Used to load and store xQuest result files. More...

#include <OpenMS/FORMAT/XQuestResultXMLFile.h>

Inheritance diagram for XQuestResultXMLFile:

Public Member Functions
	XQuestResultXMLFile ()

	~XQuestResultXMLFile () override

void	load (const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
	Load the content of the xquest.xml file into the provided data structures. More...

void	store (const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
	Stores the identifications in a xQuest XML file. 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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static void	writeXQuestXMLSpec (const String &out_file, const 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 (const String &out_file, const 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_
	Total number of hits within the result file. More...

double	min_score_
	Minimum score encountered in file. More...

double	max_score_
	Maximum score encountered in file. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

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)

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Used to load and store xQuest result files.

These files are used to store results derived from chemical cross-linking coupled to MS experiments.

A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

Constructor & Destructor Documentation

◆ XQuestResultXMLFile()

XQuestResultXMLFile ( )

◆ ~XQuestResultXMLFile()

~XQuestResultXMLFile ( )

override

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

Referenced by TOPPXFDR::loadInputFile_().

◆ 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< PeptideIdentification > &	pep_ids,
		std::vector< ProteinIdentification > &	prot_ids
	)

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

Parameters

filename	Filename of the file which is to be loaded.
pep_ids	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.

Referenced by TOPPXFDR::loadInputFile_().

◆ store()

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	poid,
		const std::vector< PeptideIdentification > &	peid
	)		const

Stores the identifications in a xQuest XML file.

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be created

Referenced by TOPPXFDR::main_(), TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

◆ 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

◆ writeXQuestXMLSpec() [1/2]

static void writeXQuestXMLSpec	(	const String &	out_file,
		const 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	(	const String &	out_file,
		const 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

Maximum score encountered in file.

◆ min_score_

double min_score_

private

Minimum score encountered in file.

◆ n_hits_

int n_hits_

private

Total number of hits within the result file.

Public Member Functions

Static Public Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ XQuestResultXMLFile()

◆ ~XQuestResultXMLFile()

Member Function Documentation

◆ getMaxScore()

◆ getMinScore()

◆ getNumberOfHits()

◆ getxQuestBase64EncodedSpectrum_()

◆ load()

◆ store()

◆ wrap_()

◆ writeXQuestXMLSpec() [1/2]

◆ writeXQuestXMLSpec() [2/2]

Member Data Documentation

◆ max_score_

◆ min_score_

◆ n_hits_