Base class for all feature grouping algorithms. More...

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

Inheritance diagram for FeatureGroupingAlgorithm:

Collaboration diagram for FeatureGroupingAlgorithm:

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

	~FeatureGroupingAlgorithm () override
	Destructor. More...

virtual void	group (const std::vector< FeatureMap > &maps, ConsensusMap &out)=0
	Applies the algorithm. The features in the input `maps` are grouped and the output is written to the consensus map `out`. More...

virtual void	group (const std::vector< ConsensusMap > &maps, ConsensusMap &out)

void	transferSubelements (const std::vector< ConsensusMap > &maps, ConsensusMap &out) const
	Transfers subelements (grouped features) from input consensus maps to the result consensus map. 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...

Protected Member Functions
template<class MapType >
void	postprocess_ (const std::vector< MapType > &maps, ConsensusMap &out)

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
	FeatureGroupingAlgorithm (const FeatureGroupingAlgorithm &)
	Copy constructor is not implemented -> private. More...

FeatureGroupingAlgorithm &	operator= (const FeatureGroupingAlgorithm &)
	Assignment operator is not implemented -> private. More...

Additional Inherited Members
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 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

Base class for all feature grouping algorithms.

These algorithms group corresponding features in one map or across maps.

Constructor & Destructor Documentation

◆ FeatureGroupingAlgorithm() [1/2]

FeatureGroupingAlgorithm ( )

Default constructor.

◆ ~FeatureGroupingAlgorithm()

~FeatureGroupingAlgorithm ( )

override

Destructor.

◆ FeatureGroupingAlgorithm() [2/2]

FeatureGroupingAlgorithm ( const FeatureGroupingAlgorithm & )

private

Copy constructor is not implemented -> private.

Member Function Documentation

◆ group() [1/2]

virtual void group	(	const std::vector< ConsensusMap > &	maps,
		ConsensusMap &	out
	)

virtual

Applies the algorithm. The consensus features in the input maps are grouped and the output is written to the consensus map out Algorithms not supporting ConsensusMap input should simply not override this method, as the base implementation will forward the data to the FeatureMap version of group()

Reimplemented in FeatureGroupingAlgorithmQT, and FeatureGroupingAlgorithmKD.

◆ group() [2/2]

virtual void group	(	const std::vector< FeatureMap > &	maps,
		ConsensusMap &	out
	)

pure virtual

Applies the algorithm. The features in the input maps are grouped and the output is written to the consensus map out.

Implemented in FeatureGroupingAlgorithmUnlabeled, FeatureGroupingAlgorithmQT, FeatureGroupingAlgorithmLabeled, and FeatureGroupingAlgorithmKD.

◆ operator=()

FeatureGroupingAlgorithm& operator= ( const FeatureGroupingAlgorithm & )

private

Assignment operator is not implemented -> private.

◆ postprocess_()

void postprocess_	(	const std::vector< MapType > &	maps,
		ConsensusMap &	out
	)

inlineprotected

after grouping by the subclasses, postprocess unassigned IDs, protein IDs and sort results in a consistent way

References ConsensusMap::getProteinIdentifications(), ConsensusMap::getUnassignedPeptideIdentifications(), ConsensusMap::sortByMaps(), ConsensusMap::sortByQuality(), and ConsensusMap::sortBySize().

◆ transferSubelements()

void transferSubelements	(	const std::vector< ConsensusMap > &	maps,
		ConsensusMap &	out
	)		const

Transfers subelements (grouped features) from input consensus maps to the result consensus map.

Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members