Simulates MS signals for a given set of peptides. More...
#include <OpenMS/SIMULATION/RawMSSignalSimulation.h>
 
  
 | Classes | |
| struct | ContaminantInfo | 
| Public Member Functions | |
| RawMSSignalSimulation & | operator= (const RawMSSignalSimulation &source) | 
| void | loadContaminants () | 
| void | generateRawSignals (FeatureMapSim &features, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, FeatureMapSim &contaminants) | 
| fill experiment with signals and noise  More... | |
| Constructors and Destructors | |
| RawMSSignalSimulation (const SimRandomNumberGenerator &rng) | |
| Constructor taking a random generator.  More... | |
| RawMSSignalSimulation (const RawMSSignalSimulation &source) | |
| Copy constructor.  More... | |
| virtual | ~RawMSSignalSimulation () | 
| Destructor.  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
|  Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor.  More... | |
| ~ProgressLogger () | |
| Destructor.  More... | |
| void | setLogType (LogType type) const | 
| Sets the progress log that should be used. The default type is NONE!  More... | |
| LogType | getLogType () const | 
| Returns the type of progress log being used.  More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const | 
| Initializes the progress display.  More... | |
| void | setProgress (SignedSize value) const | 
| Sets the current progress.  More... | |
| void | endProgress () const | 
| Ends the progress display.  More... | |
| Protected Types | |
| enum | IONIZATIONMETHOD { IM_ESI = 0, IM_MALDI = 1, IM_ALL = 2 } | 
| enum | PROFILESHAPE { RT_RECTANGULAR, RT_GAUSSIAN } | 
| enum | RESOLUTIONMODEL { RES_CONSTANT, RES_LINEAR, RES_SQRT } | 
| Protected Member Functions | |
| RawMSSignalSimulation () | |
| Default constructor.  More... | |
| void | updateMembers_ () | 
| Synchronize members with param class.  More... | |
| void | setDefaultParams_ () | 
| Set default parameters.  More... | |
| void | add1DSignal_ (Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct) | 
| Add a 1D signal for a single feature.  More... | |
| void | add2DSignal_ (Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct) | 
| Add a 2D signal for a single feature.  More... | |
| void | samplePeptideModel1D_ (const IsotopeModel &iso, const SimCoordinateType mz_start, const SimCoordinateType mz_end, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, Feature &activeFeature) | 
| Samples signals for the given 1D model.  More... | |
| void | 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) | 
| Samples signals for the given 2D model.  More... | |
| void | chooseElutionProfile_ (EGHModel *const elutionmodel, Feature &feature, const double scale, const DoubleReal rt_sampling_rate, const MSSimExperiment &experiment) | 
| Add the correct Elution profile to the passed ProductModel.  More... | |
| void | createContaminants_ (FeatureMapSim &contaminants, MSSimExperiment &exp, MSSimExperiment &exp_ct) | 
| build contaminant feature map  More... | |
| void | addShotNoise_ (MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit, SimCoordinateType maximal_mz_measurement_limit) | 
| Add shot noise to the experiment.  More... | |
| void | addWhiteNoise_ (MSSimExperiment &experiment) | 
| Add white noise to the experiment.  More... | |
| void | addDetectorNoise_ (MSSimExperiment &experiment) | 
| Add detector noise to the experiment.  More... | |
| void | addBaseLine_ (MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit) | 
| Add a base line to the experiment.  More... | |
| void | getSamplingGrid_ (std::vector< SimCoordinateType > &grid, const SimCoordinateType mz_min, const SimCoordinateType mz_max, const Int step_Da) | 
| get the mz grid where all m/z values will be mapped to  More... | |
| void | compressSignals_ (MSSimExperiment &experiment) | 
| Compress signales in a single RT scan (to merge signals which were sampled overlapping)  More... | |
| SimIntensityType | getFeatureScaledIntensity_ (const SimIntensityType feature_intensity, const SimIntensityType natural_scaling_factor) | 
| Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter natural_scaling_factor.  More... | |
| DoubleReal | getResolution_ (const DoubleReal query_mz, const DoubleReal resolution, const RESOLUTIONMODEL model) const | 
| Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z.  More... | |
| DoubleReal | getPeakWidth_ (const DoubleReal mz, const bool is_gaussian) const | 
| compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used)  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Protected Attributes | |
| Int | sampling_points_per_FWHM_ | 
| number of points sampled per peak's FWHM  More... | |
| SimCoordinateType | mz_error_mean_ | 
| Mean of peak m/z error.  More... | |
| SimCoordinateType | mz_error_stddev_ | 
| Standard deviation of peak m/z error.  More... | |
| SimIntensityType | intensity_scale_ | 
| Scaling factor of peak intensities.  More... | |
| SimIntensityType | intensity_scale_stddev_ | 
| Standard deviation of peak intensity scaling.  More... | |
| RESOLUTIONMODEL | res_model_ | 
| model of how resolution behaves with increasing m/z  More... | |
| DoubleReal | res_base_ | 
| base resolution at 400 Th  More... | |
| std::vector< SimCoordinateType > | grid_ | 
| m/z sampling grid for all signals  More... | |
| SimRandomNumberGenerator const * | rnd_gen_ | 
| Random number generator.  More... | |
| std::vector< ContaminantInfo > | contaminants_ | 
| std::vector< std::vector < double > > | threaded_random_numbers_ | 
| std::vector< Size > | threaded_random_numbers_index_ | 
| bool | contaminants_loaded_ | 
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
|  Protected Attributes inherited from ProgressLogger | |
| LogType | type_ | 
| SignedSize | begin_ | 
| SignedSize | end_ | 
| SignedSize | value_ | 
| QProgressDialog * | dlg_ | 
| StopWatch | stop_watch_ | 
| time_t | last_invoke_ | 
| Static Protected Attributes | |
| static const Size | THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500 | 
|  Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ | 
| Additional Inherited Members | |
|  Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } | 
| Possible log types.  More... | |
Simulates MS signals for a given set of peptides.
Simulates MS signals for a given set of peptides, with charge annotation, given detectabilities, predicted retention times and charge values.
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| enabled | string | true | true, false | Enable RAW signal simulation? (select 'false' if you only need feature-maps) | 
| ionization_type | string | ESI | MALDI, ESI | Type of Ionization (MALDI or ESI) | 
| peak_shape | string | Gaussian | Gaussian, Lorentzian | Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian. | 
| resolution:value | int | 50000 | Instrument resolution at 400 Th. | |
| resolution:type | string | linear | constant, linear, sqrt | How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass. | 
| baseline:scaling | float | 0 | min: 0 | Scale of baseline. Set to 0 to disable simulation of baseline. | 
| baseline:shape | float | 0.5 | min: 0 | The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x) | 
| mz:sampling_points | int | 3 | min: 2 | Number of raw data points per FWHM of the peak. | 
| contaminants:file | string | examples/simulation/contaminants.csv | Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details. | |
| variation:mz:error_stddev | float | 0 | Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors. | |
| variation:mz:error_mean | float | 0 | Average systematic m/z error (Da) | |
| variation:intensity:scale | float | 100 | min: 0 | Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file. | 
| variation:intensity:scale_stddev | float | 0 | min: 0 | Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities. | 
| noise:shot:rate | float | 0 | min: 0 | Poisson rate of shot noise per unit m/z. Set this to 0 to disable simulation of shot noise. | 
| noise:shot:intensity-mean | float | 1 | Shot noise intensity mean (exponentially distributed with given mean). | |
| noise:white:mean | float | 0 | Mean value of white noise being added to each measured signal. | |
| noise:white:stddev | float | 0 | Standard deviation of white noise being added to each measured signal. | |
| noise:detector:mean | float | 0 | Mean value of the detector noise being added to the complete measurement. | |
| noise:detector:stddev | float | 0 | Standard deviation of the detector noise being added to the complete measurement. | 
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 | protected | 
| RawMSSignalSimulation | ( | const SimRandomNumberGenerator & | rng | ) | 
Constructor taking a random generator.
| RawMSSignalSimulation | ( | const RawMSSignalSimulation & | source | ) | 
Copy constructor.
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 | virtual | 
Destructor.
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 | protected | 
Default constructor.
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 | protected | 
Add a 1D signal for a single feature.
| feature | The feature which should be simulated | 
| experiment | The experiment to which the simulated signals should be added | 
| experiment_ct | Ground truth for picked peaks | 
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 | protected | 
Add a 2D signal for a single feature.
| feature | The feature which should be simulated | 
| experiment | The experiment to which the simulated signals should be added | 
| experiment_ct | Ground truth for picked peaks | 
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 | protected | 
Add a base line to the experiment.
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 | protected | 
Add detector noise to the experiment.
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 | protected | 
Add shot noise to the experiment.
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 | protected | 
Add white noise to the experiment.
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 | protected | 
Add the correct Elution profile to the passed ProductModel.
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 | protected | 
Compress signales in a single RT scan (to merge signals which were sampled overlapping)
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 | protected | 
build contaminant feature map
| void generateRawSignals | ( | FeatureMapSim & | features, | 
| MSSimExperiment & | experiment, | ||
| MSSimExperiment & | experiment_ct, | ||
| FeatureMapSim & | contaminants | ||
| ) | 
fill experiment with signals and noise
| 
 | protected | 
Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter natural_scaling_factor. 
| feature_intensity | Intensity of the current feature. | 
| natural_scaling_factor | Additional scaling factor used by some of the sampling models. | 
| 
 | protected | 
compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used)
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 | protected | 
Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z.
| query_mz | The m/z value where the resolution should be estimated | 
| resolution | The resolution at 400 Th | 
| model | The model describing how resolution behaves, i.e. 
 | 
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 | protected | 
get the mz grid where all m/z values will be mapped to
| void loadContaminants | ( | ) | 
load the contaminants from contaminants:file param You do not have to call this function before calling generateRawSignals(), but it might be useful to check if the contaminant file is valid
| RawMSSignalSimulation& operator= | ( | const RawMSSignalSimulation & | source | ) | 
| 
 | protected | 
Samples signals for the given 1D model.
| iso | The isotope model from which the signals will be sampled | 
| mz_start | Start coordinate (in m/z dimension) of the region where the signals will be sampled | 
| mz_end | End coordinate (in m/z dimension) of the region where the signals will be sampled | 
| experiment | Experiment to which the sampled signals will be added | 
| experiment_ct | Experiment to which the centroided Ground Truth sampled signals will be added | 
| activeFeature | The current feature that is simulated | 
| 
 | protected | 
Samples signals for the given 2D model.
| pm | The product model from which the signals will be sampled | 
| mz_start | Start coordinate (in m/z dimension) of the region where the signals will be sampled | 
| mz_end | End coordinate (in m/z dimension) of the region where the signals will be sampled | 
| rt_start | Start coordinate (in rt dimension) of the region where the signals will be sampled | 
| rt_end | End coordinate (in rt dimension) of the region where the signals will be sampled | 
| experiment | Experiment to which the sampled signals will be added | 
| experiment_ct | Experiment to which the centroided Ground Truth sampled signals will be added | 
| activeFeature | The current feature that is simulated | 
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 | protected | 
Set default parameters.
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 | protectedvirtual | 
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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 | protected | 
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m/z sampling grid for all signals
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 | protected | 
Scaling factor of peak intensities.
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 | protected | 
Standard deviation of peak intensity scaling.
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Mean of peak m/z error.
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 | protected | 
Standard deviation of peak m/z error.
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base resolution at 400 Th
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model of how resolution behaves with increasing m/z
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Random number generator.
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number of points sampled per peak's FWHM
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 | staticprotected | 
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threaded_random_numbers keeps a set of random numbers for each thread simulating a feature. 
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 | protected | 
Indicates which random numbers each thread has used already and if the random number pool should be rebuild.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |