File adapter for MSP files (NIST spectra library) More...

#include <OpenMS/FORMAT/MSPFile.h>

Inheritance diagram for MSPFile:

Collaboration diagram for MSPFile:

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

	MSPFile (const MSPFile &rhs)
	Copy constructor. More...

	~MSPFile () override
	Destructor. More...

MSPFile &	operator= (const MSPFile &rhs)
	assignment operator More...

void	load (const String &filename, std::vector< PeptideIdentification > &ids, PeakMap &exp)
	Loads a map from a MSPFile file. More...

void	store (const String &filename, const PeakMap &exp) const
	Stores a map in a MSPFile file. 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
void	parseHeader_ (const String &header, PeakSpectrum &spec)
	reads the header information and stores it as metainfo in the spectrum 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...

Additional Inherited Members
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 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

File adapter for MSP files (NIST spectra library)

Parameters of this class are:

Name	Type	Default	Restrictions	Description
parse_headers	string	false	true, false	Flag whether header information should be parsed an stored for each spectrum
parse_peakinfo	string	true	true, false	Flag whether the peak annotation information should be parsed and stored for each peak
parse_firstpeakinfo_only	string	true	true, false	Flag whether only the first (default for 1:1 correspondence in SpecLibSearcher) or all peak annotation information should be parsed and stored for each peak.
instrument	string		, it, qtof, toftof	If instrument given, only spectra of these type of instrument (Inst= in header) are parsed

Note:

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

Constructor & Destructor Documentation

◆ MSPFile() [1/2]

MSPFile ( )

Default constructor.

Constructors and destructors

◆ MSPFile() [2/2]

MSPFile ( const MSPFile & rhs )

Copy constructor.

◆ ~MSPFile()

~MSPFile ( )

override

Destructor.

Member Function Documentation

◆ load()

void load	(	const String &	filename,
		std::vector< PeptideIdentification > &	ids,
		PeakMap &	exp
	)

Loads a map from a MSPFile file.

Parameters

exp	PeakMap which contains the spectra after reading
filename	the filename of the experiment
ids	output parameter which contains the peptide identifications from the spectra annotations

Exceptions

FileNotFound	is thrown if the file could not be found
ParseError	is thrown if the given file could not be parsed
ElementNotFound	is thrown if a annotated modification cannot be found in ModificationsDB (PSI-MOD definitions)

◆ operator=()

MSPFile& operator= ( const MSPFile & rhs )

assignment operator

◆ parseHeader_()

void parseHeader_	(	const String &	header,
		PeakSpectrum &	spec
	)

protected

reads the header information and stores it as metainfo in the spectrum

◆ store()

void store	(	const String &	filename,
		const PeakMap &	exp
	)		const

Stores a map in a MSPFile file.