MzIdentMLFile Class Reference

File adapter for MzIdentML files. More...

#include <OpenMS/FORMAT/MzIdentMLFile.h>

Inheritance diagram for MzIdentMLFile:

Public Member Functions
	MzIdentMLFile ()
	Default constructor. More...
	~MzIdentMLFile () override
	Destructor. More...
void	load (const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
	Loads the identifications from a MzIdentML file. More...
void	store (const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
	Stores the identifications in a MzIdentML file. More...
void	store (const String &filename, const Identification &id) const
	Stores the identifications in a MzIdentML file. More...
bool	isSemanticallyValid (const String &filename, StringList &errors, StringList &warnings)
	Checks if a file is valid with respect to the mapping file and the controlled vocabulary. 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...

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

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

isSemanticallyValid()

bool isSemanticallyValid	(	const String &	filename,
		StringList &	errors,
		StringList &	warnings
	)

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

Parameters

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

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened

load()

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	poid,
		std::vector< PeptideIdentification > &	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

Referenced by TOPPViewBase::addDataFile(), and TOPPViewBase::annotateWithID().

store() [1/2]

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

Stores the identifications in a MzIdentML file.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

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

store() [2/2]

void store	(	const String &	filename,
		const Identification &	id
	)		const

Stores the identifications in a MzIdentML file.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created