Used to load Mascot XML files. More...

Inheritance diagram for MascotXMLFile:

Collaboration diagram for MascotXMLFile:

Public Member Functions
	MascotXMLFile ()
	Constructor.

void	load (const String &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, const SpectrumMetaDataLookup &lookup)
	Loads data from a Mascot XML file.

void	load (const String &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
	Loads data from a Mascot XML file.

Public Member Functions inherited from XMLFile
	XMLFile ()
	Default constructor.

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location.

virtual	~XMLFile ()
	Destructor.

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema.

const String &	getVersion () const
	return the version of the schema

Static Public Member Functions
static void	initializeLookup (SpectrumMetaDataLookup &lookup, const PeakMap &experiment, const 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 String &filename, XMLHandler *handler)
	Parses the XML file given by `filename` using the handler given by `handler`.

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parses the in-memory buffer given by `buffer` using the handler given by `handler`.

void	save_ (const String &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`.

void	enforceEncoding_ (const String &encoding)

Protected Attributes inherited from XMLFile
String	schema_location_
	XML schema file location.

String	schema_version_
	Version string.

String	enforced_encoding_
	Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml.

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 ( )

Constructor.

static void initializeLookup	(	SpectrumMetaDataLookup &	lookup,
		const PeakMap &	experiment,
		const 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

void load	(	const 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.

void load	(	const String &	filename,
		ProteinIdentification &	protein_identification,
		PeptideIdentificationList &	id_data,
		std::map< 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 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.