TraMLFile Class Reference

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.
	~TraMLFile () override
	Destructor.
void	load (const std::string &filename, TargetedExperiment &id)
	Loads a map from a TraML file.
void	store (const std::string &filename, const TargetedExperiment &id) const
	Stores a map in a TraML 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.
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 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 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

load()

void load	(	const std::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

store()

void store	(	const std::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