| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BaseLabeler Class Referenceabstract

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 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...
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...
Labeling Hooks
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...
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...

## Protected Member Functions

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
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

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< 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 ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.

## ◆ postDigestHook()

virtual void postDigestHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

pure virtual

Labeling between digestion and rt simulation.

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

## ◆ postIonizationHook()

virtual void postIonizationHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

pure virtual

Labeling after ionization.

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

## ◆ postRawMSHook()

virtual void postRawMSHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

pure virtual

Labeling after raw signal generation.

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

## ◆ postRawTandemMSHook()

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

pure virtual

Labeling after Tandem MS (e.g. iTRAQ)

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

## ◆ postRTHook()

virtual void postRTHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

pure virtual

Labeling after rt simulation.

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

## ◆ 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 ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.

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

## Member Data Documentation

## ◆ channel_description_

String channel_description_

protected

## ◆ consensus_

ConsensusMap consensus_

protected

## ◆ rng_

SimTypes::MutableSimRandomNumberGeneratorPtr rng_

protected