| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
DetectabilitySimulation Class Reference
Simulation

Simulates peptide detectability. More...

`#include <OpenMS/SIMULATION/DetectabilitySimulation.h>`

Inheritance diagram for DetectabilitySimulation:

## Public Member Functions

DetectabilitySimulation & | operator= (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)
Constructors and Destructors
| DetectabilitySimulation ()
| Constructor taking a random generator. More...
| DetectabilitySimulation (const DetectabilitySimulation &source)
| Copy constructor. More...
| ~DetectabilitySimulation () override
| 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 &param)
| 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_ (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...
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_ () override
| Synchronize members with param class. More...

## Private Attributes

double | 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...

## 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:

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

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ DetectabilitySimulation() [1/2]

DetectabilitySimulation | ( |  | ) |

Constructor taking a random generator.

## ◆ DetectabilitySimulation() [2/2]

DetectabilitySimulation | ( | const DetectabilitySimulation & | source | ) |

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

  features | Feature 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_ | ( |  | ) |

override private virtual

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.