Simulate O-18 experiments. More...
#include <OpenMS/SIMULATION/LABELING/O18Labeler.h>
Public Member Functions | |
| O18Labeler () | |
| default constructor | |
| virtual | ~O18Labeler () |
| destructor | |
| void | preCheck (Param ¶m) 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 AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const |
Static Private Attributes | |
| static const int | LIGHT_CHANNEL_ID_ |
| Map ID for the light/unlabeled channel. | |
| static const int | MEDIUM_CHANNEL_ID_ |
| Map ID for the medium/mono-labeled channel. | |
| static const int | HEAVY_CHANNEL_ID_ |
| Map ID for the heavy/bi-labeled channel. | |
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 | min: 0 max: 1 | 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 | ( | ) |
default constructor
| virtual ~O18Labeler | ( | ) | [virtual] |
destructor
Member Function Documentation
| void addModificationToPeptideHit_ | ( | Feature & | feature, | |
| const String & | modification | |||
| ) | 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().
| Feature mergeFeatures_ | ( | Feature & | labeled_channel_feature, | |
| const AASequence & | unmodified_sequence, | |||
| std::map< AASequence, Feature > & | unlabeled_features_index | |||
| ) | 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.
Member Data Documentation
const int HEAVY_CHANNEL_ID_ [static, private] |
Map ID for the heavy/bi-labeled channel.
const int LIGHT_CHANNEL_ID_ [static, private] |
Map ID for the light/unlabeled channel.
const int MEDIUM_CHANNEL_ID_ [static, private] |
Map ID for the medium/mono-labeled channel.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |