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MascotXMLHandler Class Reference

Handler that is used for parsing MascotXML data. More...

#include <OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h>

Inheritance diagram for MascotXMLHandler:
XMLHandler DefaultHandler

List of all members.

Public Types

typedef Map< String, Real > RTMapping

Public Member Functions

 MascotXMLHandler (ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const RTMapping &rt_mapping=RTMapping())
 Constructor.
virtual ~MascotXMLHandler ()
 Destructor.
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.
virtual void characters (const XMLCh *const chars, const XMLSize_t)
 Parsing method for character data.

Private Attributes

ProteinIdentification & protein_identification_
 the protein identifications
std::vector
< PeptideIdentification > & 		id_data_
 the identifications (storing the peptide hits)
ProteinHit actual_protein_hit_
PeptideHit actual_peptide_hit_
UInt peptide_identification_index_
String tag_
DateTime date_
String date_time_string_
UInt actual_query_
ProteinIdentification::SearchParameters search_parameters_
String identifier_
String actual_title_
std::map< String, std::vector
< AASequence > > & 		modified_peptides_
String warning_msg_
StringList tags_open_
 tracking the current XML tree
String major_version_
String minor_version_
const RTMapping & rt_mapping_

Detailed Description

Handler that is used for parsing MascotXML data.

Member Typedef Documentation

typedef Map<String, Real> RTMapping

Constructor & Destructor Documentation

MascotXMLHandler ( ProteinIdentification &  protein_identification,
std::vector< PeptideIdentification > &  identifications,
const String &  filename,
std::map< String, std::vector< AASequence > > &  peptides,
const RTMapping &  rt_mapping = RTMapping() 
)

Constructor.

virtual ~MascotXMLHandler (  )  [virtual]

Destructor.

Member Function Documentation

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

Parsing method for character data.

Reimplemented from XMLHandler.

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

Parsing method for opening tags.

Reimplemented from XMLHandler.

Member Data Documentation

PeptideHit actual_peptide_hit_ [private]
ProteinHit actual_protein_hit_ [private]
UInt actual_query_ [private]
String actual_title_ [private]
DateTime date_ [private]
String date_time_string_ [private]
std::vector<PeptideIdentification>& id_data_ [private]

the identifications (storing the peptide hits)

String identifier_ [private]
String major_version_ [private]
String minor_version_ [private]
std::map<String, std::vector<AASequence> >& modified_peptides_ [private]
UInt peptide_identification_index_ [private]
ProteinIdentification& protein_identification_ [private]

the protein identifications

const RTMapping& rt_mapping_ [private]

optional mapping of scan indices to RT's if scan numbers are given; without this mapping, other sources of RT information are used (if available); if all fails, there will be no RT information for peptide hits

ProteinIdentification::SearchParameters search_parameters_ [private]
String tag_ [private]
StringList tags_open_ [private]

tracking the current XML tree

String warning_msg_ [private]
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:43:00 using doxygen 1.7.1