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

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

Inheritance diagram for BaseLabeler:

Public Member Functions
	BaseLabeler ()
	constructor
virtual	~BaseLabeler ()
	destructor
virtual Param	getDefaultParameters () const
	Returns the default parameters. Re-implement.
virtual void	setRnd (const SimRandomNumberGenerator &rng)
	Set the random number generator.
virtual void	preCheck (Param &param) const =0
	Checks the (simulation) params passed if they are consistent with the labeling technique.
ConsensusMap &	getConsensus ()
const String &	getDescription () const
	Get short description of the labeler (channels).
String	getChannelIntensityName (const Size channel_index) const
	to ensure standardized meta value names across labelers for channel intensity
Labeling Hooks

virtual void	setUpHook (FeatureMapSimVector &)=0
	Hook to prepare the simulation process.
virtual void	postDigestHook (FeatureMapSimVector &)=0
	Labeling between digestion and rt simulation.
virtual void	postRTHook (FeatureMapSimVector &)=0
	Labeling after rt simulation.
virtual void	postDetectabilityHook (FeatureMapSimVector &)=0
	Labeling after detectability simulation.
virtual void	postIonizationHook (FeatureMapSimVector &)=0
	Labeling after ionization.
virtual void	postRawMSHook (FeatureMapSimVector &)=0
	Labeling after raw signal generation.
virtual void	postRawTandemMSHook (FeatureMapSimVector &, MSSimExperiment &)=0
	Labeling after Tandem MS (e.g. iTRAQ).
Static Public Member Functions
static void	registerChildren ()
	register all derived classes here (implemented in file BaseLabeler_impl.h)
Protected Member Functions
FeatureMapSim	mergeProteinIdentificationsMaps_ (const FeatureMapSimVector &maps)
	Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in `maps`.
void	mergeProteinAccessions_ (Feature &target, const Feature &source) const
	join all protein references of two features
void	recomputeConsensus_ (const 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.
Protected Attributes
ConsensusMap	consensus_
SimRandomNumberGenerator const *	rng_
String	channel_description_

Detailed Description

Abstract base class for all kinds of labeling techniques.

Constructor & Destructor Documentation

BaseLabeler ( )

constructor

virtual ~BaseLabeler ( ) [virtual]

destructor

Member Function Documentation

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

ConsensusMap& getConsensus ( )

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.

const String& getDescription ( ) const

Get short description of the labeler (channels).

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

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

FeatureMapSim mergeProteinIdentificationsMaps_ ( const 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

virtual void postDetectabilityHook ( FeatureMapSimVector & ) [pure virtual]

Labeling after detectability simulation.

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

virtual void postDigestHook ( FeatureMapSimVector & ) [pure virtual]

Labeling between digestion and rt simulation.

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

virtual void postIonizationHook ( FeatureMapSimVector & ) [pure virtual]

Labeling after ionization.

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

virtual void postRawMSHook ( FeatureMapSimVector & ) [pure virtual]

Labeling after raw signal generation.

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

virtual void postRawTandemMSHook	(	FeatureMapSimVector &	,
		MSSimExperiment &
	)			`[pure virtual]`

Labeling after Tandem MS (e.g. iTRAQ).

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

virtual void postRTHook ( FeatureMapSimVector & ) [pure virtual]

Labeling after rt simulation.

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

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 ICPLLabeler, ITRAQLabeler, LabelFreeLabeler, O18Labeler, and SILACLabeler.

void recomputeConsensus_ ( const 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

void registerChildren ( ) [static]

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

References ICPLLabeler::create(), SILACLabeler::create(), ITRAQLabeler::create(), O18Labeler::create(), LabelFreeLabeler::create(), ICPLLabeler::getProductName(), SILACLabeler::getProductName(), ITRAQLabeler::getProductName(), O18Labeler::getProductName(), and LabelFreeLabeler::getProductName().