File adapter for HUPO PSI TraML files. More...

#include <OpenMS/FORMAT/TraMLFile.h>

Inheritance diagram for TraMLFile:

Collaboration diagram for TraMLFile:

Public Member Functions
	TraMLFile ()
	Default constructor. More...

	~TraMLFile () override
	Destructor. More...

void	load (const String &filename, TargetedExperiment &id)
	Loads a map from a TraML file. More...

void	store (const String &filename, const TargetedExperiment &id) const
	Stores a map in a TraML 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...

virtual	~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 HUPO PSI TraML files.

TraML files contain information about transitions used for targeted proteomics and metabolomics experiments:

Deutsch et al. "TraML--a standard format for exchange of selected reaction monitoring transition lists." Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040.

In OpenMS, TraML files can be generated from TSV or CSV files using the TransitionTSVFile class or the TargetedFileConverter TOPP Tool. For more information on the TSV format required by the TOPP tool, see see also the documentation of TransitionTSVFile.

Constructor & Destructor Documentation

◆ TraMLFile()

TraMLFile ( )

Default constructor.

◆ ~TraMLFile()

~TraMLFile ( )

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,
		TargetedExperiment &	id
	)

Loads a map from a TraML 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 TOPPOpenSwathBase::loadTransitionList().

◆ store()

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

Stores a map in a TraML file.

Exceptions

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TraMLFile()

◆ ~TraMLFile()

Member Function Documentation

◆ isSemanticallyValid()

◆ load()

◆ store()