OpenMS  2.8.0
List of all members
DetectabilitySimulation Class Reference

Simulates peptide detectability. More...

#include <OpenMS/SIMULATION/DetectabilitySimulation.h>

Inheritance diagram for DetectabilitySimulation:
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Collaboration diagram for DetectabilitySimulation:
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Constructors and Destructors

double min_detect_
 Minimum allowed detectability likelihood of a peptide. More...
 
OpenMS::String dt_model_file_
 Name of the svm model file. More...
 
 DetectabilitySimulation ()
 Constructor taking a random generator. More...
 
 DetectabilitySimulation (const DetectabilitySimulation &source)
 Copy constructor. More...
 
 ~DetectabilitySimulation () override
 Destructor. More...
 
DetectabilitySimulationoperator= (const DetectabilitySimulation &source)
 Assignment operator. More...
 
void filterDetectability (SimTypes::FeatureMapSim &features)
 Filters the given peptide features for detectability. More...
 
void predictDetectabilities (std::vector< String > &peptides_vector, std::vector< double > &labels, std::vector< double > &detectabilities)
 
void setDefaultParams_ ()
 Set default parameters. More...
 
void updateMembers_ () override
 Synchronize members with param class. More...
 
void svmFilter_ (SimTypes::FeatureMapSim &)
 Filter the feature map using a svm model. More...
 
void noFilter_ (SimTypes::FeatureMapSim &)
 Do not filter the feature map, just set the detectability to a default value. More...
 

Additional Inherited Members

- 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- 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< Stringsubsections_
 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...
 

Detailed Description

Simulates peptide detectability.

The peptide detectability is predicted based on a support-vector machine. Alternatively the detectability can be set to a default value for all peptides if no model is given.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
dt_simulation_on stringfalse true, falseModelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count
min_detect float0.5  Minimum peptide detectability accepted. Peptides with a lower score will be removed
dt_model_file stringSIMULATION/DTPredict.model  SVM model for peptide detectability prediction

Note:

Constructor & Destructor Documentation

◆ DetectabilitySimulation() [1/2]

Constructor taking a random generator.

◆ DetectabilitySimulation() [2/2]

Copy constructor.

◆ ~DetectabilitySimulation()

~DetectabilitySimulation ( )
override

Destructor.

Member Function Documentation

◆ filterDetectability()

void filterDetectability ( SimTypes::FeatureMapSim features)

Filters the given peptide features for detectability.

Based on the provided method (SVM or simple) all peptide features are removed that do not have a sufficient peptide detectability.

Parameters
featuresFeature map that will be filtered for detectability

◆ noFilter_()

void noFilter_ ( SimTypes::FeatureMapSim )
protected

Do not filter the feature map, just set the detectability to a default value.

◆ operator=()

DetectabilitySimulation& operator= ( const DetectabilitySimulation source)

Assignment operator.

◆ predictDetectabilities()

void predictDetectabilities ( std::vector< String > &  peptides_vector,
std::vector< double > &  labels,
std::vector< double > &  detectabilities 
)

◆ setDefaultParams_()

void setDefaultParams_ ( )
private

Set default parameters.

◆ svmFilter_()

void svmFilter_ ( SimTypes::FeatureMapSim )
protected

Filter the feature map using a svm model.

◆ updateMembers_()

void updateMembers_ ( )
overrideprivatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ dt_model_file_

OpenMS::String dt_model_file_
private

Name of the svm model file.

◆ min_detect_

double min_detect_
private

Minimum allowed detectability likelihood of a peptide.