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MascotXMLFile Class Reference

Used to load MascotXML files. More...

#include <OpenMS/FORMAT/MascotXMLFile.h>

Inheritance diagram for MascotXMLFile:
XMLFile

Public Types

typedef Internal::MascotXMLHandler::RTMapping RTMapping
 

Public Member Functions

 MascotXMLFile ()
 Constructor. More...
 
void load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, const RTMapping &rt_mapping=RTMapping(), const String &scan_regex="")
 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 RTMapping &rt_mapping=RTMapping(), const String &scan_regex="")
 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 generateRTMapping (const MSExperiment<>::ConstIterator begin, const MSExperiment<>::ConstIterator end, RTMapping &rt_mapping)
 Generates a mapping between scan numbers and retention times in raw data. 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 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 MascotXML files.

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

Member Typedef Documentation

Constructor & Destructor Documentation

Constructor.

Member Function Documentation

static void generateRTMapping ( const MSExperiment<>::ConstIterator  begin,
const MSExperiment<>::ConstIterator  end,
RTMapping rt_mapping 
)
static

Generates a mapping between scan numbers and retention times in raw data.

Parameters
beginIterator to the first spectrum
endIterator past the last spectrum
rt_mappingOutput mapping

The mapping can be used to infer retention times of identifications when a Mascot XML file is loaded.

void load ( const String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
const RTMapping rt_mapping = RTMapping(),
const String scan_regex = "" 
)

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
rt_mappingAn optional mapping of scan indices to RT, in case the file only contains scan numbers
scan_regexAn optional regular expression used to extract the scan numbers
Exceptions
Exception::FileNotFoundis thrown if the file does not exists.
Exception::ParseErroris thrown if the file does not suit to the standard.

This method serves to read in a Mascot XML file. The information can be retrieved via the load function.

void load ( const String filename,
ProteinIdentification protein_identification,
std::vector< PeptideIdentification > &  id_data,
std::map< String, std::vector< AASequence > > &  peptides,
const RTMapping rt_mapping = RTMapping(),
const String scan_regex = "" 
)

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
rt_mappingAn optional mapping of scan indices to RT, in case the file only contains scan numbers
scan_regexAn optional regular expression used to extract the scan numbers
Exceptions
Exception::FileNotFoundis thrown if the file does not exists.
Exception::ParseErroris thrown if the file does not suit to the standard.

This method serves to read in a Mascot XML file. The information can be retrieved via the load function.


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11