File adapter for MzXML 3.1 files. More...

#include <OpenMS/FORMAT/MzXMLFile.h>

Inheritance diagram for MzXMLFile:

Collaboration diagram for MzXMLFile:

Public Member Functions
	MzXMLFile ()
	Default constructor.

	~MzXMLFile () override
	Destructor.

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

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

void	setOptions (const PeakFileOptions &)
	set options for loading/storing

void	load (const std::string &filename, MapType &map)
	Loads a map from a MzXML file.

void	store (const std::string &filename, const MapType &map) const
	Stores a map in a MzXML file.

void	transform (const std::string &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false)
	Transforms a map while loading using the supplied MSDataConsumer.

void	transform (const std::string &filename_in, Interfaces::IMSDataConsumer *consumer, MapType &map, bool skip_full_count=false)
	Transforms a map while loading using the supplied MSDataConsumer.

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
void	transformFirstPass_ (const std::string &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count)
	Perform first pass through the file and retrieve the meta-data to initialize the consumer.

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.

Private Types
typedef PeakMap	MapType

Private Attributes
PeakFileOptions	options_

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

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

File adapter for MzXML 3.1 files.

Member Typedef Documentation

◆ MapType

typedef PeakMap MapType

private

Constructor & Destructor Documentation

◆ MzXMLFile()

MzXMLFile ( )

Default constructor.

◆ ~MzXMLFile()

~MzXMLFile ( )

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,
		MapType &	map
	)

Loads a map from a MzXML 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 std::string &	filename,
		const MapType &	map
	)		const

Stores a map in a MzXML file.

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

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be created

◆ transform() [1/2]

void transform	(	const std::string &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		bool	skip_full_count = `false`
	)

Transforms a map while loading using the supplied MSDataConsumer.

The result will not be stored directly but is available through the events triggered by the parser and caught by the provided IMSDataConsumer object.

This function should be used if processing and storage of the result can be performed directly in the provided IMSDataConsumer object.

Note: Transformation can be speed up by setting skip_full_count which does not require a full first pass through the file to compute the correct number of spectra and chromatograms in the input file.

Parameters

[in]	filename_in	Filename of input mzML file to transform
[in]	consumer	Consumer class to operate on the input filename (implementing a transformation)
[in]	skip_full_count	Whether to skip computing the correct number of spectra and chromatograms in the input file

◆ transform() [2/2]

void transform	(	const std::string &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		MapType &	map,
		bool	skip_full_count = `false`
	)

Transforms a map while loading using the supplied MSDataConsumer.

The result will be stored in the provided map.

This function should be used if a specific pre-processing should be applied to the data before storing them in a map (e.g. if data-reduction should be applied to the data before loading all data into memory).

Parameters

[in]	filename_in	Filename of input mzXML file to transform
[in]	consumer	Consumer class to operate on the input filename (implementing a transformation)
[out]	map	Map to store the resulting spectra and chromatograms
[in]	skip_full_count	Whether to skip computing the correct number of spectra and chromatograms in the input file

◆ transformFirstPass_()

void transformFirstPass_	(	const std::string &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		bool	skip_full_count
	)

protected

Perform first pass through the file and retrieve the meta-data to initialize the consumer.

Member Data Documentation

◆ options_

PeakFileOptions options_