Used to load (storing not supported, yet) ProtXML files. More...

#include <OpenMS/FORMAT/ProtXMLFile.h>

Inheritance diagram for ProtXMLFile:

Public Types
typedef ProteinIdentification::ProteinGroup	ProteinGroup
	A protein group (set of indices into ProteinIdentification).
Public Member Functions
	ProtXMLFile ()
	Constructor.
void	load (const String &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids)
	Loads the identifications of an ProtXML file without identifier.
void	store (const String &filename, const ProteinIdentification &protein_ids, const PeptideIdentification &peptide_ids, const String &document_id="")
	[not implemented yet!] Stores the data in an ProtXML file
Protected Member Functions
void	resetMembers_ ()
	reset members after reading/writing
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
	Docu in base class.
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
	Docu in base class.
void	registerProtein_ (const String &protein_name)
	Creates a new protein entry (if not already present) and appends it to the current group.
void	matchModification_ (const DoubleReal mass, const String &origin, String &modification_description)
	find modification name given a modified AA mass
Protected Attributes
members for loading data

ProteinIdentification *	prot_id_
	Pointer to protein identification.
PeptideIdentification *	pep_id_
	Pointer to peptide identification.
PeptideHit *	pep_hit_
	Temporary peptide hit.
ProteinGroup	protein_group_
	protein group

Detailed Description

Used to load (storing not supported, yet) ProtXML files.

This class is used to load (storing not supported, yet) documents that implement the schema of ProtXML files.

A documented schema for this format comes with the TPP.

OpenMS can only read parts of the protein_summary subtree to extract protein-peptide associations. All other parts are silently ignored.

For protein groups, only the "group leader" (which is annotated with a probability and coverage) receives these attributes. All indistinguishable proteins of the same group only have an accession and score of -1.

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

Todo:: Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris)

Member Typedef Documentation

typedef ProteinIdentification::ProteinGroup ProteinGroup

A protein group (set of indices into ProteinIdentification).

Constructor & Destructor Documentation

ProtXMLFile ( )

Constructor.

Member Function Documentation

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

Docu in base class.

void load	(	const String &	filename,
		ProteinIdentification &	protein_ids,
		PeptideIdentification &	peptide_ids
	)

Loads the identifications of an ProtXML file without identifier.

The information is read in and the information is stored in the corresponding variables

Exceptions:

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

void matchModification_	(	const DoubleReal	mass,
		const String &	origin,
		String &	modification_description
	)			`[protected]`

find modification name given a modified AA mass

Matches a mass of a modified AA to a mod in our modification db For ambigious mods, the first (arbitrary) is returned If no mod is found an error is issued and the return string is empty

Note:: A duplicate of this function is also used in PepXMLFile

Parameters:

	mass	Modified AA's mass
	origin	AA one letter code
	modification_description	[out] Name of the modification, e.g. 'Carboxymethyl (C)'

void registerProtein_ ( const String & protein_name ) [protected]

Creates a new protein entry (if not already present) and appends it to the current group.

void resetMembers_ ( ) [protected]

reset members after reading/writing

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

Docu in base class.

void store	(	const String &	filename,
		const ProteinIdentification &	protein_ids,
		const PeptideIdentification &	peptide_ids,
		const String &	document_id = `""`
	)

[not implemented yet!] Stores the data in an ProtXML file

[not implemented yet!] The data is stored in the file 'filename'.

Exceptions:

Exception::UnableToCreateFile

is thrown if the file could not be created

Member Data Documentation

PeptideHit* pep_hit_ [protected]

Temporary peptide hit.

PeptideIdentification* pep_id_ [protected]

Pointer to peptide identification.

ProteinIdentification* prot_id_ [protected]

Pointer to protein identification.

ProteinGroup protein_group_ [protected]

protein group

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1

ProtXMLFile Class Reference [File IO]

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

ProtXMLFile Class Reference
[File IO]