Simulate ICPL experiments. More...

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

Inheritance diagram for ICPLLabeler:

Public Member Functions
	ICPLLabeler ()
	default constructor
virtual	~ICPLLabeler ()
	destructor
void	preCheck (Param &param) const
	Checks the (simulation) params passed if they are consistent with the labeling technique.
void	setUpHook (FeatureMapSimVector &)
	Hook to prepare the simulation process.
void	postDigestHook (FeatureMapSimVector &)
	Labeling between digestion and rt simulation.
void	postRTHook (FeatureMapSimVector &)
	Labeling after rt simulation.
void	postDetectabilityHook (FeatureMapSimVector &)
	Labeling after detectability simulation.
void	postIonizationHook (FeatureMapSimVector &)
	Labeling after ionization.
void	postRawMSHook (FeatureMapSimVector &)
	Labeling after raw signal generation.
void	postRawTandemMSHook (FeatureMapSimVector &, MSSimExperiment &)
	Labeling after Tandem MS (e.g. iTRAQ).
Static Public Member Functions
static BaseLabeler *	create ()
	create new object (needed by Factory)
static const String	getProductName ()
	name of the model (needed by Factory)
Protected Member Functions
void	addModificationToPeptideHit_ (Feature &feature, const String &modification) const
void	addLabelToProteinHits_ (FeatureMapSim &features, const String &label) const
Feature	mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, Map< String, Feature > &unlabeled_features_index) const
void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
String	getUnmodifiedAASequence_ (const Feature &feature, const String &label) const
Protected Attributes
String	light_channel_label_
String	medium_channel_label_
String	heavy_channel_label_
Static Private Attributes
static const int	LIGHT_FEATURE_MAPID_
	Map ID for the light/unlabeled channel.
static const int	MEDIUM_FEATURE_MAPID_
	Map ID for the medium labeled channel.
static const int	HEAVY_FEATURE_MAPID_
	Map ID for the heavy labeled channel.

Detailed Description

Simulate ICPL experiments.

Add modified features to MS1 scans. Highly Experimental.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
ICPL_fixed_rtshift	float	0		Fixed retention time shift between labeled pairs. If set to 0.0 only the retention times, computed by the RT model step are used.
label_proteins	string	true	true, false	Enables protein-labeling. (select 'false' if you only need peptide-labeling)
ICPL_light_channel_label	string	UniMod:365		UniMod Id of the light channel ICPL label.
ICPL_medium_channel_label	string	UniMod:687		UniMod Id of the medium channel ICPL label.
ICPL_heavy_channel_label	string	UniMod:364		UniMod Id of the heavy channel ICPL label.

Note:

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

Constructor & Destructor Documentation

ICPLLabeler ( )

default constructor

virtual ~ICPLLabeler ( ) [virtual]

destructor

Member Function Documentation

void addLabelToProteinHits_	(	FeatureMapSim &	features,
		const String &	label
	)			const `[protected]`

void addModificationToPeptideHit_	(	Feature &	feature,
		const String &	modification
	)			const `[protected]`

static BaseLabeler* create ( ) [inline, static]

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

static const String getProductName ( ) [inline, static]

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

String getUnmodifiedAASequence_	(	const Feature &	feature,
		const String &	label
	)			const `[protected]`

Feature mergeFeatures_	(	Feature &	labeled_channel_feature,
		const AASequence &	unmodified_sequence,
		Map< String, Feature > &	unlabeled_features_index
	)			const `[protected]`

void postDetectabilityHook ( FeatureMapSimVector & ) [virtual]

Labeling after detectability simulation.

Implements BaseLabeler.

void postDigestHook ( FeatureMapSimVector & ) [virtual]

Labeling between digestion and rt simulation.

Implements BaseLabeler.

void postIonizationHook ( FeatureMapSimVector & ) [virtual]

Labeling after ionization.

Implements BaseLabeler.

void postRawMSHook ( FeatureMapSimVector & ) [virtual]

Labeling after raw signal generation.

Implements BaseLabeler.

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

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

Implements BaseLabeler.

void postRTHook ( FeatureMapSimVector & ) [virtual]

Labeling after rt simulation.

Implements BaseLabeler.

void preCheck ( Param & param ) const [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

Implements BaseLabeler.

void setUpHook ( FeatureMapSimVector & ) [virtual]

Hook to prepare the simulation process.

Implements BaseLabeler.

void updateMembers_ ( ) [protected, virtual]

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

String heavy_channel_label_ [protected]

const int HEAVY_FEATURE_MAPID_ [static, private]

Map ID for the heavy labeled channel.

String light_channel_label_ [protected]

const int LIGHT_FEATURE_MAPID_ [static, private]

Map ID for the light/unlabeled channel.

String medium_channel_label_ [protected]

const int MEDIUM_FEATURE_MAPID_ [static, private]

Map ID for the medium labeled channel.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1

ICPLLabeler Class Reference

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation