Simulate O-18 experiments. More...

#include <OpenMS/SIMULATION/LABELING/O18Labeler.h>

Inheritance diagram for O18Labeler:

Collaboration diagram for O18Labeler:

Public Member Functions
	O18Labeler ()
	default constructor More...

	~O18Labeler () override
	destructor More...

void	preCheck (Param &param) const override
	Checks the (simulation) params passed if they are consistent with the labeling technique. More...

void	setUpHook (SimTypes::FeatureMapSimVector &) override
	Hook to prepare the simulation process. More...

void	postDigestHook (SimTypes::FeatureMapSimVector &) override
	Labeling between digestion and rt simulation. More...

void	postRTHook (SimTypes::FeatureMapSimVector &) override
	Labeling after rt simulation. More...

void	postDetectabilityHook (SimTypes::FeatureMapSimVector &) override
	Labeling after detectability simulation. More...

void	postIonizationHook (SimTypes::FeatureMapSimVector &) override
	Labeling after ionization. More...

void	postRawMSHook (SimTypes::FeatureMapSimVector &) override
	Labeling after raw signal generation. More...

void	postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
	Labeling after Tandem MS (e.g. iTRAQ) More...

Public Member Functions inherited from BaseLabeler
	BaseLabeler ()
	constructor More...

	~BaseLabeler () override
	destructor More...

virtual Param	getDefaultParameters () const
	Returns the default parameters. Re-implement. More...

virtual void	setRnd (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
	Set the random number generator. More...

ConsensusMap &	getConsensus ()

const String &	getDescription () const
	Get short description of the labeler (e.g., channels used) More...

String	getChannelIntensityName (const Size channel_index) const
	to ensure standardized meta value names across labelers for channel intensity 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...

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...

Static Public Member Functions
static BaseLabeler *	create ()
	create new object (needed by Factory) More...

static const String	getProductName ()
	name of the model (needed by Factory) More...

Static Public Member Functions inherited from BaseLabeler
static void	registerChildren ()
	register all derived classes here (implemented in file BaseLabeler_impl.h) More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
void	addModificationToPeptideHit_ (Feature &feature, const String &modification) const

Feature	mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const

Protected Member Functions inherited from BaseLabeler
SimTypes::FeatureMapSim	mergeProteinIdentificationsMaps_ (const SimTypes::FeatureMapSimVector &maps)
	Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in `maps`. More...

void	mergeProteinAccessions_ (Feature &target, const Feature &source) const
	join all protein references of two features More...

void	recomputeConsensus_ (const SimTypes::FeatureMapSim &simulated_features)
	Based on the stored consensus recompute the associations for the passed features, assuming that the features where derived from the features stored in the consensus. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Static Private Attributes
static const int	LIGHT_CHANNEL_ID_
	Map ID for the light/unlabeled channel. More...

static const int	MEDIUM_CHANNEL_ID_
	Map ID for the medium/mono-labeled channel. More...

static const int	HEAVY_CHANNEL_ID_
	Map ID for the heavy/bi-labeled channel. More...

Additional Inherited Members
Protected Attributes inherited from BaseLabeler
ConsensusMap	consensus_

SimTypes::MutableSimRandomNumberGeneratorPtr	rng_

String	channel_description_

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...

Detailed Description

Simulate O-18 experiments.

Add modified features to MS1 scans.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
labeling_efficiency	float	1.0	min: 0.0 max: 1.0	Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ O18Labeler()

O18Labeler ( )

default constructor

◆ ~O18Labeler()

~O18Labeler ( )

override

destructor

Member Function Documentation

◆ addModificationToPeptideHit_()

void addModificationToPeptideHit_	(	Feature &	feature,
		const String &	modification
	)		const

protected

◆ create()

static BaseLabeler* create ( )

inlinestatic

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

◆ mergeFeatures_()

Feature mergeFeatures_	(	Feature &	labeled_channel_feature,
		const AASequence &	unmodified_sequence,
		std::map< AASequence, Feature > &	unlabeled_features_index
	)		const

protected

◆ postDetectabilityHook()

void postDetectabilityHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Labeling after detectability simulation.

Implements BaseLabeler.

◆ postDigestHook()

void postDigestHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Labeling between digestion and rt simulation.

Implements BaseLabeler.

◆ postIonizationHook()

void postIonizationHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Labeling after ionization.

Implements BaseLabeler.

◆ postRawMSHook()

void postRawMSHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Labeling after raw signal generation.

Implements BaseLabeler.

◆ postRawTandemMSHook()

void postRawTandemMSHook	(	SimTypes::FeatureMapSimVector &	,
		SimTypes::MSSimExperiment &
	)

overridevirtual

Labeling after Tandem MS (e.g. iTRAQ)

Implements BaseLabeler.

◆ postRTHook()

void postRTHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Labeling after rt simulation.

Implements BaseLabeler.

◆ preCheck()

void preCheck ( Param & param ) const

overridevirtual

Checks the (simulation) params passed if they are consistent with the labeling technique.

Parameters

param Param object containing the simulation parameters

Exceptions

Exception::InvalidParameter if the given parameters are not consistent with the labeling technique

Implements BaseLabeler.

◆ setUpHook()

void setUpHook ( SimTypes::FeatureMapSimVector & )

overridevirtual

Hook to prepare the simulation process.

Implements BaseLabeler.

Member Data Documentation

◆ HEAVY_CHANNEL_ID_

const int HEAVY_CHANNEL_ID_

staticprivate

Map ID for the heavy/bi-labeled channel.

◆ LIGHT_CHANNEL_ID_

const int LIGHT_CHANNEL_ID_

staticprivate

Map ID for the light/unlabeled channel.

◆ MEDIUM_CHANNEL_ID_

const int MEDIUM_CHANNEL_ID_

staticprivate

Map ID for the medium/mono-labeled channel.

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ O18Labeler()

◆ ~O18Labeler()

Member Function Documentation

◆ addModificationToPeptideHit_()

◆ create()

◆ getProductName()

◆ mergeFeatures_()

◆ postDetectabilityHook()

◆ postDigestHook()

◆ postIonizationHook()

◆ postRawMSHook()

◆ postRawTandemMSHook()

◆ postRTHook()

◆ preCheck()

◆ setUpHook()

Member Data Documentation

◆ HEAVY_CHANNEL_ID_

◆ LIGHT_CHANNEL_ID_

◆ MEDIUM_CHANNEL_ID_