DiaPrescore Class Reference

Scoring of an spectrum given library intensities of a transition group. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DIAPrescoring.h>

Inheritance diagram for DiaPrescore:

Collaboration diagram for DiaPrescore:

Public Member Functions
	DiaPrescore ()
	DiaPrescore (double dia_extract_window, int nr_isotopes=4, int nr_charges=4)
void	defineDefaults ()
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...
void	score (OpenSwath::SpectrumPtr spec, const std::vector< OpenSwath::LightTransition > &lt, double &dotprod, double &manhattan)
	Score a spectrum given a transition group. More...
void	operator() (OpenSwath::SpectrumAccessPtr swath_ptr, OpenSwath::LightTargetedExperiment &transition_exp_used, OpenSwath::IDataFrameWriter *ivw)
	Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment. 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...

Private Attributes
double	dia_extract_window_
int	nr_isotopes_
int	nr_charges_

Additional Inherited Members
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 inherited from DefaultParamHandler
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

Scoring of an spectrum given library intensities of a transition group.

In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:

See also class DIAScoring.

Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intensities and simulated spectrum.

Constructor & Destructor Documentation

DiaPrescore() [1/2]

DiaPrescore

(

)

DiaPrescore() [2/2]

DiaPrescore	(	double	dia_extract_window,
		int	nr_isotopes = 4,
		int	nr_charges = 4
	)

Member Function Documentation

defineDefaults()

void defineDefaults

(

)

operator()()

void operator()	(	OpenSwath::SpectrumAccessPtr	swath_ptr,
		OpenSwath::LightTargetedExperiment &	transition_exp_used,
		OpenSwath::IDataFrameWriter *	ivw
	)

Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment.

score()

void score	(	OpenSwath::SpectrumPtr	spec,
		const std::vector< OpenSwath::LightTransition > &	lt,
		double &	dotprod,
		double &	manhattan
	)

Score a spectrum given a transition group.

Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intensities and simulated spectrum.

updateMembers_()

void updateMembers_ ( )

overridevirtual

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

dia_extract_window_

double dia_extract_window_

private

nr_charges_

int nr_charges_

private

nr_isotopes_

int nr_isotopes_

private