The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...

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

Inheritance diagram for LabeledPairFinder:

Collaboration diagram for LabeledPairFinder:

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

	~LabeledPairFinder () 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...

virtual 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 () const
	Ends the progress display. More...

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 &prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
double	PValue_ (double x, double m, double sig1, double sig2)
	return the p-value at position x for the bi-Gaussian distribution with mean `m` and standard deviation `sig1` (left) and `sig2` (right) 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
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...

Private Member Functions
	LabeledPairFinder (const LabeledPairFinder &source)
	Copy constructor not implemented => private. More...

LabeledPairFinder &	operator= (const LabeledPairFinder &source)
	Assignment operator not implemented => private. More...

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

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...

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_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

The LabeledPairFinder allows the matching of labeled features (features with a fixed distance).

Finds feature pairs that have a defined distance in RT and m/z in the same map.

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.

Todo:

Implement support for labeled MRM experiments, Q1 m/z value and charges. (Andreas)

Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)

Constructor & Destructor Documentation

◆ LabeledPairFinder() [1/2]

LabeledPairFinder ( )

Default constructor.

◆ ~LabeledPairFinder()

~LabeledPairFinder ( )

inlineoverride

Destructor.

◆ LabeledPairFinder() [2/2]

LabeledPairFinder ( const LabeledPairFinder & source )

private

Copy constructor not implemented => private.

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.

◆ operator=()

LabeledPairFinder& operator= ( const LabeledPairFinder & source )

private

Assignment operator not implemented => private.

◆ PValue_()

double PValue_	(	double	x,
		double	m,
		double	sig1,
		double	sig2
	)

inlineprotected

return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right)

◆ run()

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

overridevirtual

Run 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 BaseGroupFinder.

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members