XQuestResultXMLFile Class Reference

#include <OpenMS/FORMAT/XQuestResultXMLFile.h>

Inheritance diagram for XQuestResultXMLFile:

Public Member Functions
	XQuestResultXMLFile ()
	~XQuestResultXMLFile ()
void	load (const String &filename, std::vector< std::vector< PeptideIdentification > > &csms, std::vector< ProteinIdentification > &prot_ids, Size min_n_hits_per_spectrum=0, bool load_to_peptideHit=false)
	Load the content of the xquest.xml file into the provided data structures. More...
int	getNumberOfHits () const
	Returns the total number of hits in the file. More...
double	getMinScore () const
	Returns minimum score among the hits in the file. More...
double	getMaxScore () const
	Returns maximum score among the hits in the 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	writeXQuestXML (String out_file, String base_name, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra, String precursor_mass_tolerance_unit, String fragment_mass_tolerance_unit, double precursor_mass_tolerance, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, String cross_link_name, double cross_link_mass_light, DoubleList cross_link_mass_mono_link, String in_fasta, String in_decoy_fasta, StringList cross_link_residue1, StringList cross_link_residue2, double cross_link_mass_iso_shift, String enzyme_name, Size missed_cleavages)
	Writes xquest.xml output files containing XL-MS identification results. More...
static void	writeXQuestXMLSpec (String out_file, String base_name, const OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
	Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and filtering. More...
static void	writeXQuestXMLSpec (String out_file, String base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
	Writes spec.xml output containing spectra for visualization. This version of the function is meant to be used for label-free linkers. More...

Static Private Member Functions
static String	getxQuestBase64EncodedSpectrum_ (const PeakSpectrum &spec, String header)
	Transforms a PeakSpectrum into a base 64 encoded string, which is the format used in spec.xml for xQuest. More...
static void	wrap_ (const String &input, Size width, String &output)
	A helper function, that takes one string containing one line and wraps it into several lines of a given width. More...

Private Attributes
int	n_hits_
double	min_score_
double	max_score_

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...

Constructor & Destructor Documentation

XQuestResultXMLFile()

XQuestResultXMLFile

(

)

~XQuestResultXMLFile()

~XQuestResultXMLFile

(

)

Member Function Documentation

getMaxScore()

double getMaxScore

(

)

const

Returns maximum score among the hits in the file.

Returns

Maximum score among the hits in the file.

getMinScore()

double getMinScore

(

)

const

Returns minimum score among the hits in the file.

Returns

Minimum score among the hits in the file.

getNumberOfHits()

int getNumberOfHits

(

)

const

Returns the total number of hits in the file.

Returns

total number of hits in the file

getxQuestBase64EncodedSpectrum_()

static String getxQuestBase64EncodedSpectrum_ ( const PeakSpectrum &  spec, String  header  )

staticprivate

Transforms a PeakSpectrum into a base 64 encoded string, which is the format used in spec.xml for xQuest.

Parameters

The	spectrum
A	header for the spectrum, build using the base_name parameter for writeXQuestXMLSpec and the index of the spectrum.

load()

void load	(	const String &	filename,
		std::vector< std::vector< PeptideIdentification > > &	csms,
		std::vector< ProteinIdentification > &	prot_ids,
		Size	min_n_hits_per_spectrum = 0,
		bool	load_to_peptideHit = false
	)

Load the content of the xquest.xml file into the provided data structures.

Parameters

filename	Filename of the file which is to be loaded.
csms	Where the spectra with identifications of the input file will be loaded to.
prot_ids	Where the protein identification of the input file will be loaded to.
min_n_hits_per_spectrum	How many minimum hits a spectrum must contain to be loaded to csms.
load_to_peptideHit	Whether the data will be loaded as meta values also into the peptide hits, instead just into the PeptideIdentification

wrap_()

static void wrap_ ( const String &  input, Size  width, String &  output  )

staticprivate

A helper function, that takes one string containing one line and wraps it into several lines of a given width.

Parameters

The	string as one line
The	preferred line width
String	in which the output is written

writeXQuestXML()

static void writeXQuestXML ( String  out_file, String  base_name, const std::vector< PeptideIdentification > &  peptide_ids, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &  all_top_csms, const PeakMap &  spectra, String  precursor_mass_tolerance_unit, String  fragment_mass_tolerance_unit, double  precursor_mass_tolerance, double  fragment_mass_tolerance, double  fragment_mass_tolerance_xlinks, String  cross_link_name, double  cross_link_mass_light, DoubleList  cross_link_mass_mono_link, String  in_fasta, String  in_decoy_fasta, StringList  cross_link_residue1, StringList  cross_link_residue2, double  cross_link_mass_iso_shift, String  enzyme_name, Size  missed_cleavages  )

static

Writes xquest.xml output files containing XL-MS identification results.

Parameters

Path	and filename for the output file
The	base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra.
The	PeptideIdentifications from a XL-MS search
CrossLinkSpectrumMatches,from	which the IDs were generated.
The	spectra, that were searched as a PeakMap
The	unit of the precursor mass tolerance ("Da" or "ppm")
The	unit of the fragment mass tolerance ("Da" or "ppm")
The	precursor mass tolerance
The	fragment mass tolerance for common ions
The	fragment mass tolerance for cross-linked ions
The	name of the cross-link reagent
The	mass of the cross-link reagent when linking two peptides
List	of possible masses for the cross-link, if it is attached to a peptide on one side
Path	and filename of the target protein database
Path	and filename of the decoy protein database
Residues,that	the first side of the cross-linker can react with
Residues,that	the second side of the cross-linker can react with
The	difference of mass between the two types of cross-linkers, if labeled linkers were used. Should be 0 for label-free linkers.
Name	of the Enzyme used for digestion
Number	of allowed missed cleavages

writeXQuestXMLSpec() [1/2]

static void writeXQuestXMLSpec ( String  out_file, String  base_name, const OPXLDataStructs::PreprocessedPairSpectra &  preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &  spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &  all_top_csms, const PeakMap &  spectra  )

static

Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and filtering.

Parameters

Path	and filename for the output file
The	base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra.
The	preprocessed spectra after comparing and filtering
Indices	of spectrum pairs in the input map
CrossLinkSpectrumMatches,from	which the IDs were generated. Only spectra with matches are written out.
The	spectra, that were searched as a PeakMap. The indices in spectrum_pairs correspond to spectra in this map.

writeXQuestXMLSpec() [2/2]

static void writeXQuestXMLSpec ( String  out_file, String  base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &  all_top_csms, const PeakMap &  spectra  )

static

Writes spec.xml output containing spectra for visualization. This version of the function is meant to be used for label-free linkers.

Parameters

Path	and filename for the output file
The	base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra.
CrossLinkSpectrumMatches,from	which the IDs were generated. Only spectra with matches are written out.
The	spectra, that were searched as a PeakMap.

Member Data Documentation

max_score_

double max_score_

private

min_score_

double min_score_

private

n_hits_

int n_hits_

private