MRMMapping Class Reference

A class to map targeted assays to chromatograms. More...

#include <OpenMS/ANALYSIS/TARGETED/MRMMapping.h>

Inheritance diagram for MRMMapping:

Public Member Functions
void	mapExperiment (const OpenMS::PeakMap &input_chromatograms, const OpenMS::TargetedExperiment &targeted_exp, OpenMS::PeakMap &output)
	Maps input chromatograms to assays in a targeted experiment. More...
Constructors and destructors
	MRMMapping ()
	default constructor More...
	~MRMMapping () 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...

Protected Member Functions
	MRMMapping (const MRMMapping &rhs)
	copy constructor More...
MRMMapping &	operator= (const MRMMapping &rhs)
	assignment operator More...
void	updateMembers_ () override
	Synchronize members with param class. 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	precursor_tol_
double	product_tol_
bool	map_multiple_assays_
bool	error_on_unmapped_
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 class to map targeted assays to chromatograms.

Constructor & Destructor Documentation

MRMMapping() [1/2]

MRMMapping

(

)

default constructor

~MRMMapping()

~MRMMapping ( )

inlineoverride

destructor

MRMMapping() [2/2]

MRMMapping ( const MRMMapping &  rhs )

protected

copy constructor

Member Function Documentation

mapExperiment()

void mapExperiment	(	const OpenMS::PeakMap &	input_chromatograms,
		const OpenMS::TargetedExperiment &	targeted_exp,
		OpenMS::PeakMap &	output
	)

Maps input chromatograms to assays in a targeted experiment.

The output chromatograms are an annotated copy of the input chromatograms with native id, precursor information and peptide sequence (if available) annotated in the chromatogram files.

The algorithm tries to match a given set of chromatograms and targeted assays. It iterates through all the chromatograms retrieves one or more matching targeted assay for the chromatogram. By default, the algorithm assumes that a 1:1 mapping exists. If a chromatogram cannot be mapped (does not have a corresponding assay) the algorithm issues a warning, the user can specify that the program should abort in such a case (see error_on_unmapped).

If multiple mapping is enabled (see map_multiple_assays parameter) then each mapped assay will get its own chromatogram that contains the same raw data but different meta-annotation. This *can* be useful if the same transition is used to monitor multiple analytes but may also indicate a problem with too wide mapping tolerances.

operator=()

MRMMapping& operator= ( const MRMMapping &  rhs )

protected

assignment operator

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

error_on_unmapped_

bool error_on_unmapped_

protected

map_multiple_assays_

bool map_multiple_assays_

protected

precursor_tol_

double precursor_tol_

protected

product_tol_

double product_tol_

protected