A map feature grouping algorithm for labeling techniques with two labels. More...

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

Inheritance diagram for FeatureGroupingAlgorithmLabeled:

Collaboration diagram for FeatureGroupingAlgorithmLabeled:

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

	~FeatureGroupingAlgorithmLabeled () override
	Destructor. More...

void	group (const std::vector< FeatureMap > &maps, ConsensusMap &out) override
	Applies the algorithm. More...

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

	~FeatureGroupingAlgorithm () override
	Destructor. 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...

Private Member Functions
	FeatureGroupingAlgorithmLabeled (const FeatureGroupingAlgorithmLabeled &)
	Copy constructor is not implemented -> private. More...

FeatureGroupingAlgorithmLabeled &	operator= (const FeatureGroupingAlgorithmLabeled &)
	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 Member Functions inherited from FeatureGroupingAlgorithm
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...

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

A map feature grouping algorithm for labeling techniques with two labels.

It takes one maps and searches for corresponding features with a defined distance in RT and m/z.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_estimate	string	true	true, false	If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.
rt_pair_dist	float	-20.0		optimal pair distance in RT [sec] from light to heavy feature
rt_dev_low	float	15.0	min: 0.0	maximum allowed deviation below optimal retention time distance
rt_dev_high	float	15.0	min: 0.0	maximum allowed deviation above optimal retention time distance
mz_pair_dists	float list	[4.0]		optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)
mz_dev	float	0.05	min: 0.0	maximum allowed deviation from optimal m/z distance
mrm	string	false	true, false	this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ FeatureGroupingAlgorithmLabeled() [1/2]

FeatureGroupingAlgorithmLabeled ( )

Default constructor.

◆ ~FeatureGroupingAlgorithmLabeled()

~FeatureGroupingAlgorithmLabeled ( )

override

Destructor.

◆ FeatureGroupingAlgorithmLabeled() [2/2]

FeatureGroupingAlgorithmLabeled ( const FeatureGroupingAlgorithmLabeled & )

private

Copy constructor is not implemented -> private.

Member Function Documentation

◆ group()

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

overridevirtual

Applies the algorithm.

Note: Exactly one input map has to be provided.; The output map has to have two file descriptions, containing the same file name. The file descriptions have to be labeled 'heavy' and 'light'.

Exceptions

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

Implements FeatureGroupingAlgorithm.

◆ operator=()

FeatureGroupingAlgorithmLabeled& operator= ( const FeatureGroupingAlgorithmLabeled & )

private

Assignment operator is not implemented -> private.

Public Member Functions

Private Member Functions

Additional Inherited Members