Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

IdXMLFile Class Reference
[File IO]

#include <OpenMS/FORMAT/IdXMLFile.h>

Inheritance diagram for IdXMLFile:

XMLHandler XMLFile xercesc::DefaultHandler

List of all members.


Detailed Description

Used to load and store IdXML files.

This class is used to load and store documents that implement the schema of IdXML files.

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

One file can contain several ProteinIdentification runs. Each run consists of peptide hits stored in PeptideIdentification and (optional) protein hits stored in Identification. Peptide and protein hits are connected via a string identifier. We use the search engine and the date as identifier.

Note:
This format will eventually be replaced by the HUPO-PSI AnalysisXML format!

Public Member Functions

 IdXMLFile ()
 Constructor.
void load (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids) throw (Exception::FileNotFound, Exception::ParseError)
 Loads the identifications of an IdXML file.
void store (String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids) throw (Exception::UnableToCreateFile)
 Stores the data in an IdXML file.

Protected 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.

Protected Attributes

members for loading data
std::vector
< ProteinIdentification > * 
prot_ids_
 Pointer to fill in protein identifications.
std::vector
< PeptideIdentification > * 
pep_ids_
 Pointer to fill in peptide identifications.
MetaInfoInterfacelast_meta_
 Pointer to last read object with MetaInfoInterface.
std::map< String,
ProteinIdentification::SearchParameters
parameters_
 Search parameters map (key is the "id").
ProteinIdentification::SearchParameters param_
 Temporary search parameters variable.
String id_
 Temporary id.
ProteinIdentification prot_id_
 Temporary protein ProteinIdentification.
PeptideIdentification pep_id_
 Temporary peptide ProteinIdentification.
ProteinHit prot_hit_
 Temporary protein hit.
PeptideHit pep_hit_
 Temporary peptide hit.
std::map< String, Stringproteinid_to_accession_

Constructor & Destructor Documentation

IdXMLFile (  ) 

Constructor.


Member Function Documentation

void load ( const String filename,
std::vector< ProteinIdentification > &  protein_ids,
std::vector< PeptideIdentification > &  peptide_ids 
) throw (Exception::FileNotFound, Exception::ParseError)

Loads the identifications of an IdXML file.

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

void store ( String  filename,
const std::vector< ProteinIdentification > &  protein_ids,
const std::vector< PeptideIdentification > &  peptide_ids 
) throw (Exception::UnableToCreateFile)

Stores the data in an IdXML file.

The data is read in and stored in the file 'filename'.

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

Parsing method for closing tags.

Reimplemented from XMLHandler.

virtual void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const   qname,
const xercesc::Attributes &  attrs 
) [protected, virtual]

Parsing method for opening tags.

Reimplemented from XMLHandler.


Member Data Documentation

std::vector<ProteinIdentification>* prot_ids_ [protected]

Pointer to fill in protein identifications.

std::vector<PeptideIdentification>* pep_ids_ [protected]

Pointer to fill in peptide identifications.

MetaInfoInterface* last_meta_ [protected]

Pointer to last read object with MetaInfoInterface.

std::map<String,ProteinIdentification::SearchParameters> parameters_ [protected]

Search parameters map (key is the "id").

ProteinIdentification::SearchParameters param_ [protected]

Temporary search parameters variable.

String id_ [protected]

Temporary id.

ProteinIdentification prot_id_ [protected]

Temporary protein ProteinIdentification.

PeptideIdentification pep_id_ [protected]

Temporary peptide ProteinIdentification.

ProteinHit prot_hit_ [protected]

Temporary protein hit.

PeptideHit pep_hit_ [protected]

Temporary peptide hit.

std::map<String,String> proteinid_to_accession_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1