#include <OpenMS/ANALYSIS/ID/MetaboliteSpectralMatching.h>

Inheritance diagram for MetaboliteSpectralMatching:

Collaboration diagram for MetaboliteSpectralMatching:

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

	~MetaboliteSpectralMatching () override
	Default destructor. More...

void	run (PeakMap &, PeakMap &, MzTab &, String &)
	main method of MetaboliteSpectralMatching 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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 double	computeHyperScore (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, double mz_lower_bound=0.0)
	hyperscore computation More...

static double	computeHyperScore (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, std::vector< PeptideHit::PeakAnnotation > &annotations, double mz_lower_bound=0.0)
	hyperscore computation (with output of peak annotations) 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...

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

Static Protected Member Functions
static double	computeHyperScore_ (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, std::vector< PeptideHit::PeakAnnotation > *annotations=0, double mz_lower_bound=0.0)

Private Member Functions
void	exportMzTab_ (const std::vector< SpectralMatch > &, MzTab &)
	private member functions More...

Private Attributes
double	precursor_mz_error_

double	fragment_mz_error_

String	mz_error_unit_

String	ion_mode_

String	report_mode_

bool	merge_spectra_

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

Constructor & Destructor Documentation

◆ MetaboliteSpectralMatching()

MetaboliteSpectralMatching ( )

Default constructor.

◆ ~MetaboliteSpectralMatching()

~MetaboliteSpectralMatching ( )

override

Default destructor.

Member Function Documentation

◆ computeHyperScore() [1/2]

static double computeHyperScore	(	double	fragment_mass_error,
		bool	fragment_mass_tolerance_unit_ppm,
		const MSSpectrum &	exp_spectrum,
		const MSSpectrum &	db_spectrum,
		double	mz_lower_bound = `0.0`
	)

static

hyperscore computation

Referenced by NucleicAcidSearchEngine::main_().

◆ computeHyperScore() [2/2]

static double computeHyperScore	(	double	fragment_mass_error,
		bool	fragment_mass_tolerance_unit_ppm,
		const MSSpectrum &	exp_spectrum,
		const MSSpectrum &	db_spectrum,
		std::vector< PeptideHit::PeakAnnotation > &	annotations,
		double	mz_lower_bound = `0.0`
	)

static

hyperscore computation (with output of peak annotations)

◆ computeHyperScore_()

static double computeHyperScore_	(	double	fragment_mass_error,
		bool	fragment_mass_tolerance_unit_ppm,
		const MSSpectrum &	exp_spectrum,
		const MSSpectrum &	db_spectrum,
		std::vector< PeptideHit::PeakAnnotation > *	annotations = `0`,
		double	mz_lower_bound = `0.0`
	)

staticprotected

◆ exportMzTab_()

void exportMzTab_	(	const std::vector< SpectralMatch > &	,
		MzTab &
	)

private

private member functions

◆ run()

void run	(	PeakMap &	,
		PeakMap &	,
		MzTab &	,
		String &
	)

main method of MetaboliteSpectralMatching

◆ 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

◆ fragment_mz_error_

double fragment_mz_error_

private

◆ ion_mode_

String ion_mode_

private

◆ merge_spectra_

bool merge_spectra_

private

◆ mz_error_unit_

String mz_error_unit_

private

◆ precursor_mz_error_

double precursor_mz_error_

private

◆ report_mode_

String report_mode_

private

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MetaboliteSpectralMatching()

◆ ~MetaboliteSpectralMatching()

Member Function Documentation

◆ computeHyperScore() [1/2]

◆ computeHyperScore() [2/2]

◆ computeHyperScore_()

◆ exportMzTab_()

◆ run()

◆ updateMembers_()

Member Data Documentation

◆ fragment_mz_error_

◆ ion_mode_

◆ merge_spectra_

◆ mz_error_unit_

◆ precursor_mz_error_

◆ report_mode_