The base class of all element group finding algorithms. More...

#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>

Inheritance diagram for BaseGroupFinder:

Collaboration diagram for BaseGroupFinder:

Public Member Functions
	BaseGroupFinder ()
	Default constructor. More...

	~BaseGroupFinder () override
	Destructor. More...

virtual void	run (const std::vector< ConsensusMap > &input, ConsensusMap &result)=0
	Run the algorithm. 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...

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...

virtual	~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 (UInt64 bytes_processed=0) const

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

Static Public Member Functions
static void	registerChildren ()
	Register all derived classes here. 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
void	checkIds_ (const std::vector< ConsensusMap > &maps) const
	Checks if all file descriptions have disjoint map identifiers. 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...

Private Member Functions
	BaseGroupFinder (const BaseGroupFinder &)
	Copy constructor intentionally not implemented. More...

BaseGroupFinder &	operator= (const BaseGroupFinder &)
	Assignment operator intentionally not implemented. More...

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

Detailed Description

The base class of all element group finding algorithms.

This class defines the basic interface for all element group finding algorithms.

All derived algorithms take one or several consensus maps and find corresponding features across the maps (or within one map). They return one consensus map containing the found consensus features.

The element indices of the result consensus features are the container access indices of the input maps. The map indices of the result consensus features are are the indices in the input map vector.

Constructor & Destructor Documentation

◆ BaseGroupFinder() [1/2]

BaseGroupFinder ( )

Default constructor.

◆ ~BaseGroupFinder()

~BaseGroupFinder ( )

override

Destructor.

◆ BaseGroupFinder() [2/2]

BaseGroupFinder ( const BaseGroupFinder & )

private

Copy constructor intentionally not implemented.

Member Function Documentation

◆ checkIds_()

void checkIds_ ( const std::vector< ConsensusMap > & maps ) const

protected

Checks if all file descriptions have disjoint map identifiers.

Exceptions

Exception::IllegalArgument Is thrown if a file id is found twice

◆ operator=()

BaseGroupFinder& operator= ( const BaseGroupFinder & )

private

Assignment operator intentionally not implemented.

◆ registerChildren()

static void registerChildren ( )

static

Register all derived classes here.

◆ run()

virtual void run	(	const std::vector< ConsensusMap > &	input,
		ConsensusMap &	result
	)

pure virtual

Run the algorithm.

Exceptions

Exception::IllegalArgument is thrown if the input data is not valid.

Implemented in StablePairFinder, SimplePairFinder, QTClusterFinder, and LabeledPairFinder.

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members