FeatureGroupingAlgorithmWNet Class Reference

A feature grouping algorithm using Wasserstein optimal transport. More...

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

Inheritance diagram for FeatureGroupingAlgorithmWNet:

Collaboration diagram for FeatureGroupingAlgorithmWNet:

Public Member Functions
	FeatureGroupingAlgorithmWNet ()
	Default constructor.
	~FeatureGroupingAlgorithmWNet () override
	Destructor.
void	group (const std::vector< FeatureMap > &maps, ConsensusMap &out) override
	Applies the algorithm to feature maps.
void	group (const std::vector< ConsensusMap > &maps, ConsensusMap &out) override
	Applies the algorithm to consensus maps.
Public Member Functions inherited from FeatureGroupingAlgorithm
	FeatureGroupingAlgorithm ()
	Default constructor.
	~FeatureGroupingAlgorithm () override
	Destructor.
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 inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Private Member Functions
	FeatureGroupingAlgorithmWNet (const FeatureGroupingAlgorithmWNet &)=delete
FeatureGroupingAlgorithmWNet &	operator= (const FeatureGroupingAlgorithmWNet &)=delete
	FeatureGroupingAlgorithmWNet (FeatureGroupingAlgorithmWNet &&)=delete
FeatureGroupingAlgorithmWNet &	operator= (FeatureGroupingAlgorithmWNet &&)=delete
template<typename MapType >
void	group_ (const std::vector< MapType > &maps, ConsensusMap &out)

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
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.
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

A feature grouping algorithm using Wasserstein optimal transport.

Groups corresponding features across multiple maps by solving a minimum-cost network flow problem. Each pair of maps is aligned independently using WNetAligner<2> (2D: m/z and RT), and pairwise matchings are merged into consensus groups via union-find.

Features are matched by minimizing the total transport cost between their (m/z, RT) positions, with unmatched features assigned to a "trash" node at a configurable cost. This produces a 1-to-1 consensus matching per pair.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
distance_metric	string	LINF	L1, L2, LINF	Distance metric for comparing feature positions
max_rt_shift	float	100.0	min: 0.0	Maximum allowed RT difference (in seconds) for matching features.
mz_unit	string	ppm	Da, ppm	Unit for the m/z tolerance. 'Da' uses max_mz_shift_da; 'ppm' uses max_mz_shift_ppm and log-transforms the m/z axis.
max_mz_shift_da	float	0.3	min: 0.0	Maximum allowed m/z difference in Daltons. Used when mz_unit is 'Da'.
max_mz_shift_ppm	float	10.0	min: 0.0	Maximum allowed m/z difference in ppm. Used when mz_unit is 'ppm'.
trash_cost	float	0.0	min: 0.0	Cost of leaving a feature unmatched (in seconds). Set to 0 to auto-derive from max_rt_shift (a match at the boundary costs the same as no match). Increase to prefer matching over leaving features unmatched.
normalize_intensities	string	true	true, false	Normalize feature intensities per map before alignment so that total intensity is equal across maps.
decharge_mz	string	false	true, false	Convert observed m/z values to their singly-charged (z=1) equivalent before alignment. Features with charge z>1 are projected to [M+H]+ m/z, making features of the same compound but different charge states directly comparable. If a feature carries a 'dc_charge_adduct_mass' MetaValue (set by MetaboliteFeatureDeconvolution), the stored adduct mass is used; otherwise pure H+ adducts are assumed. Features with unknown charge (z=0) are left unchanged.

Note:

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

Constructor & Destructor Documentation

FeatureGroupingAlgorithmWNet() [1/3]

FeatureGroupingAlgorithmWNet

(

)

Default constructor.

~FeatureGroupingAlgorithmWNet()

~FeatureGroupingAlgorithmWNet ( )

override

Destructor.

FeatureGroupingAlgorithmWNet() [2/3]

FeatureGroupingAlgorithmWNet ( const FeatureGroupingAlgorithmWNet &  )

privatedelete

FeatureGroupingAlgorithmWNet() [3/3]

FeatureGroupingAlgorithmWNet ( FeatureGroupingAlgorithmWNet &&  )

privatedelete

Member Function Documentation

group() [1/2]

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

overridevirtual

Applies the algorithm to consensus maps.

Precondition

The data ranges of the input maps have to be up-to-date (use ConsensusMap::updateRanges).

Parameters

[in]	maps	Input consensus maps (at least two required).
[out]	out	Resulting consensus map with grouped features.

Exceptions

IllegalArgument

is thrown if less than two input maps are given.

Reimplemented from FeatureGroupingAlgorithm.

group() [2/2]

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

overridevirtual

Applies the algorithm to feature maps.

Precondition

The data ranges of the input maps have to be up-to-date (use FeatureMap::updateRanges).

Parameters

[in]	maps	Input feature maps (at least two required).
[out]	out	Resulting consensus map with grouped features.

Exceptions

IllegalArgument

is thrown if less than two input maps are given.

Implements FeatureGroupingAlgorithm.

group_()

template<typename MapType >

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

private

operator=() [1/2]

FeatureGroupingAlgorithmWNet & operator= ( const FeatureGroupingAlgorithmWNet &  )

privatedelete

operator=() [2/2]

FeatureGroupingAlgorithmWNet & operator= ( FeatureGroupingAlgorithmWNet &&  )

privatedelete