FeatureXMLFile Class Reference

This class provides Input/Output functionality for feature maps. More...

#include <OpenMS/FORMAT/FeatureXMLFile.h>

Inheritance diagram for FeatureXMLFile:

Collaboration diagram for FeatureXMLFile:

Constructors and Destructor
FeatureFileOptions	options_
	Options that can be set.
	FeatureXMLFile ()
	Default constructor.
	~FeatureXMLFile () override
	Destructor.
void	load (const std::string &filename, FeatureMap &feature_map)
	loads the file with name filename into map and calls updateRanges().
Size	loadSize (const std::string &filename)
void	store (const std::string &filename, const FeatureMap &feature_map)
	stores the map feature_map in file with name filename.
FeatureFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const FeatureFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
void	setOptions (const FeatureFileOptions &)
	setter for options for loading/storing

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

This class provides Input/Output functionality for feature maps.

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

Todo:

Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on OPENMS_LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

Constructor & Destructor Documentation

FeatureXMLFile()

FeatureXMLFile

(

)

Default constructor.

~FeatureXMLFile()

~FeatureXMLFile ( )

override

Destructor.

Member Function Documentation

getOptions() [1/2]

FeatureFileOptions & getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const FeatureFileOptions & getOptions

(

)

const

Non-mutable access to the options for loading/storing.

load()

void load	(	const std::string &	filename,
		FeatureMap &	feature_map
	)

loads the file with name filename into map and calls updateRanges().

Exceptions

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

loadSize()

Size loadSize

(

const std::string &

filename

)

setOptions()

void setOptions

(

const FeatureFileOptions &

)

setter for options for loading/storing

store()

void store	(	const std::string &	filename,
		const FeatureMap &	feature_map
	)

stores the map feature_map in file with name filename.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

Member Data Documentation

options_

FeatureFileOptions options_

protected

Options that can be set.