This class implements a simple point pair finding algorithm. More...

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

Inheritance diagram for SimplePairFinder:

Collaboration diagram for SimplePairFinder:

Public Types
typedef BaseGroupFinder	Base
	Base class. More...

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	SimplePairFinder ()
	Constructor. More...

	~SimplePairFinder () override
	Destructor. More...

void	run (const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map) override
	Run the algorithm. More...

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

	~BaseGroupFinder () override
	Destructor. 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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static BaseGroupFinder *	create ()
	returns an instance of this class More...

static const String	getProductName ()
	returns the name of this module More...

Static Public Member Functions inherited from BaseGroupFinder
static void	registerChildren ()
	Register all derived classes here. 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...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

double	similarity_ (ConsensusFeature const &left, ConsensusFeature const &right) const
	Compute the similarity for a pair of elements. More...

Protected Member Functions inherited from BaseGroupFinder
void	checkIds_ (const std::vector< ConsensusMap > &maps) const
	Checks if all file descriptions have disjoint map identifiers. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
double	diff_exponent_ [2]
	A parameter for similarity_(). More...

double	diff_intercept_ [2]
	A parameter for similarity_(). More...

double	pair_min_quality_
	Minimal pair quality. 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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class implements a simple point pair finding algorithm.

It offers a method to find element pairs across two element maps.

The similarity value should express our confidence that one element might possibly be matched to the other. Larger quality values are better, the maximal similarity is one. Let \(\Delta_\textit{RT}\) and \(\Delta_\textit{MZ}\) be the absolute values of the RT and MZ differences in the data. Then the similarity value is

\[ \frac{1}{ \big( 1 + \Delta_\textit{RT} \cdot \textit{diff\_intercept\_RT} \big)^\textit{diff\_exponent\_RT} \cdot \big( 1 + \Delta_\textit{MZ} \cdot \textit{diff\_intercept\_MZ} \big)^\textit{diff\_exponent\_MZ} } \]

Choosing diff_exponent: This parameter controls the growth rate of the penalty for differences. It is for example possible to search for pairs using the absolute distance in RT (which should not be very susceptible to outliers) and the squared distance in MZ (where small difference occur frequently, but large differences indicate a mismatch).

Choosing diff_intercept: Since we are taking the reciprocal value ("1/..."), we include an offset to avoid division by zero in case \(\Delta=0\). To set this parameter, ask yourself: How much worse is a difference of 1 compared to no difference?

The following image illustrates the influence of these parameters:

Influence of the parameters intercept and exponent

Parameters of this class are:

Name	Type	Default	Description
similarity:pair_min_quality	float	0.01	Minimum required pair quality.
similarity:diff_intercept:RT	float	1.0	This parameter controls the asymptotic decay rate for large differences (for more details see the similarity measurement).
similarity:diff_intercept:MZ	float	0.1	This parameter controls the asymptotic decay rate for large differences (for more details see the similarity measurement).
similarity:diff_exponent:RT	float	2.0	This parameter is important for small differences (for more details see the similarity measurement).
similarity:diff_exponent:MZ	float	1.0	This parameter is important for small differences (for more details see the similarity measurement).

Note:

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

Member Typedef Documentation

◆ Base

typedef BaseGroupFinder Base

Base class.

Constructor & Destructor Documentation

◆ SimplePairFinder()

SimplePairFinder ( )

Constructor.

◆ ~SimplePairFinder()

~SimplePairFinder ( )

inlineoverride

Destructor.

Member Function Documentation

◆ create()

static BaseGroupFinder* create ( )

inlinestatic

returns an instance of this class

◆ getProductName()

static const String getProductName ( )

inlinestatic

returns the name of this module

◆ run()

void run	(	const std::vector< ConsensusMap > &	input_maps,
		ConsensusMap &	result_map
	)

overridevirtual

Run the algorithm.

Note: Exactly two input maps must be provided.; All two input maps must be provided.

Exceptions

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

Implements BaseGroupFinder.

◆ similarity_()

double similarity_	(	ConsensusFeature const &	left,
		ConsensusFeature const &	right
	)		const

protected

Compute the similarity for a pair of elements.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ diff_exponent_

double diff_exponent_[2]

protected

A parameter for similarity_().

◆ diff_intercept_

double diff_intercept_[2]

protected

A parameter for similarity_().

◆ pair_min_quality_

double pair_min_quality_

protected

Minimal pair quality.

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

Constructor & Destructor Documentation

◆ SimplePairFinder()

◆ ~SimplePairFinder()

Member Function Documentation

◆ create()

◆ getProductName()

◆ run()

◆ similarity_()

◆ updateMembers_()

Member Data Documentation

◆ diff_exponent_

◆ diff_intercept_

◆ pair_min_quality_