MSPGenericFile Class Reference

Load MSP text file and save it into an `MSExperiment`. More...

#include <OpenMS/FORMAT/MSPGenericFile.h>

Inheritance diagram for MSPGenericFile:

Collaboration diagram for MSPGenericFile:

Public Member Functions
	MSPGenericFile ()
	Default constructor. More...
	MSPGenericFile (const String &filename, MSExperiment &library)
	Constructor with filename and output library. More...
	~MSPGenericFile ()=default
	Destructor. More...
void	getDefaultParameters (Param &params)
	Get the class' default parameters. More...
void	load (const String &filename, MSExperiment &library)
	Load the file's data and metadata, and save it into an `MSExperiment`. More...
void	store (const String &filename, const MSExperiment &library) const
	Save data and metadata into a 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...

Private Member Functions
void	updateMembers_ ()
	Overrides `DefaultParamHandler`'s method. More...
void	addSpectrumToLibrary (MSSpectrum &spectrum, MSExperiment &library)

Private Attributes
std::set< String >	loaded_spectra_names_
	To keep track of which spectra have already been loaded and avoid duplicates. More...
std::vector< String >	synonyms_
String	synonyms_separator_
	The separator to be used in "Synon" metaValue. More...

Friends
class	MSPGenericFile_friend
	To test private and protected methods. More...

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

Load MSP text file and save it into an `MSExperiment`.

This class is specialized for metabolites data. The required fields are: Name, Num Peaks, and the peaks data

Points (meaning x and y info) may be separated by a space or a colon. Peaks may be separated by a space or a semicolon.

An example of the expected format: > Name: foo > Num Peaks: 11 > 35 310; 36 1230; 37 27; 38 303; 47 5240; > 66 203; 67 68; 68 77; 82 63; 83 240; > 136 350;

Another supported format: > Name: bar > Num Peaks: 11 > 35:310 36:1230 37:27 38:303 47:5240 > 66:203 67:68 68:77 82:63 83:240 > 136:350

Constructor & Destructor Documentation

MSPGenericFile() [1/2]

MSPGenericFile

(

)

Default constructor.

MSPGenericFile() [2/2]

MSPGenericFile	(	const String &	filename,
		MSExperiment &	library
	)

Constructor with filename and output library.

~MSPGenericFile()

~MSPGenericFile ( )

default

Destructor.

Member Function Documentation

addSpectrumToLibrary()

void addSpectrumToLibrary ( MSSpectrum &  spectrum, MSExperiment &  library  )

private

Validate and add a spectrum to a spectral library

The spectrum is added to the library if all following criteria are met:

• Name field is present and not empty
• The number of peaks parsed matches the value of Num Peaks
• A spectrum of the same name has not already been added

Exceptions

MissingInformation	If the spectrum doesn't have a name or Num Peaks info is missing
ParseError	If Num Peaks' value doesn't match with the number of raw peaks parsed

Parameters

	[in/out]	spectrum The spectrum to be added
[out]	library	The spectrum is added into this `MSExperiment` library

Referenced by MSPGenericFile_friend::addSpectrumToLibrary().

getDefaultParameters()

void getDefaultParameters

(

Param &

params

)

Get the class' default parameters.

load()

void load	(	const String &	filename,
		MSExperiment &	library
	)

Load the file's data and metadata, and save it into an `MSExperiment`.

Parameters

[in]	filename	Path to the MSP input file
[out]	library	The variable into which the extracted information will be saved

Exceptions

FileNotFound

If the file could not be found

store()

void store	(	const String &	filename,
		const MSExperiment &	library
	)		const

Save data and metadata into a file.

Parameters

[in]	filename	Path to the MSP input file
[out]	library	The variable from which extracted information will be saved

Exceptions

FileNotWritable

If the file is not writable

updateMembers_()

void updateMembers_ ( )

privatevirtual

Overrides `DefaultParamHandler`'s method.

Reimplemented from DefaultParamHandler.

Friends And Related Function Documentation

MSPGenericFile_friend

friend class MSPGenericFile_friend

friend

To test private and protected methods.

Member Data Documentation

loaded_spectra_names_

std::set<String> loaded_spectra_names_

private

To keep track of which spectra have already been loaded and avoid duplicates.

synonyms_

std::vector<String> synonyms_

private

synonyms_separator_

String synonyms_separator_

private

The separator to be used in "Synon" metaValue.