File adapter for MzML files. More...

#include <OpenMS/FORMAT/MzMLFile.h>

Inheritance diagram for MzMLFile:

Collaboration diagram for MzMLFile:

Classes
struct	SpecInfo

Public Member Functions
	MzMLFile ()
	Default constructor. More...

	~MzMLFile () 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, PeakMap &map)
	Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions). More...

void	loadBuffer (const std::string &buffer, PeakMap &map)
	Loads a map from a MzML file stored in a buffer (in memory). More...

void	loadSize (const String &filename, Size &scount, Size &ccount)
	Only count the number of spectra and chromatograms from a file. More...

void	store (const String &filename, const PeakMap &map) const
	Stores a map in an MzML file. More...

void	storeBuffer (std::string &output, const PeakMap &map) const
	Stores a map in an output string. More...

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

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

bool	isValid (const String &filename, std::ostream &os=std::cerr)
	Checks if a file validates against the XML schema. 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...

std::map< UInt, SpecInfo >	getCentroidInfo (const String &filename, const Size first_n_spectra_only=10)
	Check type of spectra based on their metadata (if available) or by inspecting the peaks itself. 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
void	transformFirstPass_ (const 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. More...

void	safeParse_ (const String &filename, Internal::XMLHandler *handler)
	Safe parse that catches exceptions and handles them accordingly. 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)

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

String	indexed_schema_location_
	Location of indexed mzML schema. More...

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

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 MzML files.

This implementation does currently not support the whole functionality of MzML.

Class Documentation

◆ OpenMS::MzMLFile::SpecInfo

struct OpenMS::MzMLFile::SpecInfo

Collaboration diagram for MzMLFile::SpecInfo:

[legend]

Class Members
Size	count_centroided
Size	count_profile
Size	count_unknown

Constructor & Destructor Documentation

◆ MzMLFile()

MzMLFile ( )

Default constructor.

◆ ~MzMLFile()

~MzMLFile ( )

override

Destructor.

Member Function Documentation

◆ getCentroidInfo()

std::map<UInt, SpecInfo> getCentroidInfo	(	const String &	filename,
		const Size	first_n_spectra_only = `10`
	)

Check type of spectra based on their metadata (if available) or by inspecting the peaks itself.

By default, only the first first_n_spectra_only, which are NOT 'unknown' are checked to save time. The current PeakFileOptions, e.g. which MS-level to read/skip, are honored, e.g. skipped spectra do not count towards first_n_spectra_only.

You can use this function to estimate the spectrum type, but it should be done for each MS-level separately. Otherwise you might get mixed (PROFILE+CENTROIDED) results.

Parameters

filename	File name of the mzML file to be checked
first_n_spectra_only	Only inspect this many spectra (UNKNOWN spectra do not count) and then end parsing the file

Returns: Map of MS level to counts (centroided, profile, unknown)

Exceptions

Exception::FileNotFound is thrown if the file could not be opened

◆ getOptions() [1/2]

PeakFileOptions& getOptions ( )

Mutable access to the options for loading/storing.

Referenced by NucleicAcidSearchEngine::main_().

◆ 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

◆ isValid()

bool isValid	(	const String &	filename,
		std::ostream &	os = `std::cerr`
	)

Checks if a file validates against the XML schema.

Exceptions

Exception::FileNotFound is thrown if the file cannot be found.

◆ load()

void load	(	const String &	filename,
		PeakMap &	map
	)

Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions).

Parameters

filename	The filename with the data
map	Is an MSExperiment

Exceptions

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

Referenced by CachedSwathFileConsumer::ensureMapsAreFilled_(), TOPPGNPSExport::main_(), and NucleicAcidSearchEngine::main_().

◆ loadBuffer()

void loadBuffer	(	const std::string &	buffer,
		PeakMap &	map
	)

Loads a map from a MzML file stored in a buffer (in memory).

Parameters

[in]	buffer	The buffer with the data (i.e. string with content of an mzML file)
[out]	map	Is an MSExperiment

Exceptions

Exception::ParseError is thrown if an error occurs during parsing

◆ loadSize()

void loadSize	(	const String &	filename,
		Size &	scount,
		Size &	ccount
	)

Only count the number of spectra and chromatograms from a file.

This method honors PeakOptions (if specified) for spectra, i.e. only spectra within the specified RT range and MS levels are counted. If PeakOptions have no filters set (the default), then spectra and chromatogram counts are taken from the counts attribute of the spectrumList/chromatogramList tags (the parsing skips all intermediate data and ends as soon as both counts are available).

◆ safeParse_()

void safeParse_	(	const String &	filename,
		Internal::XMLHandler *	handler
	)

protected

Safe parse that catches exceptions and handles them accordingly.

◆ setOptions()

void setOptions ( const PeakFileOptions & )

set options for loading/storing

Referenced by IndexedMzMLFileLoader::store().

◆ store()

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

Stores a map in an MzML file.

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

Exceptions

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

Referenced by NucleicAcidSearchEngine::main_(), TOPPViewBase::runTOPPTool_(), and IndexedMzMLFileLoader::store().

◆ storeBuffer()

void storeBuffer	(	std::string &	output,
		const PeakMap &	map
	)		const

Stores a map in an output string.

output An empty string to store the result map has to be an MSExperiment

◆ transform() [1/2]

void transform	(	const String &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		bool	skip_full_count = `false`,
		bool	skip_first_pass = `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

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

◆ transform() [2/2]

void transform	(	const String &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		PeakMap &	map,
		bool	skip_full_count = `false`,
		bool	skip_first_pass = `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

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

◆ transformFirstPass_()

void transformFirstPass_	(	const 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

◆ indexed_schema_location_

String indexed_schema_location_

private

Location of indexed mzML schema.

◆ options_

PeakFileOptions options_

private

Options for loading / storing.

Classes

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::MzMLFile::SpecInfo

Constructor & Destructor Documentation

◆ MzMLFile()

◆ ~MzMLFile()

Member Function Documentation

◆ getCentroidInfo()

◆ getOptions() [1/2]

◆ getOptions() [2/2]

◆ isSemanticallyValid()

◆ isValid()

◆ load()

◆ loadBuffer()

◆ loadSize()

◆ safeParse_()

◆ setOptions()

◆ store()

◆ storeBuffer()

◆ transform() [1/2]

◆ transform() [2/2]

◆ transformFirstPass_()

Member Data Documentation

◆ indexed_schema_location_

◆ options_