#include <OpenMS/ANALYSIS/ID/BayesianProteinInferenceAlgorithm.h>

Inheritance diagram for BayesianProteinInferenceAlgorithm:

Public Member Functions
	BayesianProteinInferenceAlgorithm ()
	Constructor. More...

	~BayesianProteinInferenceAlgorithm () override=default
	Destructor. More...

void	inferPosteriorProbabilities (std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs)
	Perform inference. Writes its results into proteins (as new score) and peptides. More...

void	inferPosteriorProbabilities (const StringList &idXMLs, const String db, const ExperimentalDesign &expDesign, ProteinIdentification &proteinIDs, std::vector< PeptideIdentification > &peptideIDs)
	Load and merge ID files one by one from disk. Then perform inference. More...

void	inferPosteriorProbabilities (std::vector< PeptideIdentification > pepIdReplicates, ProteinIdentification &proteinIds, const String &db)

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Attributes
GridSearch< double, double, double >	grid {{0.008,0.032,0.128},{0.001},{0.5}}
	The grid search object initialized with a default grid. More...

std::vector< std::pair< double, Size > >	debug_times_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

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...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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< 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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Constructor & Destructor Documentation

◆ BayesianProteinInferenceAlgorithm()

BayesianProteinInferenceAlgorithm ( )

Constructor.

◆ ~BayesianProteinInferenceAlgorithm()

~BayesianProteinInferenceAlgorithm ( )

overridedefault

Destructor.

Member Function Documentation

◆ inferPosteriorProbabilities() [1/3]

void inferPosteriorProbabilities	(	std::vector< ProteinIdentification > &	proteinIDs,
		std::vector< PeptideIdentification > &	peptideIDs
	)

Perform inference. Writes its results into proteins (as new score) and peptides.

Referenced by TOPPBayesianProteinInference::main_(), and UTILProteomicsLFQ::main_().

◆ inferPosteriorProbabilities() [2/3]

void inferPosteriorProbabilities	(	const StringList &	idXMLs,
		const String	db,
		const ExperimentalDesign &	expDesign,
		ProteinIdentification &	proteinIDs,
		std::vector< PeptideIdentification > &	peptideIDs
	)

Load and merge ID files one by one from disk. Then perform inference.

◆ inferPosteriorProbabilities() [3/3]

void inferPosteriorProbabilities	(	std::vector< PeptideIdentification >	pepIdReplicates,
		ProteinIdentification &	proteinIds,
		const String &	db
	)

Member Data Documentation

◆ debug_times_

std::vector<std::pair<double,Size> > debug_times_

private

◆ grid

GridSearch<double,double,double> grid {{0.008,0.032,0.128},{0.001},{0.5}}