MzDataFile Class Reference

File adapter for MzData files. More...

#include <OpenMS/FORMAT/MzDataFile.h>

Inheritance diagram for MzDataFile:

Collaboration diagram for MzDataFile:

Public Member Functions
	MzDataFile ()
	Default constructor. More...
	~MzDataFile () override
	Destructor. 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...
void	setOptions (const PeakFileOptions &)
	set options for loading/storing More...
void	load (const String &filename, MapType &map)
	Loads a map from a MzData file. More...
void	store (const String &filename, const MapType &map) const
	Stores a map in a MzData file. More...
bool	isSemanticallyValid (const String &filename, StringList &errors, StringList &warnings)
	Checks if a file is valid with respect to the mapping file and the controlled vocabulary. 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...

Private Types
typedef PeakMap	MapType

Private Attributes
PeakFileOptions	options_
	Options for loading / storing. More...

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...
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

File adapter for MzData files.

Member Typedef Documentation

MapType

typedef PeakMap MapType

private

Constructor & Destructor Documentation

MzDataFile()

MzDataFile

(

)

Default constructor.

~MzDataFile()

~MzDataFile ( )

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.

isSemanticallyValid()

bool isSemanticallyValid	(	const String &	filename,
		StringList &	errors,
		StringList &	warnings
	)

Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

Parameters

filename	File name of the file to be checked.
errors	Errors during the validation are returned in this output parameter.
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 String &	filename,
		MapType &	map
	)

Loads a map from a MzData file.

map has to be a MSExperiment or have the same interface.

Exceptions

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

setOptions()

void setOptions

(

const PeakFileOptions &

)

set options for loading/storing

store()

void store	(	const String &	filename,
		const MapType &	map
	)		const

Stores a map in a MzData file.

map has to be a MSExperiment or have the same interface.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

Member Data Documentation

options_

PeakFileOptions options_

private

Options for loading / storing.