OpenMS
BaseLabeler Class Referenceabstract

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

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

Inheritance diagram for BaseLabeler:
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Collaboration diagram for BaseLabeler:
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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...
 
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 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...
 
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...
 
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< 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...
 

Detailed Description

Abstract base class for all kinds of labeling techniques.

Constructor & Destructor Documentation

◆ 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
mapsVector 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
paramParam object containing the simulation parameters
Exceptions
Exception::InvalidParameterif 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_featuresFeatureMap containing features derived from the ones, stored in the consensus

◆ registerChildren()

◆ 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_