MzMLFile Class Reference

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.
	~MzMLFile () 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, PeakMap &map)
	Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions).
void	loadBuffer (const std::string &buffer, PeakMap &map)
	Loads a map from a MzML file stored in a buffer (in memory).
void	loadSize (const std::string &filename, Size &scount, Size &ccount)
	Only count the number of spectra and chromatograms from a file.
void	store (const std::string &filename, const PeakMap &map) const
	Stores a map in an MzML file.
void	storeBuffer (std::string &output, const PeakMap &map) const
	Stores a map in an output string.
void	transform (const std::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.
void	transform (const std::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.
bool	isValid (const std::string &filename, std::ostream &os=std::cerr)
	Checks if a file validates against the XML schema.
bool	isSemanticallyValid (const std::string &filename, StringList &errors, StringList &warnings)
	Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
bool	hasIndex (const std::string &filename)
	Checks if a file is an indexed MzML file or not.
std::map< UInt, SpecInfo >	getCentroidInfo (const std::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.
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.
void	safeParse_ (const std::string &filename, Internal::XMLHandler *handler)
	Safe parse that catches exceptions and handles them accordingly.
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 Attributes
PeakFileOptions	options_
	Options for loading / storing.
std::string	indexed_schema_location_
	Location of indexed mzML schema.

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 MzML files.

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

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Class Documentation

OpenMS::MzMLFile::SpecInfo

struct OpenMS::MzMLFile::SpecInfo

Collaboration diagram for MzMLFile::SpecInfo:

Class Members
Size	count_centroided = 0
Size	count_profile = 0
Size	count_unknown = 0

Constructor & Destructor Documentation

MzMLFile()

MzMLFile

(

)

Default constructor.

~MzMLFile()

~MzMLFile ( )

override

Destructor.

Member Function Documentation

getCentroidInfo()

std::map< UInt, SpecInfo > getCentroidInfo	(	const std::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

[in]	filename	File name of the mzML file to be checked
[in]	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 NuXLRTPrediction::train().

getOptions() [2/2]

const PeakFileOptions & getOptions

(

)

const

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

hasIndex()

bool hasIndex

(

const std::string &

filename

)

Checks if a file is an indexed MzML file or not.

Parameters

[in]

filename

File name of the file to be checked.

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened

isSemanticallyValid()

bool isSemanticallyValid	(	const std::string &	filename,
		StringList &	errors,
		StringList &	warnings
	)

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

Parameters

[in]	filename	File name of the file to be checked.
[out]	errors	Errors during the validation are returned in this output parameter.
[out]	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 std::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 std::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

[in]	filename	The filename with the data
[out]	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 NuXLRTPrediction::train().

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 std::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 std::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

store()

void store	(	const std::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

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 std::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

[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
[in]	skip_first_pass	Skip first file parsing pass, which hands only meta-data (number of spectra/chroms and experimental settings) to the consumer

transform() [2/2]

void transform	(	const std::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

[in]	filename_in	Filename of input mzML file to transform
[in]	consumer	Consumer class to operate on the input filename (implementing a transformation)
[in]	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
[in]	skip_first_pass	Skip first file parsing pass, which hands only meta-data (number of spectra/chroms and experimental settings) to the consumer

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

indexed_schema_location_

std::string indexed_schema_location_

private

Location of indexed mzML schema.

options_

PeakFileOptions options_

private

Options for loading / storing.