OpenMS: SILACLabeler Class Reference

| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Static Private Attributes | List of all members
SILACLabeler Class Reference

Simulate SILAC experiments. More...

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

Inheritance diagram for SILACLabeler:

## 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...
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...
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 BaseLabeler * | create ()
| 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...

## Protected Member Functions

void | addModificationToPeptideHit_ (Feature &feature, const String &modification) const
Feature | mergeFeatures_ (Feature &labeled_channel_feature, const String &unmodified_sequence, 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, Map< String, Feature > &light_channel_feature_index, 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< 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...

## 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:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
fixed_rtshift | float | 1.0e-04 | min: 0.0 | Fixed 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 | string | UniMod:481 |  | Modification of Lysine in the medium SILAC channel
medium_channel:modification_arginine | string | UniMod:188 |  | Modification of Arginine in the medium SILAC channel
heavy_channel:modification_lysine | string | UniMod:259 |  | Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed.
heavy_channel:modification_arginine | string | UniMod: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()

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,
|  | Map< String, Feature > & | light_channel_feature_index,
|  | Map< String, Feature > & | medium_channel_feature_index
| ) |  | const

protected

## ◆ mergeFeatures_()

Feature mergeFeatures_ | ( | Feature & | labeled_channel_feature,
|  | const String & | unmodified_sequence,
|  | 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

  param | Param object containing the simulation parameters

Exceptions

  Exception::InvalidParameter | if 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.