add1DSignal_(Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct) | RawMSSignalSimulation | protected |
add2DSignal_(Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct) | RawMSSignalSimulation | protected |
addBaseLine_(MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit) | RawMSSignalSimulation | protected |
addDetectorNoise_(MSSimExperiment &experiment) | RawMSSignalSimulation | protected |
addShotNoise_(MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit, SimCoordinateType maximal_mz_measurement_limit) | RawMSSignalSimulation | protected |
addWhiteNoise_(MSSimExperiment &experiment) | RawMSSignalSimulation | protected |
begin_ | ProgressLogger | mutableprotected |
check_defaults_ | DefaultParamHandler | protected |
chooseElutionProfile_(EGHModel *const elutionmodel, Feature &feature, const double scale, const DoubleReal rt_sampling_rate, const MSSimExperiment &experiment) | RawMSSignalSimulation | protected |
CMD enum value | ProgressLogger | |
compressSignals_(MSSimExperiment &experiment) | RawMSSignalSimulation | protected |
contaminants_ | RawMSSignalSimulation | protected |
contaminants_loaded_ | RawMSSignalSimulation | protected |
createContaminants_(FeatureMapSim &contaminants, MSSimExperiment &exp, MSSimExperiment &exp_ct) | RawMSSignalSimulation | protected |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
defaults_ | DefaultParamHandler | protected |
defaultsToParam_() | DefaultParamHandler | protected |
dlg_ | ProgressLogger | mutableprotected |
end_ | ProgressLogger | mutableprotected |
endProgress() const | ProgressLogger | |
error_name_ | DefaultParamHandler | protected |
generateRawSignals(FeatureMapSim &features, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, FeatureMapSim &contaminants) | RawMSSignalSimulation | |
getDefaults() const | DefaultParamHandler | |
getFeatureScaledIntensity_(const SimIntensityType feature_intensity, const SimIntensityType natural_scaling_factor) | RawMSSignalSimulation | protected |
getLogType() const | ProgressLogger | |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getPeakWidth_(const DoubleReal mz, const bool is_gaussian) const | RawMSSignalSimulation | protected |
getResolution_(const DoubleReal query_mz, const DoubleReal resolution, const RESOLUTIONMODEL model) const | RawMSSignalSimulation | protected |
getSamplingGrid_(std::vector< SimCoordinateType > &grid, const SimCoordinateType mz_min, const SimCoordinateType mz_max, const Int step_Da) | RawMSSignalSimulation | protected |
getSubsections() const | DefaultParamHandler | |
grid_ | RawMSSignalSimulation | protected |
GUI enum value | ProgressLogger | |
IM_ALL enum value | RawMSSignalSimulation | protected |
IM_ESI enum value | RawMSSignalSimulation | protected |
IM_MALDI enum value | RawMSSignalSimulation | protected |
intensity_scale_ | RawMSSignalSimulation | protected |
intensity_scale_stddev_ | RawMSSignalSimulation | protected |
IONIZATIONMETHOD enum name | RawMSSignalSimulation | protected |
last_invoke_ | ProgressLogger | mutableprotected |
loadContaminants() | RawMSSignalSimulation | |
LogType enum name | ProgressLogger | |
mz_error_mean_ | RawMSSignalSimulation | protected |
mz_error_stddev_ | RawMSSignalSimulation | protected |
NONE enum value | ProgressLogger | |
operator=(const RawMSSignalSimulation &source) | RawMSSignalSimulation | |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
param_ | DefaultParamHandler | protected |
PROFILESHAPE enum name | RawMSSignalSimulation | protected |
ProgressLogger() | ProgressLogger | |
RawMSSignalSimulation(const SimRandomNumberGenerator &rng) | RawMSSignalSimulation | |
RawMSSignalSimulation(const RawMSSignalSimulation &source) | RawMSSignalSimulation | |
RawMSSignalSimulation() | RawMSSignalSimulation | protected |
recursion_depth_ | ProgressLogger | protectedstatic |
res_base_ | RawMSSignalSimulation | protected |
RES_CONSTANT enum value | RawMSSignalSimulation | protected |
RES_LINEAR enum value | RawMSSignalSimulation | protected |
res_model_ | RawMSSignalSimulation | protected |
RES_SQRT enum value | RawMSSignalSimulation | protected |
RESOLUTIONMODEL enum name | RawMSSignalSimulation | protected |
rnd_gen_ | RawMSSignalSimulation | protected |
RT_GAUSSIAN enum value | RawMSSignalSimulation | protected |
RT_RECTANGULAR enum value | RawMSSignalSimulation | protected |
samplePeptideModel1D_(const IsotopeModel &iso, const SimCoordinateType mz_start, const SimCoordinateType mz_end, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, Feature &activeFeature) | RawMSSignalSimulation | protected |
samplePeptideModel2D_(const ProductModel< 2 > &pm, const SimCoordinateType mz_start, const SimCoordinateType mz_end, SimCoordinateType rt_start, SimCoordinateType rt_end, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, Feature &activeFeature) | RawMSSignalSimulation | protected |
sampling_points_per_FWHM_ | RawMSSignalSimulation | protected |
setDefaultParams_() | RawMSSignalSimulation | protected |
setLogType(LogType type) const | ProgressLogger | |
setName(const String &name) | DefaultParamHandler | |
setParameters(const Param ¶m) | DefaultParamHandler | |
setProgress(SignedSize value) const | ProgressLogger | |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
stop_watch_ | ProgressLogger | mutableprotected |
subsections_ | DefaultParamHandler | protected |
THREADED_RANDOM_NUMBER_POOL_SIZE_ | RawMSSignalSimulation | protectedstatic |
threaded_random_numbers_ | RawMSSignalSimulation | protected |
threaded_random_numbers_index_ | RawMSSignalSimulation | protected |
type_ | ProgressLogger | mutableprotected |
updateMembers_() | RawMSSignalSimulation | protectedvirtual |
value_ | ProgressLogger | mutableprotected |
warn_empty_defaults_ | DefaultParamHandler | protected |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~ProgressLogger() | ProgressLogger | |
~RawMSSignalSimulation() | RawMSSignalSimulation | virtual |