OpenMS  2.7.0
Public Member Functions | Static Public Member Functions | List of all members
MascotXMLFile Class Reference

Used to load Mascot XML files. More...

#include <OpenMS/FORMAT/MascotXMLFile.h>

Inheritance diagram for MascotXMLFile:
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Collaboration diagram for MascotXMLFile:
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Public Member Functions

 MascotXMLFile ()
 Constructor. More...
 
void load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, const SpectrumMetaDataLookup &lookup)
 Loads data from a Mascot XML file. More...
 
void load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
 Loads data from a Mascot XML file. More...
 
- Public Member Functions inherited from XMLFile
 XMLFile ()
 Default constructor. More...
 
 XMLFile (const String &schema_location, const String &version)
 Constructor that sets the schema location. More...
 
virtual ~XMLFile ()
 Destructor. More...
 
bool isValid (const String &filename, std::ostream &os)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Static Public Member Functions

static void initializeLookup (SpectrumMetaDataLookup &lookup, const PeakMap &experiment, const String &scan_regex="")
 Initializes a helper object for looking up spectrum meta data (RT, m/z) More...
 

Additional Inherited Members

- Protected Member Functions inherited from XMLFile
void parse_ (const String &filename, XMLHandler *handler)
 Parses the XML file given by filename using the handler given by handler. More...
 
void parseBuffer_ (const std::string &buffer, XMLHandler *handler)
 Parses the in-memory buffer given by buffer using the handler given by handler. More...
 
void save_ (const String &filename, XMLHandler *handler) const
 Stores the contents of the XML handler given by handler in the file given by filename. More...
 
void enforceEncoding_ (const String &encoding)
 
- Protected Attributes inherited from XMLFile
String schema_location_
 XML schema file location. More...
 
String schema_version_
 Version string. More...
 
String enforced_encoding_
 Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
 

Detailed Description

Used to load Mascot XML files.

This class is used to load documents that implement the schema of Mascot XML files.

Constructor & Destructor Documentation

◆ MascotXMLFile()

Constructor.

Member Function Documentation

◆ initializeLookup()

static void initializeLookup ( SpectrumMetaDataLookup lookup,
const PeakMap experiment,
const String scan_regex = "" 
)
static

Initializes a helper object for looking up spectrum meta data (RT, m/z)

Parameters
lookupHelper object to initialize
experimentExperiment containing the spectra
scan_regexOptional regular expression for extracting information from references to spectra

◆ load() [1/2]

void load ( const String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
const SpectrumMetaDataLookup lookup 
)

Loads data from a Mascot XML file.

Parameters
filenamethe file to be loaded
protein_identificationprotein identifications belonging to the whole experiment
id_datathe identifications with m/z and RT
lookuphelper object for looking up spectrum meta data
Exceptions
Exception::FileNotFoundis thrown if the file does not exists.
Exception::ParseErroris thrown if the file does not suit to the standard.

◆ load() [2/2]

void load ( const String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
std::map< String, std::vector< AASequence > > &  peptides,
const SpectrumMetaDataLookup lookup 
)

Loads data from a Mascot XML file.

Parameters
filenamethe file to be loaded
protein_identificationprotein identifications belonging to the whole experiment
id_datathe identifications with m/z and RT
peptidesa map of modified peptides identified by the String title
lookuphelper object for looking up spectrum meta data
Exceptions
Exception::FileNotFoundis thrown if the file does not exists.
Exception::ParseErroris thrown if the file does not suit to the standard.