| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | List of all members
IDDecoyProbability Class Reference
Analysis » Identification

IDDecoyProbability calculates probabilities using decoy approach. More...

`#include <OpenMS/ANALYSIS/ID/IDDecoyProbability.h>`

Inheritance diagram for IDDecoyProbability:

## Classes

struct | Transformation_
| struct to be used to store a transformation (used for fitting) More...

## Public Member Functions

| IDDecoyProbability ()
| Default constructor. More...
| IDDecoyProbability (const IDDecoyProbability &rhs)
| Copy constructor. More...
| ~IDDecoyProbability () override
| Destructor. More...
IDDecoyProbability & | operator= (const IDDecoyProbability &rhs)
| assignment operator More...
void | apply (std::vector< PeptideIdentification > &prob_ids, const std::vector< PeptideIdentification > &fwd_ids, const std::vector< PeptideIdentification > &rev_ids)
void | apply (std::vector< PeptideIdentification > &ids)
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 | normalizeBins_ (const std::vector< double > &scores, std::vector< double > &binned, Transformation_ &trafo)
double | getProbability_ (const Math::GammaDistributionFitter::GammaDistributionFitResult &result_gamma, const Transformation_ &gamma_trafo, const Math::GaussFitter::GaussFitResult &result_gauss, const Transformation_ &gauss_trafo, double score)
void | generateDistributionImage_ (const std::vector< double > &ids, const String &formula, const String &filename)
void | generateDistributionImage_ (const std::vector< double > &all_ids, const Transformation_ &all_trans, const String &fwd_formula, const String &rev_formula, const String &filename)
void | apply_ (std::vector< PeptideIdentification > &ids, const std::vector< double > &rev_scores, const std::vector< double > &fwd_scores, const std::vector< double > &all_scores)
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...

## 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

IDDecoyProbability calculates probabilities using decoy approach.

This class calculates the probabilities using a target decoy approach. Like in peptide prophet the forward distribution is modeled using a gaussian distribution the reverse scores are modeled using a gamma distribution.

## Constructor & Destructor Documentation

## ◆ IDDecoyProbability() [1/2]

IDDecoyProbability | ( |  | ) |

Default constructor.

## ◆ IDDecoyProbability() [2/2]

IDDecoyProbability | ( | const IDDecoyProbability & | rhs | ) |

Copy constructor.

## ◆ ~IDDecoyProbability()

~IDDecoyProbability | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ apply() [1/2]

void apply | ( | std::vector< PeptideIdentification > & | prob_ids,
|  | const std::vector< PeptideIdentification > & | fwd_ids,
|  | const std::vector< PeptideIdentification > & | rev_ids
| ) |  |

converts the forward and reverse identification into probabilities

Parameters

  prob_ids | Output of the algorithm which includes identifications with probability based scores
  fwd_ids | Input parameter which represents the identifications of the forward search
  rev_ids | Input parameter which represents the identifications of the reversed search

## ◆ apply() [2/2]

void apply | ( | std::vector< PeptideIdentification > & | ids | ) |

## ◆ apply_()

void apply_ | ( | std::vector< PeptideIdentification > & | ids,
|  | const std::vector< double > & | rev_scores,
|  | const std::vector< double > & | fwd_scores,
|  | const std::vector< double > & | all_scores
| ) |  |

protected

## ◆ generateDistributionImage_() [1/2]

void generateDistributionImage_ | ( | const std::vector< double > & | ids,
|  | const String & | formula,
|  | const String & | filename
| ) |  |

protected

## ◆ generateDistributionImage_() [2/2]

void generateDistributionImage_ | ( | const std::vector< double > & | all_ids,
|  | const Transformation_ & | all_trans,
|  | const String & | fwd_formula,
|  | const String & | rev_formula,
|  | const String & | filename
| ) |  |

protected

## ◆ getProbability_()

double getProbability_ | ( | const Math::GammaDistributionFitter::GammaDistributionFitResult & | result_gamma,
|  | const Transformation_ & | gamma_trafo,
|  | const Math::GaussFitter::GaussFitResult & | result_gauss,
|  | const Transformation_ & | gauss_trafo,
|  | double | score
| ) |  |

protected

## ◆ normalizeBins_()

void normalizeBins_ | ( | const std::vector< double > & | scores,
|  | std::vector< double > & | binned,
|  | Transformation_ & | trafo
| ) |  |

protected

## ◆ operator=()

IDDecoyProbability& operator= | ( | const IDDecoyProbability & | rhs | ) |

assignment operator