This class provides Input/Output functionality for feature maps. More...

#include <OpenMS/FORMAT/FeatureXMLFile.h>

Inheritance diagram for FeatureXMLFile:

Public Member Functions
void	load (const String &filename, FeatureMap<> &feature_map)
	loads the file with name `filename` into `map`.
Size	loadSize (const String &filename)
void	store (const String &filename, const FeatureMap<> &feature_map)
	stores the map `feature_map` in file with name `filename`.
FeatureFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const FeatureFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
Constructors and Destructor

	FeatureXMLFile ()
	Default constructor.
	~FeatureXMLFile ()
	Destructor.
Protected Member Functions
void	resetMembers_ ()
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)
virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
void	writeFeature_ (const String &filename, std::ostream &os, const Feature &feat, const String &identifier_prefix, UInt64 identifier, UInt indentation_level)
	Writes a feature to a stream.
void	writePeptideIdentification_ (const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level)
	Writes a peptide identification to a stream (for assigned/unassigned peptide identifications).
void	updateCurrentFeature_ (bool create)
	update the pointer to the current feature
Protected Attributes
Int	disable_parsing_
Feature *	current_feature_
	points to the last open <feature> tag (possibly a subordinate feature)
FeatureMap< Feature > *	map_
	Feature map pointer for reading.
FeatureFileOptions	options_
	Options that can be set.
bool	size_only_
	only parse until "count" tag is reached (used in loadSize())
Size	expected_size_
	holds the putative size given in count
UInt	dim_
	current dimension of the feature position, quality, or convex hull point
bool	in_description_
	for downward compatibility, all tags in the old description must be ignored
Int	subordinate_feature_level_
	level in Feature stack during parsing
MetaInfoInterface *	last_meta_
	Pointer to last read object as a MetaInfoInterface, or null.
ProteinIdentification	prot_id_
	Temporary protein ProteinIdentification.
PeptideIdentification	pep_id_
	Temporary peptide ProteinIdentification.
ProteinHit	prot_hit_
	Temporary protein hit.
PeptideHit	pep_hit_
	Temporary peptide hit.
Map< String, String >	proteinid_to_accession_
	Map from protein id to accession.
Map< String, Size >	accession_to_id_
	Map from search identifier concatenated with protein accession to id.
Map< String, String >	identifier_id_
	Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run).
Map< String, String >	id_identifier_
	Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run).
ProteinIdentification::SearchParameters	search_param_
	Temporary search parameters file.
temporary data structures to hold parsed data

ModelDescription< 2 >	model_desc_
Param	param_
ConvexHull2D::PointArrayType	current_chull_
DPosition< 2 >	hull_position_

Detailed Description

This class provides Input/Output functionality for feature maps.

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

Todo:: Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

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

Constructor & Destructor Documentation

FeatureXMLFile ( )

Default constructor.

~FeatureXMLFile ( )

Destructor.

Member Function Documentation

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

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

const FeatureFileOptions& getOptions ( ) const

Non-mutable access to the options for loading/storing.

FeatureFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

void load	(	const String &	filename,
		FeatureMap<> &	feature_map
	)

loads the file with name filename into map.

Exceptions:

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

Size loadSize ( const String & filename )

void resetMembers_ ( ) [protected]

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

void store	(	const String &	filename,
		const FeatureMap<> &	feature_map
	)

stores the map feature_map in file with name filename.

Exceptions:

Exception::UnableToCreateFile

is thrown if the file could not be created

void updateCurrentFeature_ ( bool create ) [protected]

update the pointer to the current feature

Parameters:

create

If true, a new (empty) Feature is added at the appropriate subordinate_feature_level_

void writeFeature_	(	const String &	filename,
		std::ostream &	os,
		const Feature &	feat,
		const String &	identifier_prefix,
		UInt64	identifier,
		UInt	indentation_level
	)			`[protected]`

Writes a feature to a stream.

void writePeptideIdentification_	(	const String &	filename,
		std::ostream &	os,
		const PeptideIdentification &	id,
		const String &	tag_name,
		UInt	indentation_level
	)			`[protected]`

Writes a peptide identification to a stream (for assigned/unassigned peptide identifications).

Member Data Documentation

Map<String, Size> accession_to_id_ [protected]

Map from search identifier concatenated with protein accession to id.

ConvexHull2D::PointArrayType current_chull_ [protected]

Feature* current_feature_ [protected]

points to the last open <feature> tag (possibly a subordinate feature)

UInt dim_ [protected]

current dimension of the feature position, quality, or convex hull point

Int disable_parsing_ [protected]

allows for early return in parsing functions when certain sections should be ignored <=0 - parsing ON >0 - this number of tags have been entered that forbid parsing and need to be exited before parsing continues

Size expected_size_ [protected]

holds the putative size given in count

DPosition<2> hull_position_ [protected]

Map<String, String> id_identifier_ [protected]

Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run).

Map<String, String> identifier_id_ [protected]

Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run).

bool in_description_ [protected]

for downward compatibility, all tags in the old description must be ignored

MetaInfoInterface* last_meta_ [protected]

Pointer to last read object as a MetaInfoInterface, or null.

FeatureMap<Feature>* map_ [protected]