Abstract base class for all kinds of labeling techniques. More...
#include <OpenMS/SIMULATION/LABELING/LabelFreeLabeler.h>
Public Member Functions | |
| LabelFreeLabeler () | |
| default constructor More... | |
| virtual | ~LabelFreeLabeler () |
| destructor More... | |
| void | preCheck (Param ¶m) const |
| Checks the (simulation) params passed if they are consistent with the labeling technique. More... | |
| void | setUpHook (FeatureMapSimVector &) |
| Hook to prepare the simulation process. More... | |
| void | postDigestHook (FeatureMapSimVector &) |
| Labeling between digestion and rt simulation. More... | |
| void | postRTHook (FeatureMapSimVector &) |
| Labeling after rt simulation. More... | |
| void | postDetectabilityHook (FeatureMapSimVector &) |
| Labeling after detectability simulation. More... | |
| void | postIonizationHook (FeatureMapSimVector &) |
| Labeling after ionization. More... | |
| void | postRawMSHook (FeatureMapSimVector &) |
| Labeling after raw signal generation. More... | |
| void | postRawTandemMSHook (FeatureMapSimVector &, 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 (const SimRandomNumberGenerator &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 GaussModel 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... | |
Additional Inherited Members | |
Protected Member Functions inherited from BaseLabeler | |
| FeatureMapSim | mergeProteinIdentificationsMaps_ (const 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 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 inherited from BaseLabeler | |
| ConsensusMap | consensus_ |
| SimRandomNumberGenerator const * | 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.
| LabelFreeLabeler | ( | ) |
default constructor
|
virtual |
destructor
|
inlinestatic |
create new GaussModel object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
|
inlinestatic |
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
|
virtual |
Labeling after detectability simulation.
Implements BaseLabeler.
|
virtual |
Labeling between digestion and rt simulation.
Implements BaseLabeler.
|
virtual |
Labeling after ionization.
Implements BaseLabeler.
|
virtual |
Labeling after raw signal generation.
Implements BaseLabeler.
|
virtual |
Labeling after Tandem MS (e.g. iTRAQ)
Implements BaseLabeler.
|
virtual |
Labeling after rt simulation.
Implements BaseLabeler.
|
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 |
Implements BaseLabeler.
|
virtual |
Hook to prepare the simulation process.
Implements BaseLabeler.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |