OpenMS
2.5.0
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Abstract base class for all kinds of labeling techniques. More...
#include <OpenMS/SIMULATION/LABELING/LabelFreeLabeler.h>
Public Member Functions | |
LabelFreeLabeler () | |
default constructor More... | |
~LabelFreeLabeler () override | |
destructor More... | |
void | preCheck (Param ¶m) const override |
Checks the (simulation) params passed if they are consistent with the labeling technique. More... | |
void | setUpHook (SimTypes::FeatureMapSimVector &) override |
Hook to prepare the simulation process. More... | |
void | postDigestHook (SimTypes::FeatureMapSimVector &) override |
Labeling between digestion and rt simulation. More... | |
void | postRTHook (SimTypes::FeatureMapSimVector &) override |
Labeling after rt simulation. More... | |
void | postDetectabilityHook (SimTypes::FeatureMapSimVector &) override |
Labeling after detectability simulation. More... | |
void | postIonizationHook (SimTypes::FeatureMapSimVector &) override |
Labeling after ionization. More... | |
void | postRawMSHook (SimTypes::FeatureMapSimVector &) override |
Labeling after raw signal generation. More... | |
void | postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override |
Labeling after Tandem MS (e.g. iTRAQ) More... | |
Public Member Functions inherited from BaseLabeler | |
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... | |
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 | |
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 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... | |
Abstract base class for all kinds of labeling techniques.
LabelFreeLabeler | ( | ) |
default constructor
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override |
destructor
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inlinestatic |
create new GaussModel object (needed by Factory)
Referenced by BaseLabeler::registerChildren().
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inlinestatic |
name of the model (needed by Factory)
Referenced by BaseLabeler::registerChildren().
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overridevirtual |
Labeling after detectability simulation.
Implements BaseLabeler.
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overridevirtual |
Labeling between digestion and rt simulation.
Implements BaseLabeler.
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overridevirtual |
Labeling after ionization.
Implements BaseLabeler.
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overridevirtual |
Labeling after raw signal generation.
Implements BaseLabeler.
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overridevirtual |
Labeling after Tandem MS (e.g. iTRAQ)
Implements BaseLabeler.
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overridevirtual |
Labeling after rt simulation.
Implements BaseLabeler.
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overridevirtual |
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.
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overridevirtual |
Hook to prepare the simulation process.
Implements BaseLabeler.