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

Inheritance diagram for MzQuantMLHandler:

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

	MzQuantMLHandler (const MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler.
	MzQuantMLHandler (MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler.
virtual	~MzQuantMLHandler ()
	Destructor.
Protected Member Functions
void	handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const String &name, const String &value, const xercesc::Attributes &attributes, const String &cv_ref, const String &unit_accession="")
	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	writeCVParams_ (String &s, const Map< String, std::vector< CVTerm > > &, UInt indent)
	Write CV term.
void	writeUserParams_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent)
	Writes user terms.
void	writeUserParams_ (String &s, const MetaInfoInterface &meta, UInt indent)
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.
void	writeFeature_ (std::ostream &os, const String &identifier_prefix, UInt64 identifier, UInt indentation_level)
	Helper method that writes a feature.
Protected Attributes
const ProgressLogger &	logger_
	Progress logger.
ControlledVocabulary	cv_
	Controlled vocabulary (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo).
String	tag_
MSQuantifications *	msq_
const MSQuantifications *	cmsq_
Private Member Functions
	MzQuantMLHandler ()
	Helper method that writes a source file.
	MzQuantMLHandler (const MzQuantMLHandler &rhs)
MzQuantMLHandler &	operator= (const MzQuantMLHandler &rhs)
Private Attributes
std::map< String, std::vector < ExperimentalSettings > >	current_files_
String	current_id_
String	current_cf_id_
Size	current_count_
std::vector< MetaInfo >	up_stack_
std::vector< CVTerm >	cvp_stack_
MSQuantifications::Assay	current_assay_
std::multimap< String, String >	cm_cf_ids_
std::map< String, String >	f_cf_ids_
std::map< String, ConsensusFeature >	cf_cf_obj_
std::map< String, FeatureHandle >	f_f_obj_
std::map< String, ConsensusFeature::Ratio >	r_rtemp_
std::map< String, String >	numden_r_ids_
std::map< String, ConsensusFeature::Ratio >	r_r_obj_
std::map< String, Software >	current_sws_
std::map< int, DataProcessing >	current_orderedps_
std::pair< int, DataProcessing >	current_dp_
std::set < DataProcessing::ProcessingAction >	current_pas_
std::vector< String >	current_col_types_
std::vector< DoubleReal >	current_dm_values_
std::vector< DoubleReal >	current_row_

Detailed Description

XML handler for MzQuantMLFile.

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

Constructor & Destructor Documentation

MzQuantMLHandler	(	const MSQuantifications &	msq,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

MzQuantMLHandler	(	MSQuantifications &	msq,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

virtual ~MzQuantMLHandler ( ) [virtual]

Destructor.

MzQuantMLHandler ( ) [private]

Helper method that writes a source file.

MzQuantMLHandler ( const MzQuantMLHandler & 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 String &	name,
		const String &	value,
		const xercesc::Attributes &	attributes,
		const String &	cv_ref,
		const String &	unit_accession = `""`
	)			`[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]`