Used to load and store idXML files. More...

#include <OpenMS/FORMAT/IdXMLFile.h>

Inheritance diagram for IdXMLFile:

Public Member Functions
	IdXMLFile ()
	Constructor.
void	load (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
	Loads the identifications of an idXML file without identifier.
void	load (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, String &document_id)
	Loads the identifications of an idXML file.
void	store (String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
	Stores the data in an idXML file.
Protected Member Functions
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
void	addProteinGroups_ (MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::map< String, UInt > &accession_to_id)
	Add data from ProteinGroups to a MetaInfoInterface.
void	getProteinGroups_ (std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
	Read and store ProteinGroup data.
Protected Attributes
members for loading data

std::vector < ProteinIdentification > *	prot_ids_
	Pointer to fill in protein identifications.
std::vector < PeptideIdentification > *	pep_ids_
	Pointer to fill in peptide identifications.
MetaInfoInterface *	last_meta_
	Pointer to last read object with MetaInfoInterface.
std::map< String, ProteinIdentification::SearchParameters >	parameters_
	Search parameters map (key is the "id").
ProteinIdentification::SearchParameters	param_
	Temporary search parameters variable.
String	id_
	Temporary id.
ProteinIdentification	prot_id_
	Temporary protein ProteinIdentification.
PeptideIdentification	pep_id_
	Temporary peptide ProteinIdentification.
ProteinHit	prot_hit_
	Temporary protein hit.
PeptideHit	pep_hit_
	Temporary peptide hit.
std::map< String, String >	proteinid_to_accession_
	Map from protein id to accession.
String *	document_id_
	Document identitifier.
bool	prot_id_in_run_
	true if a prot id is contained in the current run

Detailed Description

Used to load and store idXML files.

This class is used to load and store documents that implement the schema of idXML files.

A documented schema for this format can be found at http://open-ms.sourceforge.net/schemas/.

One file can contain several ProteinIdentification runs. Each run consists of peptide hits stored in PeptideIdentification and (optional) protein hits stored in Identification. Peptide and protein hits are connected via a string identifier. We use the search engine and the date as identifier.

Note:: This format will eventually be replaced by the HUPO-PSI (mzIdentML and mzQuantML)) AnalysisXML formats!

Constructor & Destructor Documentation

IdXMLFile ( )

Constructor.

Member Function Documentation

void addProteinGroups_	(	MetaInfoInterface &	meta,
		const std::vector< ProteinIdentification::ProteinGroup > &	groups,
		const String &	group_name,
		const std::map< String, UInt > &	accession_to_id
	)			`[protected]`

Add data from ProteinGroups to a MetaInfoInterface.

virtual void endElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname
	)			`[protected, virtual]`

void getProteinGroups_	(	std::vector< ProteinIdentification::ProteinGroup > &	groups,
		const String &	group_name
	)			`[protected]`

Read and store ProteinGroup data.

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	protein_ids,
		std::vector< PeptideIdentification > &	peptide_ids
	)

Loads the identifications of an idXML file without identifier.

The information is read in and the information is stored in the corresponding variables

Exceptions:

	Exception::FileNotFound	is thrown if the file could not be opened
	Exception::ParseError	is thrown if an error occurs during parsing

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	protein_ids,
		std::vector< PeptideIdentification > &	peptide_ids,
		String &	document_id
	)

Loads the identifications of an idXML file.

The information is read in and the information is stored in the corresponding variables

Exceptions:

	Exception::FileNotFound	is thrown if the file could not be opened
	Exception::ParseError	is thrown if an error occurs during parsing

virtual void startElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)			`[protected, virtual]`

void store	(	String	filename,
		const std::vector< ProteinIdentification > &	protein_ids,
		const std::vector< PeptideIdentification > &	peptide_ids,
		const String &	document_id = `""`
	)