ConsensusXMLFile Class Reference

This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...

#include <OpenMS/FORMAT/ConsensusXMLFile.h>

Inheritance diagram for ConsensusXMLFile:

Collaboration diagram for ConsensusXMLFile:

Public Member Functions
	ConsensusXMLFile ()
	Default constructor.
	~ConsensusXMLFile () override
	Destructor.
void	load (const std::string &filename, ConsensusMap &map)
	Loads a consensus map from file and calls updateRanges.
void	store (const std::string &filename, const ConsensusMap &consensus_map)
	Stores a consensus map to file.
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
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 Attributes
PeakFileOptions	options_
	Options that can be set.
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_

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.
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.

This class can be used to load the content of a consensusXML file into a ConsensusMap or to save the content of an ConsensusMap object into an XML file.

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 ConsensusXMLFile::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

ConsensusXMLFile()

ConsensusXMLFile

(

)

Default constructor.

~ConsensusXMLFile()

~ConsensusXMLFile ( )

override

Destructor.

Member Function Documentation

getOptions() [1/2]

PeakFileOptions & getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const PeakFileOptions & getOptions

(

)

const

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

load()

void load	(	const std::string &	filename,
		ConsensusMap &	map
	)

Loads a consensus map from file 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
Exception::MissingInformation	is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps

store()

void store	(	const std::string &	filename,
		const ConsensusMap &	consensus_map
	)

Stores a consensus map to file.

Exceptions

Exception::UnableToCreateFile	is thrown if the file name is not writable
Exception::IllegalArgument	is thrown if the consensus map is not valid
Exception::MissingInformation	is thrown if source files are missing/duplicated or map-IDs are referencing non-existing maps

Member Data Documentation

options_

PeakFileOptions options_

protected

Options that can be set.