OpenMS
2.4.0
|
Abstract base class for all kinds of labeling techniques. More...
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
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 ¶m) 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 ¶m) |
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... | |
Abstract base class for all kinds of labeling techniques.
BaseLabeler | ( | ) |
constructor
|
override |
destructor
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
ConsensusMap& getConsensus | ( | ) |
|
virtual |
Returns the default parameters. Re-implement.
Re-implement if you derive a class and have to incorporate sub-algorithm default parameters.
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.
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.
target | |
source |
|
protected |
Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in maps
.
maps | Vector of FeatureMaps containing the features that will be merged |
|
pure virtual |
Labeling after detectability simulation.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Labeling between digestion and rt simulation.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Labeling after ionization.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Labeling after raw signal generation.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Labeling after Tandem MS (e.g. iTRAQ)
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Labeling after rt simulation.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
pure virtual |
Checks the (simulation) params passed if they are consistent with the labeling technique.
param | Param object containing the simulation parameters |
Exception::InvalidParameter | if the given parameters are not consistent with the labeling technique |
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
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.
simulated_features | FeatureMap containing features derived from the ones, stored in the consensus |
|
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().
|
virtual |
Set the random number generator.
Internally a pointer to the RNG is stored.
|
pure virtual |
Hook to prepare the simulation process.
Implemented in ITRAQLabeler, SILACLabeler, ICPLLabeler, O18Labeler, and LabelFreeLabeler.
|
protected |
|
protected |
|
protected |