Simulate ICPL experiments. More...
#include <OpenMS/SIMULATION/LABELING/ICPLLabeler.h>
Inheritance diagram for ICPLLabeler:
Public Member Functions | |
| ICPLLabeler () | |
| default constructor More... | |
| virtual | ~ICPLLabeler () |
| destructor More... | |
| void | preCheck (Param ¶m) const |
| Checks the (simulation) params passed if they are consistent with the labeling technique. More... | |
| void | setUpHook (SimTypes::FeatureMapSimVector &) |
| Hook to prepare the simulation process. More... | |
| void | postDigestHook (SimTypes::FeatureMapSimVector &) |
| Labeling between digestion and rt simulation. More... | |
| void | postRTHook (SimTypes::FeatureMapSimVector &) |
| Labeling after rt simulation. More... | |
| void | postDetectabilityHook (SimTypes::FeatureMapSimVector &) |
| Labeling after detectability simulation. More... | |
| void | postIonizationHook (SimTypes::FeatureMapSimVector &) |
| Labeling after ionization. More... | |
| void | postRawMSHook (SimTypes::FeatureMapSimVector &) |
| Labeling after raw signal generation. More... | |
| void | postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) |
| Labeling after Tandem MS (e.g. iTRAQ) More... | |
 Public Member Functions inherited from BaseLabeler | |
| BaseLabeler () | |
| constructor More... | |
| virtual | ~BaseLabeler () |
| 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 ¶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 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 |
| void | addLabelToProteinHits_ (SimTypes::FeatureMapSim &features, const String &label) const |
| Feature | mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, Map< String, Feature > &unlabeled_features_index) const |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. More... | |
| String | getUnmodifiedAASequence_ (const Feature &feature, const String &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 | light_channel_label_ |
| String | medium_channel_label_ |
| String | heavy_channel_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 ICPL experiments.
Add modified features to MS1 scans. Highly Experimental.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| ICPL_fixed_rtshift | float | 0 | Fixed retention time shift between labeled pairs. If set to 0.0 only the retention times, computed by the RT model step are used. | |
| label_proteins | string | true | true, false | Enables protein-labeling. (select 'false' if you only need peptide-labeling) |
| ICPL_light_channel_label | string | UniMod:365 | UniMod Id of the light channel ICPL label. | |
| ICPL_medium_channel_label | string | UniMod:687 | UniMod Id of the medium channel ICPL label. | |
| ICPL_heavy_channel_label | string | UniMod:364 | UniMod Id of the heavy channel ICPL label. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ ICPLLabeler()
| ICPLLabeler | ( | ) |
default constructor
◆ ~ICPLLabeler()
|
virtual |
destructor
Member Function Documentation
◆ addLabelToProteinHits_()
|
protected |
◆ addModificationToPeptideHit_()
|
protected |
◆ create()
|
inlinestatic |
create new object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
◆ getProductName()
|
inlinestatic |
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
◆ getUnmodifiedAASequence_()
◆ mergeFeatures_()
|
protected |
◆ postDetectabilityHook()
|
virtual |
Labeling after detectability simulation.
Implements BaseLabeler.
◆ postDigestHook()
|
virtual |
Labeling between digestion and rt simulation.
Implements BaseLabeler.
◆ postIonizationHook()
|
virtual |
Labeling after ionization.
Implements BaseLabeler.
◆ postRawMSHook()
|
virtual |
Labeling after raw signal generation.
Implements BaseLabeler.
◆ postRawTandemMSHook()
|
virtual |
Labeling after Tandem MS (e.g. iTRAQ)
Implements BaseLabeler.
◆ postRTHook()
|
virtual |
Labeling after rt simulation.
Implements BaseLabeler.
◆ preCheck()
|
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()
|
virtual |
Hook to prepare the simulation process.
Implements BaseLabeler.
◆ updateMembers_()
|
protectedvirtual |
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_label_
|
protected |
◆ HEAVY_FEATURE_MAPID_
|
staticprivate |
Map ID for the heavy labeled channel.
◆ light_channel_label_
|
protected |
◆ LIGHT_FEATURE_MAPID_
|
staticprivate |
Map ID for the light/unlabeled channel.
◆ medium_channel_label_
|
protected |
◆ MEDIUM_FEATURE_MAPID_
|
staticprivate |
Map ID for the medium labeled channel.