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