IDDecoyProbability Class Reference

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