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