MzIdentMLFile Class Reference

File adapter for MzIdentML files. More...

#include <OpenMS/FORMAT/MzIdentMLFile.h>

Inheritance diagram for MzIdentMLFile:

Collaboration diagram for MzIdentMLFile:

Public Member Functions
	MzIdentMLFile ()
	Default constructor.
	~MzIdentMLFile () override
	Destructor.
void	load (const std::string &filename, std::vector< ProteinIdentification > &poid, PeptideIdentificationList &peid)
	Loads the identifications from a MzIdentML file.
void	store (const std::string &filename, const std::vector< ProteinIdentification > &poid, const PeptideIdentificationList &peid) const
	Stores the identifications in a MzIdentML file.
bool	isSemanticallyValid (const std::string &filename, StringList &errors, StringList &warnings)
	Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
bool	isValid (const std::string &filename, std::ostream &os, std::string &used_version)
	Checks if a file validates against the mzIdentML schema that matches its declared version.
std::string	detectVersion (const std::string &filename) const
	Detect the mzIdentML version declared in filename (e.g. "1.1.0").
Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; schema_location_ remains unset, so isValid cannot be used until derived-class logic initializes schema_location_ before calling isValid.
	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.
virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.
bool	isValid (const std::string &filename, std::ostream &os)
	Check if filename validates against the bound XML schema.
const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

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 std::string &filename, XMLHandler *handler)
	Parse the XML file at filename through handler.
void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through handler.
void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by handler in the file given by filename.
void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.
Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws NotImplemented).
std::string	schema_version_
	Schema version string returned by getVersion.
std::string	enforced_encoding_
	Optional XML encoding override applied to the InputSource in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.
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

File adapter for MzIdentML files.

This file adapter exposes the internal MzIdentML processing capabilities to the library. The file adapter interface is kept the same as idXML file adapter for downward capability reasons. For now, read-in will be performed with DOM write-out with STREAM

Note

due to the limited capabilities of idXML/PeptideIdentification/ProteinIdentification not all MzIdentML features can be supported. Development for these structures will be discontinued, a new interface with appropriate structures will be provided.

If a critical error occurs due to the missing functionality, Exception::NotImplemented is thrown.

All PSM will be read into PeptideIdentification, even the passThreshold=false, threshold will be read into ProteinIdentification (i.e. one id run), considered at writing also will only be the threshold set in ProteinIdentification

All PSM will be read into PeptideIdentification, even the passThreshold=false

Constructor & Destructor Documentation

MzIdentMLFile()

MzIdentMLFile

(

)

Default constructor.

~MzIdentMLFile()

~MzIdentMLFile ( )

override

Destructor.

Member Function Documentation

detectVersion()

std::string detectVersion

(

const std::string &

filename

)

const

Detect the mzIdentML version declared in filename (e.g. "1.1.0").

Reads the version attribute / target namespace from the document header. Falls back to the adapter's default version (1.3.0) if no version can be determined or no matching schema exists.

isSemanticallyValid()

bool isSemanticallyValid	(	const std::string &	filename,
		StringList &	errors,
		StringList &	warnings
	)

Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

Parameters

[in]	filename	File name of the file to be checked.
[out]	errors	Errors during the validation are returned in this output parameter.
[out]	warnings	Warnings during the validation are returned in this output parameter.

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened

isValid()

bool isValid	(	const std::string &	filename,
		std::ostream &	os,
		std::string &	used_version
	)

Checks if a file validates against the mzIdentML schema that matches its declared version.

Unlike the base-class Internal::XMLFile::isValid (which always validates against the schema the file adapter was constructed with), this overload first detects the mzIdentML version declared in filename and validates against the corresponding schema (1.1.0, 1.2.0 or 1.3.0). This keeps older, still-valid mzIdentML files from being reported as invalid just because OpenMS now writes 1.3.0. The schema version actually used is returned via used_version.

Parameters

[in]	filename	File name of the file to be checked.
[in,out]	os	Error-message sink for validation errors.
[out]	used_version	Receives the schema version the file was validated against.

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened

load()

void load	(	const std::string &	filename,
		std::vector< ProteinIdentification > &	poid,
		PeptideIdentificationList &	peid
	)

Loads the identifications from a MzIdentML file.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

store()

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

Stores the identifications in a MzIdentML file.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created