OpenMS
SILACLabeler Class Reference

Simulate SILAC experiments. More...

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

Inheritance diagram for SILACLabeler:
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Collaboration diagram for SILACLabeler:
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Public Member Functions

 SILACLabeler ()
 default constructor More...
 
 ~SILACLabeler () override
 destructor More...
 
void preCheck (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...
 
ConsensusMapgetConsensus ()
 
const StringgetDescription () 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 BaseLabelercreate ()
 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 String &unmodified_sequence, std::map< String, Feature > &unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const
 
Feature mergeAllChannelFeatures_ (Feature &heavy_channel_feature, const String &unmodified_feature_sequence, std::map< String, Feature > &light_channel_feature_index, std::map< String, Feature > &medium_channel_feature_index) const
 
bool canModificationBeApplied_ (const String &modification_id, const String &aa) const
 
void applyLabelToProteinHit_ (SimTypes::FeatureMapSim &protein_hit, const String &arginine_label, const String &lysine_label) const
 
void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
String getUnmodifiedSequence_ (const Feature &feature, const String &arginine_label, const String &lysine_label) 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
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

String medium_channel_lysine_label_
 
String medium_channel_arginine_label_
 
String heavy_channel_lysine_label_
 
String heavy_channel_arginine_label_
 
- 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< Stringsubsections_
 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...
 

Static Private Attributes

static const int LIGHT_FEATURE_MAPID_
 Map ID for the light/unlabeled channel. More...
 
static const int MEDIUM_FEATURE_MAPID_
 Map ID for the medium labeled channel. More...
 
static const int HEAVY_FEATURE_MAPID_
 Map ID for the heavy labeled channel. More...
 

Detailed Description

Simulate SILAC experiments.

Add modified features to MS1 scans.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
fixed_rtshift float1.0e-04 min: 0.0Fixed retention time shift between labeled peptides. If set to 0.0 only the retention times computed by the RT model step are used.
medium_channel:modification_lysine stringUniMod:481  Modification of Lysine in the medium SILAC channel
medium_channel:modification_arginine stringUniMod:188  Modification of Arginine in the medium SILAC channel
heavy_channel:modification_lysine stringUniMod:259  Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed.
heavy_channel:modification_arginine stringUniMod:267  Modification of Arginine in the heavy SILAC channel. If left empty, two-channel SILAC is assumed.

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

Constructor & Destructor Documentation

◆ SILACLabeler()

default constructor

◆ ~SILACLabeler()

~SILACLabeler ( )
override

destructor

Member Function Documentation

◆ addModificationToPeptideHit_()

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

◆ applyLabelToProteinHit_()

void applyLabelToProteinHit_ ( SimTypes::FeatureMapSim protein_hit,
const String arginine_label,
const String lysine_label 
) const
protected

◆ canModificationBeApplied_()

bool canModificationBeApplied_ ( const String modification_id,
const String aa 
) 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().

◆ getUnmodifiedSequence_()

String getUnmodifiedSequence_ ( const Feature feature,
const String arginine_label,
const String lysine_label 
) const
protected

◆ mergeAllChannelFeatures_()

Feature mergeAllChannelFeatures_ ( Feature heavy_channel_feature,
const String unmodified_feature_sequence,
std::map< String, Feature > &  light_channel_feature_index,
std::map< String, Feature > &  medium_channel_feature_index 
) const
protected

◆ mergeFeatures_()

Feature mergeFeatures_ ( Feature labeled_channel_feature,
const String unmodified_sequence,
std::map< String, Feature > &  unlabeled_features_index,
Int  index_channel_id,
Int  labeled_channel_id 
) 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
paramParam object containing the simulation parameters
Exceptions
Exception::InvalidParameterif 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.

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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

◆ heavy_channel_arginine_label_

String heavy_channel_arginine_label_
protected

◆ heavy_channel_lysine_label_

String heavy_channel_lysine_label_
protected

◆ HEAVY_FEATURE_MAPID_

const int HEAVY_FEATURE_MAPID_
staticprivate

Map ID for the heavy labeled channel.

◆ LIGHT_FEATURE_MAPID_

const int LIGHT_FEATURE_MAPID_
staticprivate

Map ID for the light/unlabeled channel.

◆ medium_channel_arginine_label_

String medium_channel_arginine_label_
protected

◆ medium_channel_lysine_label_

String medium_channel_lysine_label_
protected

◆ MEDIUM_FEATURE_MAPID_

const int MEDIUM_FEATURE_MAPID_
staticprivate

Map ID for the medium labeled channel.