| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | List of all members
MascotXMLFile Class Reference
Format » File IO

Used to load Mascot XML files. More...

`#include <OpenMS/FORMAT/MascotXMLFile.h>`

Inheritance diagram for MascotXMLFile:

## 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 String & | getVersion () 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()

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

  lookup | Helper object to initialize
  experiment | Experiment containing the spectra
  scan_regex | Optional 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

  filename | the file to be loaded
  protein_identification | protein identifications belonging to the whole experiment
  id_data | the identifications with m/z and RT
  lookup | helper object for looking up spectrum meta data

Exceptions

  Exception::FileNotFound | is thrown if the file does not exists.
  Exception::ParseError | is 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

  filename | the file to be loaded
  protein_identification | protein identifications belonging to the whole experiment
  id_data | the identifications with m/z and RT
  peptides | a map of modified peptides identified by the String title
  lookup | helper object for looking up spectrum meta data

Exceptions

  Exception::FileNotFound | is thrown if the file does not exists.
  Exception::ParseError | is thrown if the file does not suit to the standard.