This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...

#include <OpenMS/FORMAT/ConsensusXMLFile.h>

Inheritance diagram for ConsensusXMLFile:

List of all members.

Public Member Functions
	ConsensusXMLFile ()
	Default constructor.
	~ConsensusXMLFile ()
	Destructor.
void	load (const String &filename, ConsensusMap &map)
	Loads a consensus map from file.
void	store (const String &filename, const ConsensusMap &consensus_map)
	Stores a consensus map to file.
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
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)
virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
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).
Protected Attributes
PeakFileOptions	options_
	Options that can be set.
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.
UInt	progress_
Temporary variables for parsing

ConsensusMap *	consensus_map_
ConsensusFeature	act_cons_element_
DPosition< 2 >	pos_
DoubleReal	it_
UInt	last_map_

Detailed Description

This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.

This class can be used to load the content of a consensusXML file into a ConsensusMap or to save the content of an ConsensusMap object into an XML file.

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 ConsensusXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

Constructor & Destructor Documentation

ConsensusXMLFile ( )

Default constructor.

~ConsensusXMLFile ( )

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]`

PeakFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

const PeakFileOptions& getOptions ( ) const

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

void load	(	const String &	filename,
		ConsensusMap &	map
	)

Loads a consensus map from file.

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	(	const String &	filename,
		const ConsensusMap &	consensus_map
	)

Stores a consensus map to file.

Exceptions:

	Exception::UnableToCreateFile	is thrown if the file name is not writable
	Exception::IllegalArgument	is thrown if the consensus map is not valid

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