| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Private Attributes | List of all members
O18Labeler Class Reference

Simulate O-18 experiments. More...

`#include <OpenMS/SIMULATION/LABELING/O18Labeler.h>`

Inheritance diagram for O18Labeler:

## Public Member Functions

| O18Labeler ()
| default constructor More...
| ~O18Labeler () override
| destructor More...
void | preCheck (Param &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 AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) 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
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...

## Static Private Attributes

static const int | LIGHT_CHANNEL_ID_
| Map ID for the light/unlabeled channel. More...
static const int | MEDIUM_CHANNEL_ID_
| Map ID for the medium/mono-labeled channel. More...
static const int | HEAVY_CHANNEL_ID_
| Map ID for the heavy/bi-labeled channel. More...

## Additional Inherited Members

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...

## Detailed Description

Simulate O-18 experiments.

Add modified features to MS1 scans.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
labeling_efficiency | float | 1.0 | min: 0.0 max: 1.0 | Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)

Note:

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

## Constructor & Destructor Documentation

## ◆ O18Labeler()

O18Labeler | ( |  | ) |

default constructor

## ◆ ~O18Labeler()

~O18Labeler | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addModificationToPeptideHit_()

void addModificationToPeptideHit_ | ( | Feature & | feature,
|  | const String & | modification
| ) |  | const

protected

## ◆ create()

static BaseLabeler* create | ( |  | ) |

inline static

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

## ◆ mergeFeatures_()

Feature mergeFeatures_ | ( | Feature & | labeled_channel_feature,
|  | const AASequence & | unmodified_sequence,
|  | std::map< AASequence, Feature > & | unlabeled_features_index
| ) |  | const

protected

## ◆ postDetectabilityHook()

void postDetectabilityHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling after detectability simulation.

Implements BaseLabeler.

## ◆ postDigestHook()

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

override virtual

Labeling between digestion and rt simulation.

Implements BaseLabeler.

## ◆ postIonizationHook()

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

override virtual

Labeling after ionization.

Implements BaseLabeler.

## ◆ postRawMSHook()

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

override virtual

Labeling after raw signal generation.

Implements BaseLabeler.

## ◆ postRawTandemMSHook()

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

override virtual

Labeling after Tandem MS (e.g. iTRAQ)

Implements BaseLabeler.

## ◆ postRTHook()

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

override virtual

Labeling after rt simulation.

Implements BaseLabeler.

## ◆ preCheck()

void preCheck | ( | Param & | param | ) | const

override 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.

## ◆ setUpHook()

void setUpHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Hook to prepare the simulation process.

Implements BaseLabeler.

## Member Data Documentation

## ◆ HEAVY_CHANNEL_ID_

const int HEAVY_CHANNEL_ID_

static private

Map ID for the heavy/bi-labeled channel.

## ◆ LIGHT_CHANNEL_ID_

const int LIGHT_CHANNEL_ID_

static private

Map ID for the light/unlabeled channel.

## ◆ MEDIUM_CHANNEL_ID_

const int MEDIUM_CHANNEL_ID_

static private

Map ID for the medium/mono-labeled channel.