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PepXMLFileMascot Class Reference
[File IO]

Used to load Mascot PepXML files. More...

#include <OpenMS/FORMAT/PepXMLFileMascot.h>

Inheritance diagram for PepXMLFileMascot:
XMLHandler XMLFile DefaultHandler

List of all members.

Public Member Functions

 PepXMLFileMascot ()
 Constructor.
void load (const String &filename, std::map< String, std::vector< AASequence > > &peptides)
 Loads peptide sequences with modifications out of a PepXML file.

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)
void matchModification_ (DoubleReal mass, String &modification_description)

Protected Attributes

members for loading data

String actual_title_
 Pointer to fill in protein identifications.
String actual_sequence_
 The sequence of the actual peptide hit.
std::vector< std::pair< String,
UInt > > 		actual_modifications_
 The modifications of the actual peptide hit (position is 1-based).
std::map< String, std::vector
< AASequence > > * 		peptides_
 The peptides together with the spectrum title.
std::vector< AASequence > actual_aa_sequences_
 stores the actual peptide sequences
std::vector< String > fixed_modifications_
 stores the fixed residue modifications
std::vector< std::pair< String,
DoubleReal > > 		variable_modifications_
 stores the variable residue modifications

Detailed Description

Used to load Mascot PepXML files.

A schema for this format can be found at http://www.matrixscience.com/xmlns/schema/pepXML_v18/pepXML_v18.xsd.

Constructor & Destructor Documentation

PepXMLFileMascot (  ) 

Constructor.

Member Function Documentation

virtual void endElement ( const XMLCh *  const,
const XMLCh *  const,
const XMLCh *const   qname 
) [protected, virtual]
void load ( const String &  filename,
std::map< String, std::vector< AASequence > > &  peptides 
)

Loads peptide sequences with modifications out of a PepXML file.

Exceptions:
Exception::FileNotFound is thrown if the file could not be opened
Exception::ParseError is thrown if an error occurs during parsing
void matchModification_ ( DoubleReal  mass,
String &  modification_description 
) [protected]
virtual void startElement ( const XMLCh *  const,
const XMLCh *  const,
const XMLCh *const   qname,
const xercesc::Attributes &  attributes 
) [protected, virtual]

Member Data Documentation

std::vector<AASequence> actual_aa_sequences_ [protected]

stores the actual peptide sequences

std::vector<std::pair<String, UInt> > actual_modifications_ [protected]

The modifications of the actual peptide hit (position is 1-based).

String actual_sequence_ [protected]

The sequence of the actual peptide hit.

String actual_title_ [protected]

Pointer to fill in protein identifications.

The title of the actual spectrum

std::vector<String> fixed_modifications_ [protected]

stores the fixed residue modifications

std::map<String, std::vector<AASequence> >* peptides_ [protected]

The peptides together with the spectrum title.

std::vector<std::pair<String, DoubleReal> > variable_modifications_ [protected]

stores the variable residue modifications

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1