Simulates peptide detectability. More...
#include <OpenMS/SIMULATION/DetectabilitySimulation.h>
Public Member Functions | |
| DetectabilitySimulation & | operator= (const DetectabilitySimulation &source) |
| Assignment operator. More... | |
| void | filterDetectability (FeatureMapSim &features) |
| Filters the given peptide features for detectibility. More... | |
| void | predictDetectabilities (std::vector< String > &peptides_vector, std::vector< DoubleReal > &labels, std::vector< DoubleReal > &detectabilities) |
Constructors and Destructors | |
| DetectabilitySimulation () | |
| Constructor taking a random generator. More... | |
| DetectabilitySimulation (const DetectabilitySimulation &source) | |
| Copy constructor. More... | |
| virtual | ~DetectabilitySimulation () |
| Destructor. 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... | |
Protected Member Functions | |
| void | svmFilter_ (FeatureMapSim &) |
| Filter the feature map using a svm model. More... | |
| void | noFilter_ (FeatureMapSim &) |
| Do not filter the feature map, just set the detectability to a default value. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Private Member Functions | |
| void | setDefaultParams_ () |
| Set default parameters. More... | |
| void | updateMembers_ () |
| Synchronize members with param class. More... | |
Private Attributes | |
| DoubleReal | min_detect_ |
| Minimum allowed detectability likelihood of a peptide. More... | |
| OpenMS::String | dt_model_file_ |
| Name of the svm model file. More... | |
Additional Inherited Members | |
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... | |
Simulates peptide detectability.
The peptide detectability is predicted based on a support-vector machine. Alternativly the detectability can be set to a default value for all peptides if no model is given.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| dt_simulation_on | string | false | true, false | Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count |
| min_detect | float | 0.5 | Minimum peptide detectability accepted. Peptides with a lower score will be removed | |
| dt_model_file | string | examples/simulation/DTPredict.model | SVM model for peptide detectability prediction |
Constructor taking a random generator.
| DetectabilitySimulation | ( | const DetectabilitySimulation & | source | ) |
Copy constructor.
|
virtual |
Destructor.
| void filterDetectability | ( | FeatureMapSim & | features | ) |
Filters the given peptide features for detectibility.
Based on the provided method (SVM or simple) all peptide features are removed that do not have a sufficient peptide detectibility.
| features | Feature map that will be filtered for detectibility |
|
protected |
Do not filter the feature map, just set the detectability to a default value.
| DetectabilitySimulation& operator= | ( | const DetectabilitySimulation & | source | ) |
Assignment operator.
| void predictDetectabilities | ( | std::vector< String > & | peptides_vector, |
| std::vector< DoubleReal > & | labels, | ||
| std::vector< DoubleReal > & | detectabilities | ||
| ) |
|
private |
Set default parameters.
|
protected |
Filter the feature map using a svm model.
|
privatevirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
|
private |
Name of the svm model file.
|
private |
Minimum allowed detectability likelihood of a peptide.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |