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

Inheritance diagram for TraMLHandler:

Public Types
typedef std::vector < ReactionMonitoringTransition::Product >	ProductListType
typedef std::vector < ReactionMonitoringTransition::Configuration >	ConfigurationListType
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

	TraMLHandler (const TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler.
	TraMLHandler (TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler.
virtual	~TraMLHandler ()
	Destructor.
Protected Member Functions
void	handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const CVTerm &cv_term)
	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.
void	writeUserParams_ (std::ostream &os, const std::vector< MetaInfoInterface > &meta, UInt indent) const
void	writeCVParams_ (std::ostream &os, const CVTermList &cv_terms, UInt indent) const
void	writeTarget_ (std::ostream &os, const std::vector< IncludeExcludeTarget >::const_iterator &it) const
void	writeProduct_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Product >::const_iterator &prod_it) const
void	writeConfiguration_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &cit) const
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).
String	tag_
TargetedExperiment *	exp_
const TargetedExperiment *	cexp_
TargetedExperiment::Publication	actual_publication_
TargetedExperiment::Contact	actual_contact_
TargetedExperiment::Instrument	actual_instrument_
TargetedExperiment::Prediction	actual_prediction_
Software	actual_software_
TargetedExperiment::Protein	actual_protein_
TargetedExperiment::RetentionTime	actual_rt_
TargetedExperiment::Peptide	actual_peptide_
TargetedExperiment::Compound	actual_compound_
ReactionMonitoringTransition	actual_transition_
IncludeExcludeTarget	actual_target_
CVTermList	actual_validation_
CVTermList	actual_interpretation_
std::vector < ReactionMonitoringTransition::Product >	actual_intermediate_products_
ReactionMonitoringTransition::Product	actual_product_
ReactionMonitoringTransition::Configuration	actual_configuration_
SourceFile	actual_sourcefile_
Private Member Functions
	TraMLHandler ()
	Helper method that writes a source file.
	TraMLHandler (const TraMLHandler &rhs)
TraMLHandler &	operator= (const TraMLHandler &rhs)

Detailed Description

XML handler for TraMLFile.

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

Member Typedef Documentation

typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType

typedef std::vector<ReactionMonitoringTransition::Product> ProductListType

Constructor & Destructor Documentation

TraMLHandler	(	const TargetedExperiment &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

TraMLHandler	(	TargetedExperiment &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

virtual ~TraMLHandler ( ) [virtual]

Destructor.

TraMLHandler ( ) [private]

Helper method that writes a source file.

TraMLHandler ( const TraMLHandler & 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 CVTerm &	cv_term
	)			`[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]`