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. More...

	FeatureXMLFile ()
	Default constructor. More...

	~FeatureXMLFile () override
	Destructor. More...

void	load (const String &filename, FeatureMap &feature_map)
	loads the file with name `filename` into `map` and calls updateRanges(). More...

Size	loadSize (const String &filename)

void	store (const String &filename, const FeatureMap &feature_map)
	stores the map `feature_map` in file with name `filename`. More...

FeatureFileOptions &	getOptions ()
	Mutable access to the options for loading/storing. More...

const FeatureFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing. More...

void	setOptions (const FeatureFileOptions &)
	setter for options for loading/storing More...

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

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

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)

Note: This format will eventually be replaced by the HUPO-PSI AnalysisXML (mzIdentML and mzQuantML) formats!

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 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

Referenced by TOPPViewBase::addDataFile().

◆ loadSize()

Size loadSize ( const String & filename )

◆ setOptions()

void setOptions ( const FeatureFileOptions & )

setter for options for loading/storing

◆ store()

void store	(	const 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

Referenced by TOPPViewBase::runTOPPTool_().

Member Data Documentation

◆ options_

FeatureFileOptions options_

protected

Options that can be set.

Constructors and Destructor

Additional Inherited Members