Abstract base class for all kinds of labeling techniques. More...

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

Inheritance diagram for BaseLabeler:

Collaboration diagram for BaseLabeler:

Public Member Functions
	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...

virtual void	preCheck (Param &param) const =0
	Checks the (simulation) params passed if they are consistent with the labeling technique. 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...

Static Public Member Functions
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...

Labeling Hooks
ConsensusMap	consensus_

SimTypes::MutableSimRandomNumberGeneratorPtr	rng_

String	channel_description_

virtual void	setUpHook (SimTypes::FeatureMapSimVector &)=0
	Hook to prepare the simulation process. More...

virtual void	postDigestHook (SimTypes::FeatureMapSimVector &)=0
	Labeling between digestion and rt simulation. More...

virtual void	postRTHook (SimTypes::FeatureMapSimVector &)=0
	Labeling after rt simulation. More...

virtual void	postDetectabilityHook (SimTypes::FeatureMapSimVector &)=0
	Labeling after detectability simulation. More...

virtual void	postIonizationHook (SimTypes::FeatureMapSimVector &)=0
	Labeling after ionization. More...

virtual void	postRawMSHook (SimTypes::FeatureMapSimVector &)=0
	Labeling after raw signal generation. More...

virtual void	postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &)=0
	Labeling after Tandem MS (e.g. iTRAQ) 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...

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...

Additional Inherited Members
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...

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

Abstract base class for all kinds of labeling techniques.

Constructor & Destructor Documentation

◆ BaseLabeler()

BaseLabeler ( )

constructor

◆ ~BaseLabeler()

~BaseLabeler ( )

override

destructor

Member Function Documentation

◆ getChannelIntensityName()

String getChannelIntensityName ( const Size channel_index ) const

to ensure standardized meta value names across labelers for channel intensity

Use this function to get the name of the meta value which holds intensity for channel channel_index

◆ getConsensus()

ConsensusMap& getConsensus ( )

◆ getDefaultParameters()

virtual Param getDefaultParameters ( ) const

virtual

Returns the default parameters. Re-implement.

Re-implement if you derive a class and have to incorporate sub-algorithm default parameters.

◆ getDescription()

const String& getDescription ( ) const

Get short description of the labeler (e.g., channels used)

Used to add a short description to the labeling section within the INI file.

◆ mergeProteinAccessions_()

void mergeProteinAccessions_	(	Feature &	target,
		const Feature &	source
	)		const

protected

join all protein references of two features

When merging peptides from different channels, the protein accessions should remain intact. Usually joining features is based on peptide sequence, so all protein hits should be valid.

Parameters

target
source

◆ mergeProteinIdentificationsMaps_()

SimTypes::FeatureMapSim mergeProteinIdentificationsMaps_ ( const SimTypes::FeatureMapSimVector & maps )

protected

Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in maps.

Parameters

maps	Vector of FeatureMaps containing the features that will be merged

Returns: A FeatureMap containing all ProteinIdentifications of the input maps

◆ postDetectabilityHook()

virtual void postDetectabilityHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Labeling after detectability simulation.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ postDigestHook()

virtual void postDigestHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Labeling between digestion and rt simulation.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ postIonizationHook()

virtual void postIonizationHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Labeling after ionization.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ postRawMSHook()

virtual void postRawMSHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Labeling after raw signal generation.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ postRawTandemMSHook()

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

pure virtual

Labeling after Tandem MS (e.g. iTRAQ)

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ postRTHook()

virtual void postRTHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Labeling after rt simulation.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

◆ preCheck()

virtual void preCheck ( Param & param ) const

pure virtual

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

Implemented in O18Labeler, LabelFreeLabeler, ITRAQLabeler, ICPLLabeler, and SILACLabeler.

◆ recomputeConsensus_()

void recomputeConsensus_ ( const SimTypes::FeatureMapSim & simulated_features )

protected

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.

Parameters

simulated_features FeatureMap containing features derived from the ones, stored in the consensus

◆ registerChildren()

void registerChildren ( )

static

register all derived classes here (implemented in file BaseLabeler_impl.h)

References ICPLLabeler::create(), ITRAQLabeler::create(), LabelFreeLabeler::create(), O18Labeler::create(), SILACLabeler::create(), ICPLLabeler::getProductName(), ITRAQLabeler::getProductName(), LabelFreeLabeler::getProductName(), O18Labeler::getProductName(), SILACLabeler::getProductName(), and Factory< FactoryProduct >::registerProduct().

◆ setRnd()

virtual void setRnd ( SimTypes::MutableSimRandomNumberGeneratorPtr rng )

virtual

Set the random number generator.

Internally a pointer to the RNG is stored.

◆ setUpHook()

virtual void setUpHook ( SimTypes::FeatureMapSimVector & )

pure virtual

Hook to prepare the simulation process.

Implemented in SILACLabeler, O18Labeler, LabelFreeLabeler, ITRAQLabeler, and ICPLLabeler.

Member Data Documentation

◆ channel_description_

String channel_description_

protected

◆ consensus_

ConsensusMap consensus_

protected

◆ rng_

SimTypes::MutableSimRandomNumberGeneratorPtr rng_

protected

Public Member Functions

Static Public Member Functions

Labeling Hooks

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BaseLabeler()

◆ ~BaseLabeler()

Member Function Documentation

◆ getChannelIntensityName()

◆ getConsensus()

◆ getDefaultParameters()

◆ getDescription()

◆ mergeProteinAccessions_()

◆ mergeProteinIdentificationsMaps_()

◆ postDetectabilityHook()

◆ postDigestHook()

◆ postIonizationHook()

◆ postRawMSHook()

◆ postRawTandemMSHook()

◆ postRTHook()

◆ preCheck()

◆ recomputeConsensus_()

◆ registerChildren()

◆ setRnd()

◆ setUpHook()

Member Data Documentation

◆ channel_description_

◆ consensus_

◆ rng_