Simulate SILAC experiments. More...
#include <OpenMS/SIMULATION/LABELING/SILACLabeler.h>
Inheritance diagram for SILACLabeler:
Public Member Functions | |
| SILACLabeler () | |
| default constructor | |
| virtual | ~SILACLabeler () |
| destructor | |
| void | preCheck (Param &) const |
| Checks the (simulation) params passed if they are consistent with the labeling technique. | |
| void | setUpHook (FeatureMapSimVector &) |
| Hook to prepare the simulation process. | |
| void | postDigestHook (FeatureMapSimVector &) |
| Labeling between digestion and rt simulation. | |
| void | postRTHook (FeatureMapSimVector &) |
| Labeling after rt simulation. | |
| void | postDetectabilityHook (FeatureMapSimVector &) |
| Labeling after detectability simulation. | |
| void | postIonizationHook (FeatureMapSimVector &) |
| Labeling after ionization. | |
| void | postRawMSHook (FeatureMapSimVector &) |
| Labeling after raw signal generation. | |
| void | postRawTandemMSHook (FeatureMapSimVector &, MSSimExperiment &) |
| Labeling after Tandem MS (e.g. iTRAQ). | |
Static Public Member Functions | |
| static BaseLabeler * | create () |
| create new object (needed by Factory) | |
| static const String | getProductName () |
| name of the model (needed by Factory) | |
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_ (FeatureMapSim &protein_hit, const String &arginine_label, const String &lysine_label) const |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. | |
| String | getUnmodifiedSequence_ (const Feature &feature, const String &arginine_label, const String &lysine_label) const |
Protected Attributes | |
| String | medium_channel_lysine_label_ |
| String | medium_channel_arginine_label_ |
| String | heavy_channel_lysine_label_ |
| String | heavy_channel_arginine_label_ |
Static Private Attributes | |
| static const int | LIGHT_FEATURE_MAPID_ |
| Map ID for the light/unlabeled channel. | |
| static const int | MEDIUM_FEATURE_MAPID_ |
| Map ID for the medium labeled channel. | |
| static const int | HEAVY_FEATURE_MAPID_ |
| Map ID for the heavy labeled channel. | |
Detailed Description
Simulate SILAC experiments.
Add modified features to MS1 scans.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| fixed_rtshift | float | 0.0001 | min: 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 | ( | ) |
default constructor
| virtual ~SILACLabeler | ( | ) | [virtual] |
destructor
Member Function Documentation
| void addModificationToPeptideHit_ | ( | Feature & | feature, | |
| const String & | modification | |||
| ) | const [protected] |
| void applyLabelToProteinHit_ | ( | FeatureMapSim & | protein_hit, | |
| const String & | arginine_label, | |||
| const String & | lysine_label | |||
| ) | const [protected] |
| bool canModificationBeApplied_ | ( | const String & | modification_id, | |
| const String & | aa | |||
| ) | const [protected] |
| static BaseLabeler* create | ( | ) | [inline, static] |
create new object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
| static const String getProductName | ( | ) | [inline, static] |
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
| String getUnmodifiedSequence_ | ( | const Feature & | feature, | |
| const String & | arginine_label, | |||
| const String & | lysine_label | |||
| ) | const [protected] |
| 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] |
| 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] |
| void postDetectabilityHook | ( | FeatureMapSimVector & | ) | [virtual] |
Labeling after detectability simulation.
Implements BaseLabeler.
| void postDigestHook | ( | FeatureMapSimVector & | ) | [virtual] |
Labeling between digestion and rt simulation.
Implements BaseLabeler.
| void postIonizationHook | ( | FeatureMapSimVector & | ) | [virtual] |
Labeling after ionization.
Implements BaseLabeler.
| void postRawMSHook | ( | FeatureMapSimVector & | ) | [virtual] |
Labeling after raw signal generation.
Implements BaseLabeler.
| void postRawTandemMSHook | ( | FeatureMapSimVector & | , | |
| MSSimExperiment & | ||||
| ) | [virtual] |
Labeling after Tandem MS (e.g. iTRAQ).
Implements BaseLabeler.
| void postRTHook | ( | FeatureMapSimVector & | ) | [virtual] |
Labeling after rt simulation.
Implements BaseLabeler.
| void preCheck | ( | Param & | param | ) | const [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.
| void setUpHook | ( | FeatureMapSimVector & | ) | [virtual] |
Hook to prepare the simulation process.
Implements BaseLabeler.
| void updateMembers_ | ( | ) | [protected, virtual] |
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
String heavy_channel_arginine_label_ [protected] |
String heavy_channel_lysine_label_ [protected] |
const int HEAVY_FEATURE_MAPID_ [static, private] |
Map ID for the heavy labeled channel.
const int LIGHT_FEATURE_MAPID_ [static, private] |
Map ID for the light/unlabeled channel.
String medium_channel_arginine_label_ [protected] |
String medium_channel_lysine_label_ [protected] |
const int MEDIUM_FEATURE_MAPID_ [static, private] |
Map ID for the medium labeled channel.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |