35 #ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
36 #define OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
80 void preCheck(
Param & param)
const;
102 void addModificationToPeptideHit_(
Feature & feature,
const String & modification,
const Size & pos)
const;
113 Feature mergeFeatures_(
Feature & labeled_channel_feature,
const AASequence & unmodified_sequence, std::map<AASequence, Feature> & unlabeled_features_index)
const;
116 void updateMembers_();
143 #endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H
A more convenient string class.
Definition: String.h:56
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:132
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:135
A container for features.
Definition: FeatureMap.h:111
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:57
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:74
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:59
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:58
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:68
An LC-MS feature.
Definition: Feature.h:66
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:128
Management and storage of parameters / INI files.
Definition: Param.h:69
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:52
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:80
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:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:54
DoubleReal y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:138
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access...
Definition: Matrix.h:79