#include <OpenMS/FORMAT/IdXMLFile.h>
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.
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. | |
MetaInfoInterface * | last_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, String > | proteinid_to_accession_ |
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.
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] |
virtual void startElement | ( | const XMLCh * | uri, | |
const XMLCh * | localname, | |||
const XMLCh *const | qname, | |||
const xercesc::Attributes & | attrs | |||
) | [protected, virtual] |
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.
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] |
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |