OpenMS  3.0.0
RawMSSignalSimulation.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
39 
42 
44 
45 namespace OpenMS
46 {
47 
48  class IsotopeModel;
49 
60  class OPENMS_DLLAPI RawMSSignalSimulation :
61  public DefaultParamHandler,
62  public ProgressLogger
63  {
64 
65 public:
71 
74 
77 
79  ~RawMSSignalSimulation() override;
81 
82  RawMSSignalSimulation& operator=(const RawMSSignalSimulation& source);
83 
87  void loadContaminants();
88 
90  void generateRawSignals(SimTypes::FeatureMapSim& features,
91  SimTypes::MSSimExperiment& experiment,
92  SimTypes::MSSimExperiment& experiment_ct,
93  SimTypes::FeatureMapSim& contaminants);
94 
95 protected:
96 
97  enum IONIZATIONMETHOD {IM_ESI = 0, IM_MALDI = 1, IM_ALL = 2};
98  enum PROFILESHAPE {RT_RECTANGULAR, RT_GAUSSIAN};
99  enum RESOLUTIONMODEL {RES_CONSTANT, RES_LINEAR, RES_SQRT};
100 
102  void updateMembers_() override;
103 
105  void setDefaultParams_();
106 
114  void add1DSignal_(Feature& feature, SimTypes::MSSimExperiment& experiment, SimTypes::MSSimExperiment& experiment_ct);
115 
123  void add2DSignal_(Feature& feature, SimTypes::MSSimExperiment& experiment, SimTypes::MSSimExperiment& experiment_ct);
124 
135  void samplePeptideModel1D_(const IsotopeModel& iso,
136  const SimTypes::SimCoordinateType mz_start,
137  const SimTypes::SimCoordinateType mz_end,
138  SimTypes::MSSimExperiment& experiment,
139  SimTypes::MSSimExperiment& experiment_ct,
140  Feature& activeFeature);
141 
154  void samplePeptideModel2D_(const ProductModel<2>& pm,
155  const SimTypes::SimCoordinateType mz_start,
156  const SimTypes::SimCoordinateType mz_end,
159  SimTypes::MSSimExperiment& experiment,
160  SimTypes::MSSimExperiment& experiment_ct,
161  Feature& activeFeature);
162 
166  void chooseElutionProfile_(EGHModel* const elutionmodel,
167  Feature& feature,
168  const double scale,
169  const double rt_sampling_rate,
170  const SimTypes::MSSimExperiment& experiment);
171 
175  void createContaminants_(SimTypes::FeatureMapSim& contaminants, SimTypes::MSSimExperiment& exp, SimTypes::MSSimExperiment& exp_ct);
176 
178  void addShotNoise_(SimTypes::MSSimExperiment& experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit, SimTypes::SimCoordinateType maximal_mz_measurement_limit);
179 
181  void addWhiteNoise_(SimTypes::MSSimExperiment& experiment);
182 
184  void addDetectorNoise_(SimTypes::MSSimExperiment& experiment);
185 
187  void addBaseLine_(SimTypes::MSSimExperiment& experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit);
188 
190  void getSamplingGrid_(std::vector<SimTypes::SimCoordinateType>& grid,
191  const SimTypes::SimCoordinateType mz_min,
192  const SimTypes::SimCoordinateType mz_max,
193  const Int step_Da);
194 
196  void compressSignals_(SimTypes::MSSimExperiment& experiment);
197 
200 
205 
214  SimTypes::SimIntensityType getFeatureScaledIntensity_(const SimTypes::SimIntensityType feature_intensity,
215  const SimTypes::SimIntensityType natural_scaling_factor);
216 
217 
229  double getResolution_(const double query_mz, const double resolution, const RESOLUTIONMODEL model) const;
230 
234  double getPeakWidth_(const double mz, const bool is_gaussian) const;
235 
240 
241 
245  double res_base_;
247  std::vector<SimTypes::SimCoordinateType> grid_;
248 
251 
253  {
256  double rt_start, rt_end, intensity;
260  };
261 
262  std::vector<ContaminantInfo> contaminants_;
263 
267  std::vector<std::vector<double> > threaded_random_numbers_;
268 
274 
275  static const Size THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500;
276 
278  };
279 
280 }
281 
DefaultParamHandler.h
OpenMS::RawMSSignalSimulation::IONIZATIONMETHOD
IONIZATIONMETHOD
Definition: RawMSSignalSimulation.h:97
OpenMS::RawMSSignalSimulation::sampling_points_per_FWHM_
Int sampling_points_per_FWHM_
number of points sampled per peak's FWHM
Definition: RawMSSignalSimulation.h:199
OpenMS::RawMSSignalSimulation::contaminants_
std::vector< ContaminantInfo > contaminants_
Definition: RawMSSignalSimulation.h:262
SimTypes.h
OpenMS::RawMSSignalSimulation::intensity_scale_stddev_
SimTypes::SimIntensityType intensity_scale_stddev_
Standard deviation of peak intensity scaling.
Definition: RawMSSignalSimulation.h:239
double
OpenMS::RawMSSignalSimulation::threaded_random_numbers_
std::vector< std::vector< double > > threaded_random_numbers_
Definition: RawMSSignalSimulation.h:267
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RawMSSignalSimulation::res_base_
double res_base_
base resolution at 400 Th
Definition: RawMSSignalSimulation.h:245
OpenMS::RawMSSignalSimulation::ContaminantInfo::sf
EmpiricalFormula sf
Definition: RawMSSignalSimulation.h:255
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::IsotopeModel
Isotope distribution approximated using linear interpolation.
Definition: IsotopeModel.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::EGHModel
Exponential-Gaussian hybrid distribution model for elution profiles.
Definition: EGHModel.h:53
OpenMS::ProductModel< 2 >
The class template is only implemented for D=2 because we use Peak2D here.
Definition: ProductModel.h:64
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::RawMSSignalSimulation
Simulates MS signals for a given set of peptides.
Definition: RawMSSignalSimulation.h:60
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
ProductModel.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RawMSSignalSimulation::res_model_
RESOLUTIONMODEL res_model_
model of how resolution behaves with increasing m/z
Definition: RawMSSignalSimulation.h:243
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::RawMSSignalSimulation::grid_
std::vector< SimTypes::SimCoordinateType > grid_
m/z sampling grid for all signals
Definition: RawMSSignalSimulation.h:247
OpenMS::RawMSSignalSimulation::rnd_gen_
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
Random number generator.
Definition: RawMSSignalSimulation.h:250
OpenMS::RawMSSignalSimulation::ContaminantInfo::im
IONIZATIONMETHOD im
Definition: RawMSSignalSimulation.h:259
OpenMS::RawMSSignalSimulation::mz_error_mean_
SimTypes::SimCoordinateType mz_error_mean_
Mean of peak m/z error.
Definition: RawMSSignalSimulation.h:202
OpenMS::RawMSSignalSimulation::mz_error_stddev_
SimTypes::SimCoordinateType mz_error_stddev_
Standard deviation of peak m/z error.
Definition: RawMSSignalSimulation.h:204
OpenMS::RawMSSignalSimulation::ContaminantInfo::rt_start
double rt_start
Definition: RawMSSignalSimulation.h:256
OpenMS::RawMSSignalSimulation::PROFILESHAPE
PROFILESHAPE
Definition: RawMSSignalSimulation.h:98
OpenMS::RawMSSignalSimulation::RT_RECTANGULAR
Definition: RawMSSignalSimulation.h:98
OpenMS::RawMSSignalSimulation::threaded_random_numbers_index_
std::vector< Size > threaded_random_numbers_index_
Definition: RawMSSignalSimulation.h:273
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
EGHModel.h
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::RawMSSignalSimulation::ContaminantInfo
Definition: RawMSSignalSimulation.h:252
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
float
OpenMS::RawMSSignalSimulation::ContaminantInfo::q
Int q
Definition: RawMSSignalSimulation.h:257
OpenMS::RawMSSignalSimulation::ContaminantInfo::name
String name
Definition: RawMSSignalSimulation.h:254
OpenMS::RawMSSignalSimulation::ContaminantInfo::shape
PROFILESHAPE shape
Definition: RawMSSignalSimulation.h:258
OpenMS::RawMSSignalSimulation::contaminants_loaded_
bool contaminants_loaded_
Definition: RawMSSignalSimulation.h:277
OpenMS::RawMSSignalSimulation::intensity_scale_
SimTypes::SimIntensityType intensity_scale_
Scaling factor of peak intensities.
Definition: RawMSSignalSimulation.h:237
OpenMS::RawMSSignalSimulation::RESOLUTIONMODEL
RESOLUTIONMODEL
Definition: RawMSSignalSimulation.h:99