SONARScoring Class Reference

Scoring of an spectrum using SONAR data. More...

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

Inheritance diagram for SONARScoring:

Collaboration diagram for SONARScoring:

Constructors and Destructor
double	dia_extract_window_
bool	dia_centroided_
bool	dia_extraction_ppm_
	SONARScoring ()
	Default constructor. More...
	~SONARScoring () override
	Destructor. More...
void	computeSonarScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< OpenSwath::LightTransition > &transitions, const std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath_Scores &scores) const
void	computeXCorr_ (std::vector< std::vector< double > > &sonar_profiles, double &xcorr_coelution_score, double &xcorr_shape_score) const
	SONARScoring (const SONARScoring &rhs)
	Copy constructor (algorithm class) More...
SONARScoring &	operator= (const SONARScoring &rhs)
	Assignment operator (algorithm class) More...
void	updateMembers_ () override
	Synchronize members with param class. More...

Additional Inherited Members
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...
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 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 using SONAR data.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
dia_extraction_window	float	0.05	min: 0.0	DIA extraction window in Th or ppm.
dia_extraction_unit	string	Th	Th, ppm	DIA extraction window unit
dia_centroided	string	false	true, false	Use centroided DIA data.

Note:

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

Constructor & Destructor Documentation

SONARScoring() [1/2]

SONARScoring

(

)

Default constructor.

~SONARScoring()

~SONARScoring ( )

inlineoverride

Destructor.

SONARScoring() [2/2]

SONARScoring ( const SONARScoring &  rhs )

private

Copy constructor (algorithm class)

Member Function Documentation

computeSonarScores()

void computeSonarScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< OpenSwath::LightTransition > &	transitions,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		OpenSwath_Scores &	scores
	)		const

computeXCorr_()

void computeXCorr_ ( std::vector< std::vector< double > > &  sonar_profiles, double &  xcorr_coelution_score, double &  xcorr_shape_score  ) const

private

operator=()

SONARScoring& operator= ( const SONARScoring &  rhs )

private

Assignment operator (algorithm class)

updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

dia_centroided_

bool dia_centroided_

private

dia_extract_window_

double dia_extract_window_

private

dia_extraction_ppm_

bool dia_extraction_ppm_

private