36 #define OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
81 void preCheck(
Param& param)
const;
103 void addModificationToPeptideHit_(
Feature& feature,
const String& modification,
const Size& pos)
const;
114 Feature mergeFeatures_(
Feature& labeled_channel_feature,
const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index)
const;
117 void updateMembers_();
120 double getRTProfileIntensity_(
const Feature& f,
const double MS2_RT_time)
const;
144 #endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H
A more convenient string class.
Definition: String.h:57
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:133
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:136
A container for features.
Definition: FeatureMap.h:93
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:58
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:75
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:60
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:59
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:69
An LC-MS feature.
Definition: Feature.h:70
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:129
Management and storage of parameters / INI files.
Definition: Param.h:75
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:50
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:103
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:139
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:53
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:96
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