A map feature grouping algorithm for unlabeled data. More...

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

Inheritance diagram for FeatureGroupingAlgorithmUnlabeled:

Collaboration diagram for FeatureGroupingAlgorithmUnlabeled:

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

	~FeatureGroupingAlgorithmUnlabeled () override
	Destructor. More...

template<typename MapType >
void	setReference (int map_id, const MapType &map)
	Sets the reference map for the algorithm. More...

ConsensusMap &	getResultMap ()
	Returns the computed consensus map (after calling addToGroup with all maps) More...

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

void	addToGroup (int map_id, const FeatureMap &feature_map)
	Adds one map to the group. 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
	FeatureGroupingAlgorithmUnlabeled (const FeatureGroupingAlgorithmUnlabeled &)
	Copy constructor intentionally not implemented -> private. More...

FeatureGroupingAlgorithmUnlabeled &	operator= (const FeatureGroupingAlgorithmUnlabeled &)
	Assignment operator intentionally not implemented -> private. More...

Private Attributes
std::vector< ConsensusMap >	pairfinder_input_

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 unlabeled data.

It takes multiple maps and searches for corresponding features. The corresponding features must be aligned, but may have small position deviations.

There are two ways to run the algorithm:

a) Simply call "group" with all maps in memory.
b) Call "setReference", "addToGroup" (n times), "getResultMap" in that order.

The second way is more memory efficient because at all times, only the reference map and the current map need to be in memory

Parameters of this class are:

Name	Type	Default	Restrictions	Description
second_nearest_gap	float	2.0	min: 1.0	Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.
use_identifications	string	false	true, false	Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).
ignore_charge	string	false	true, false	false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state
ignore_adduct	string	true	true, false	true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts
distance_RT:max_difference	float	100.0	min: 0.0	Never pair features with a larger RT distance (in seconds).
distance_RT:exponent	float	1.0	min: 0.0	Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_RT:weight	float	1.0	min: 0.0	Final RT distances are weighted by this factor
distance_MZ:max_difference	float	0.3	min: 0.0	Never pair features with larger m/z distance (unit defined by 'unit')
distance_MZ:unit	string	Da	Da, ppm	Unit of the 'max_difference' parameter
distance_MZ:exponent	float	2.0	min: 0.0	Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_MZ:weight	float	1.0	min: 0.0	Final m/z distances are weighted by this factor
distance_intensity:exponent	float	1.0	min: 0.0	Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_intensity:weight	float	0.0	min: 0.0	Final intensity distances are weighted by this factor
distance_intensity:log_transform	string	disabled	enabled, disabled	Log-transform intensities? If disabled, d = \|int_f2 - int_f1\| / int_max. If enabled, d = \|log(int_f2 + 1) - log(int_f1 + 1)\| / log(int_max + 1))

Note:

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

Constructor & Destructor Documentation

◆ FeatureGroupingAlgorithmUnlabeled() [1/2]

FeatureGroupingAlgorithmUnlabeled ( )

Default constructor.

◆ ~FeatureGroupingAlgorithmUnlabeled()

~FeatureGroupingAlgorithmUnlabeled ( )

override

Destructor.

◆ FeatureGroupingAlgorithmUnlabeled() [2/2]

FeatureGroupingAlgorithmUnlabeled ( const FeatureGroupingAlgorithmUnlabeled & )

private

Copy constructor intentionally not implemented -> private.

Member Function Documentation

◆ addToGroup()

void addToGroup	(	int	map_id,
		const FeatureMap &	feature_map
	)

Adds one map to the group.

This assumes that setReference has been called before. It is the callers responsibility to provide a valid map_id. Note that all calls to addToGroup _must_ use different map_ids and they all need to be different from the one used to call setReference!

Exceptions

IllegalArgument is thrown if the map_id has been used before

◆ 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)

◆ getResultMap()

ConsensusMap& getResultMap ( )

inline

Returns the computed consensus map (after calling addToGroup with all maps)

◆ group()

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

overridevirtual

Applies the algorithm.

Exceptions

IllegalArgument is thrown if less than two input maps are given.

Implements FeatureGroupingAlgorithm.

◆ operator=()

FeatureGroupingAlgorithmUnlabeled& operator= ( const FeatureGroupingAlgorithmUnlabeled & )

private

Assignment operator intentionally not implemented -> private.

◆ setReference()

void setReference	(	int	map_id,
		const MapType &	map
	)

inline

Sets the reference map for the algorithm.

This will store the input map in the first argument of the pairfinder_input_ vector.

Note that map_id needs to be unique (see addToGroup docu).

References MapConversion::convert().

Member Data Documentation

◆ pairfinder_input_

std::vector<ConsensusMap> pairfinder_input_

private

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FeatureGroupingAlgorithmUnlabeled() [1/2]

◆ ~FeatureGroupingAlgorithmUnlabeled()

◆ FeatureGroupingAlgorithmUnlabeled() [2/2]

Member Function Documentation

◆ addToGroup()

◆ create()

◆ getProductName()

◆ getResultMap()

◆ group()

◆ operator=()

◆ setReference()

Member Data Documentation

◆ pairfinder_input_