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. More...
	~ConsensusXMLFile () override
	Destructor. More...
void	load (const String &filename, ConsensusMap &map)
	Loads a consensus map from file and calls updateRanges. More...
void	store (const String &filename, const ConsensusMap &consensus_map)
	Stores a consensus map to file. More...
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing. More...
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing. 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 (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Attributes
PeakFileOptions	options_
	Options that can be set. 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_

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...
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 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

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), and TOPPGNPSExport::main_().

store()

void store	(	const 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.