35 #ifndef OPENMS_SIMULATION_IONIZATIONSIMULATION_H 
   36 #define OPENMS_SIMULATION_IONIZATIONSIMULATION_H 
  109     class CompareCmpByEF_;
 
  118     inline bool isFeatureValid_(
const Feature & feature);
 
  121     void setFeatureProperties_(
Feature & f,
 
  123                                const String & adduct_formula,
 
  126                                const Size parent_index);
 
  129     void setDefaultParams_();
 
  132     void updateMembers_();
 
Feature::ChargeType SimChargeType
Charge of a peptide. 
Definition: SimTypes.h:65
A more convenient string class. 
Definition: String.h:56
Simulates Protein ionization. 
Definition: IonizationSimulation.h:64
A container for features. 
Definition: FeatureMap.h:111
IonizationType
possible ionization methods 
Definition: IonizationSimulation.h:71
A container for consensus elements. 
Definition: ConsensusMap.h:60
Representation of a peptide/protein sequence. 
Definition: AASequence.h:84
std::vector< Adduct > AdductsType
Definition: Adduct.h:50
Size max_adduct_charge_
Maximal charge that any impure adduct from parameter list has. 
Definition: IonizationSimulation.h:172
std::vector< double > esi_impurity_probabilities_
Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+...
Definition: IonizationSimulation.h:161
std::set< String > basic_residues_
Definition: IonizationSimulation.h:150
SimCoordinateType minimal_mz_measurement_limit_
Minimum m/z detected by mass analyser. 
Definition: IonizationSimulation.h:183
Adduct::AdductsType esi_adducts_
Corresponding table to esi_impurity_probabilities_ holding the actual element and its charge...
Definition: IonizationSimulation.h:167
std::vector< double > maldi_probabilities_
Preprocessed table of discrete distribution (MALDI charges) 
Definition: IonizationSimulation.h:178
An LC-MS feature. 
Definition: Feature.h:66
IonizationType ionization_type_
ESI or MALDI ionization. 
Definition: IonizationSimulation.h:145
Wrapper class for random number generators used by the simulation classes. 
Definition: SimTypes.h:99
Peak2D::IntensityType SimIntensityType
Abundance of proteins/peptides. 
Definition: SimTypes.h:62
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
DoubleReal esi_probability_
Probability for the binomial distribution of ESI charge states. 
Definition: IonizationSimulation.h:155
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
SimCoordinateType maximal_mz_measurement_limit_
Maximum m/z detected by mass analyser. 
Definition: IonizationSimulation.h:181
SimRandomNumberGenerator const * rnd_gen_
Random number generator. 
Definition: IonizationSimulation.h:187
Definition: IonizationSimulation.h:73