#include <OpenMS/FORMAT/HANDLERS/MzIdentMLHandler.h>

Inheritance diagram for MzIdentMLHandler:

Public Member Functions
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
	Parsing method for closing tags.
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
	Parsing method for opening tags.
virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
	Parsing method for character data.
virtual void	writeTo (std::ostream &os)
	Writes the contents to a stream.
Constructors and destructor

	MzIdentMLHandler (const Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler.
	MzIdentMLHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler for internal identification structures.
	MzIdentMLHandler (Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler.
	MzIdentMLHandler (std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler for internal identification structures.
virtual	~MzIdentMLHandler ()
	Destructor.
Protected Member Functions
void	handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref)
	Handles CV terms.
void	handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
	Handles user terms.
void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes user terms.
ControlledVocabulary::CVTerm	getChildWithName_ (const String &parent_accession, const String &name) const
	Looks up a child CV term of `parent_accession` with the name `name`. If no such term is found, an empty term is returned.
Protected Attributes
const ProgressLogger &	logger_
	Progress logger.
ControlledVocabulary	cv_
	Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo).
ControlledVocabulary	unimod_
	Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo).
String	tag_
	XML tag parse element.
Identification *	id_
	Identification Item.
std::vector < ProteinIdentification > *	pro_id_
	internal Identification Item for proteins
std::vector < PeptideIdentification > *	pep_id_
	Identification Item for peptides.
const Identification *	cid_
const std::vector < ProteinIdentification > *	cpro_id_
const std::vector < PeptideIdentification > *	cpep_id_
SpectrumIdentification	current_spectrum_id_
	SpectrumIdentification Item.
IdentificationHit	current_id_hit_
	IdentificationHit Item.
Private Member Functions
	MzIdentMLHandler ()
	Helper method that writes a source file.
	MzIdentMLHandler (const MzIdentMLHandler &rhs)
MzIdentMLHandler &	operator= (const MzIdentMLHandler &rhs)
Private Attributes
Map< String, AASequence >	pep_sequences_
AASequence	actual_peptide_
Int	current_mod_location_
ProteinHit	actual_protein_

Detailed Description

XML handler for MzIdentMLFile.

Note:: Do not use this class. It is only needed in MzIdentMLFile.

Constructor & Destructor Documentation

MzIdentMLHandler	(	const Identification &	id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

MzIdentMLHandler	(	const std::vector< ProteinIdentification > &	pro_id,
		const std::vector< PeptideIdentification > &	pep_id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler for internal identification structures.

MzIdentMLHandler	(	Identification &	id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

MzIdentMLHandler	(	std::vector< ProteinIdentification > &	pro_id,
		std::vector< PeptideIdentification > &	pep_id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler for internal identification structures.

virtual ~MzIdentMLHandler ( ) [virtual]

Destructor.

MzIdentMLHandler ( ) [private]

Helper method that writes a source file.

MzIdentMLHandler ( const MzIdentMLHandler & rhs ) [private]

Member Function Documentation

virtual void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)			`[virtual]`

Parsing method for character data.

Reimplemented from XMLHandler.

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

ControlledVocabulary::CVTerm getChildWithName_	(	const String &	parent_accession,
		const String &	name
	)			const `[protected]`

Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.

void handleCVParam_	(	const String &	parent_parent_tag,
		const String &	parent_tag,
		const String &	accession,
		const xercesc::Attributes &	attributes,
		const String &	cv_ref
	)			`[protected]`

Handles CV terms.

void handleUserParam_	(	const String &	parent_parent_tag,
		const String &	parent_tag,
		const String &	name,
		const String &	type,
		const String &	value
	)			`[protected]`