MSSim Class Reference

Central class for simulation of mass spectrometry experiments. More...

#include <OpenMS/SIMULATION/MSSim.h>

Inheritance diagram for MSSim:

Public Member Functions
void	simulate (SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels &peptides)
	General purpose function to simulate a mass spectrometry run. More...
const SimTypes::MSSimExperiment &	getExperiment () const
	Access the simulated experiment. More...
const SimTypes::FeatureMapSim &	getSimulatedFeatures () const
	Access the simulated features. More...
ConsensusMap &	getChargeConsensus ()
	Access the charge consensus map of simulated features. More...
const SimTypes::FeatureMapSim &	getContaminants () const
	Access the contaminants feature map of simulated features. More...
ConsensusMap &	getLabelingConsensus ()
	Access the labeling consensus map of simulated features. More...
const SimTypes::MSSimExperiment &	getPeakMap () const
	Access the picked (centroided) experiment. More...
void	getMS2Identifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const
	Access the simulated MS2 identifications (proteins and peptides) More...
Param	getParameters () const
	Returns the default parameters for simulation including the labeling technique with name labeling_name. More...
Constructors and Destructors
	MSSim ()
	Default constructor. More...
virtual	~MSSim ()
	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 &param)
	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...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. 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 Member Functions
void	syncParams_ (Param &p, bool to_outer)
	handle global params More...
void	createFeatureMap_ (const SimTypes::SampleProteins &peptides, SimTypes::FeatureMapSim &features, Size map_index)
	Convert a list of peptides with given abundance values into a FeatureMap. More...
void	updateMembers_ ()
	Synchronize members with param class. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Attributes
SimTypes::MSSimExperiment	experiment_
	Holds the simulated data. More...
SimTypes::MSSimExperiment	peak_map_
	Holds the ground-truth on generated peaks positions and intensities. More...
SimTypes::FeatureMapSimVector	feature_maps_
	Holds the ground-truth on generated features. More...
ConsensusMap	consensus_map_
	Holds consensus ground-truth about the charge associations. More...
SimTypes::FeatureMapSim	contaminants_map_
	Holds the ground-truth on generated contaminants. More...
BaseLabeler *	labeler_
	Labeling functionality. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
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_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Central class for simulation of mass spectrometry experiments.

This implementation is an extended and rewritten version of the concepts and ideas presented in:

Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gropl, Oliver Kohlbacher, and Knut Reinert.
LC-MSsim - A simulation software for liquid chromatography mass spectrometry data.
BMC Bioinformatics 9:423, 2008.

See also

DetectabilitySimulation

DigestSimulation

IonizationSimulation

RawMSSignalSimulation

RTSimulation

Constructor & Destructor Documentation

MSSim

(

)

Default constructor.

virtual ~MSSim ( )

virtual

Destructor.

Member Function Documentation

void createFeatureMap_ ( const SimTypes::SampleProteins &  peptides, SimTypes::FeatureMapSim &  features, Size  map_index  )

protected

Convert a list of peptides with given abundance values into a FeatureMap.

ConsensusMap& getChargeConsensus

(

)

Access the charge consensus map of simulated features.

const SimTypes::FeatureMapSim& getContaminants

(

)

const

Access the contaminants feature map of simulated features.

const SimTypes::MSSimExperiment& getExperiment

(

)

const

Access the simulated experiment.

ConsensusMap& getLabelingConsensus

(

)

Access the labeling consensus map of simulated features.

void getMS2Identifications	(	std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides
	)		const

Access the simulated MS2 identifications (proteins and peptides)

Parameters

proteins	Will be filled with a single ProteinIdentification holding all ProteinHits used in the simulated MS2 spectra.
peptides	Will be filled with PeptideIdentifications for each simulated MS2 spectra holding all contributing peptides scored by their intensity contribution.

Param getParameters

(

)

const

Returns the default parameters for simulation including the labeling technique with name labeling_name.

const SimTypes::MSSimExperiment& getPeakMap

(

)

const

Access the picked (centroided) experiment.

const SimTypes::FeatureMapSim& getSimulatedFeatures

(

)

const

Access the simulated features.

void simulate	(	SimTypes::MutableSimRandomNumberGeneratorPtr	rnd_gen,
		SimTypes::SampleChannels &	peptides
	)

General purpose function to simulate a mass spectrometry run.

Parameters

rnd_gen	random number generator which will be passed to the different classes
peptides	List of peptides and abundances that will be simulated

void syncParams_ ( Param &  p, bool  to_outer  )

protected

handle global params

void updateMembers_ ( )

protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

ConsensusMap consensus_map_

private

Holds consensus ground-truth about the charge associations.

SimTypes::FeatureMapSim contaminants_map_

private

Holds the ground-truth on generated contaminants.

SimTypes::MSSimExperiment experiment_

private

Holds the simulated data.

SimTypes::FeatureMapSimVector feature_maps_

private

Holds the ground-truth on generated features.

BaseLabeler* labeler_

private

Labeling functionality.

SimTypes::MSSimExperiment peak_map_

private

Holds the ground-truth on generated peaks positions and intensities.