MascotXMLFile Class Reference

Used to load Mascot XML files. More...

#include <OpenMS/FORMAT/MascotXMLFile.h>

Inheritance diagram for MascotXMLFile:

Collaboration diagram for MascotXMLFile:

Public Member Functions
	MascotXMLFile ()
	Constructor.
void	load (const std::string &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, const SpectrumMetaDataLookup &lookup)
	Loads data from a Mascot XML file.
void	load (const std::string &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, std::map< std::string, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
	Loads data from a Mascot XML file.
Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; schema_location_ remains unset, so isValid cannot be used until derived-class logic initializes schema_location_ before calling isValid.
	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.
virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.
bool	isValid (const std::string &filename, std::ostream &os)
	Check if filename validates against the bound XML schema.
const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Static Public Member Functions
static void	initializeLookup (SpectrumMetaDataLookup &lookup, const PeakMap &experiment, const std::string &scan_regex="")
	Initializes a helper object for looking up spectrum meta data (RT, m/z)

Additional Inherited Members
Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler)
	Parse the XML file at filename through handler.
void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through handler.
void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by handler in the file given by filename.
void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.
Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws NotImplemented).
std::string	schema_version_
	Schema version string returned by getVersion.
std::string	enforced_encoding_
	Optional XML encoding override applied to the InputSource in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.

Detailed Description

Used to load Mascot XML files.

This class is used to load documents that implement the schema of Mascot XML files.

Constructor & Destructor Documentation

MascotXMLFile()

MascotXMLFile

(

)

Constructor.

Member Function Documentation

initializeLookup()

static void initializeLookup ( SpectrumMetaDataLookup &  lookup, const PeakMap &  experiment, const std::string &  scan_regex = ""  )

static

Initializes a helper object for looking up spectrum meta data (RT, m/z)

Parameters

[in]	lookup	Helper object to initialize
[in]	experiment	Experiment containing the spectra
[in]	scan_regex	Optional regular expression for extracting information from references to spectra

load() [1/2]

void load	(	const std::string &	filename,
		ProteinIdentification &	protein_identification,
		PeptideIdentificationList &	id_data,
		const SpectrumMetaDataLookup &	lookup
	)

Loads data from a Mascot XML file.

Parameters

[in]	filename	the file to be loaded
[in]	protein_identification	protein identifications belonging to the whole experiment
[in]	id_data	the identifications with m/z and RT
[in]	lookup	helper object for looking up spectrum meta data

Exceptions

Exception::FileNotFound	is thrown if the file does not exists.
Exception::ParseError	is thrown if the file does not suit to the standard.

load() [2/2]

void load	(	const std::string &	filename,
		ProteinIdentification &	protein_identification,
		PeptideIdentificationList &	id_data,
		std::map< std::string, std::vector< AASequence > > &	peptides,
		const SpectrumMetaDataLookup &	lookup
	)

Loads data from a Mascot XML file.

Parameters

[in]	filename	the file to be loaded
[in]	protein_identification	protein identifications belonging to the whole experiment
[in]	id_data	the identifications with m/z and RT
[in,out]	peptides	a map of modified peptides identified by the std::string title
[in]	lookup	helper object for looking up spectrum meta data

Exceptions

Exception::FileNotFound	is thrown if the file does not exists.
Exception::ParseError	is thrown if the file does not suit to the standard.