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...

Static Public Member Functions
static FeatureGroupingAlgorithm *	create ()
	Creates a new instance of this class (for Factory) More...

static String	getProductName ()
	Returns the product name (for the Factory) More...

Static Public Member Functions inherited from FeatureGroupingAlgorithm
static void	registerChildren ()
	Register all derived classes in this method. 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...

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
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

◆ create()

static FeatureGroupingAlgorithm* create ( )

inlinestatic

Creates a new instance of this class (for Factory)

◆ getProductName()

static String getProductName ( )

inlinestatic

Returns the product name (for the Factory)

◆ 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

Static Public Member Functions

Private Member Functions

Additional Inherited Members