File adapter for Swath files. More...

#include <OpenMS/FORMAT/SwathFile.h>

Inheritance diagram for SwathFile:

Public Member Functions
std::vector< OpenSwath::SwathMap >	loadSplit (StringList file_list, const std::string &tmp, std::shared_ptr< ExperimentalSettings > &exp_meta, const std::string &readoptions="normal")
	Loads a Swath run from a list of split mzML files.

std::vector< OpenSwath::SwathMap >	loadMzML (const std::string &file, const std::string &tmp, std::shared_ptr< ExperimentalSettings > &exp_meta, const std::string &readoptions="normal", Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	Loads a Swath run from a single mzML file.

std::vector< OpenSwath::SwathMap >	loadFromMSExperiment (const std::shared_ptr< PeakMap > &exp, const std::string &tmp, std::shared_ptr< ExperimentalSettings > &exp_meta, const std::string &readoptions="normal")
	Loads a Swath run from a pre-loaded in-memory MSExperiment.

std::vector< FAIMSSwathMapGroup >	loadFromMSExperimentByFAIMSCV (PeakMap &&exp, const std::string &tmp, std::shared_ptr< ExperimentalSettings > &exp_meta, const std::string &readoptions="normal")
	Partition a pre-loaded experiment once by FAIMS CV and convert each group to SWATH maps.

std::vector< OpenSwath::SwathMap >	loadMzXML (const std::string &file, const std::string &tmp, std::shared_ptr< ExperimentalSettings > &exp_meta, const std::string &readoptions="normal")
	Loads a Swath run from a single mzXML file.

std::vector< OpenSwath::SwathMap >	loadSqMass (const std::string &file, std::shared_ptr< ExperimentalSettings > &)
	Loads a Swath run from a single sqMass file.

std::vector< OpenSwath::SwathMap >	loadOnDisc (const std::shared_ptr< IMSExperimentRandomAccess > &experiment, std::shared_ptr< ExperimentalSettings > &exp_meta, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	SWATH maps that read the spectra on access from a random-access experiment ("onDisc")

std::vector< OpenSwath::SwathMap >	loadOnDisc (const std::string &file, std::shared_ptr< ExperimentalSettings > &exp_meta, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	Loads a Swath run with readoptions "onDisc": the file is indexed once and the spectra are read on access.

std::vector< FAIMSSwathMapGroup >	loadOnDiscByFAIMSCV (const std::shared_ptr< IMSExperimentRandomAccess > &experiment, std::shared_ptr< ExperimentalSettings > &exp_meta, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	Like loadOnDisc(), but partitions MS1 and MS2 spectra by FAIMS compensation voltage first.

std::vector< FAIMSSwathMapGroup >	loadOnDiscByFAIMSCV (const std::string &file, std::shared_ptr< ExperimentalSettings > &exp_meta, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	loadOnDiscByFAIMSCV() on a file; the backend is chosen as in loadOnDisc(const std::string&, ...)

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
std::vector< OpenSwath::SwathMap >	buildOnDiscMaps_ (const std::shared_ptr< IMSExperimentRandomAccess > &experiment, const PeakMap &metadata, const std::vector< Size > &indices)
	SpectrumAccessOnDisc maps for the spectra `indices` of `experiment` (`metadata:` all spectra without peaks)

void	passOnDiscToPlugin_ (IMSExperimentRandomAccess &experiment, const PeakMap &metadata, ExperimentalSettings &exp_meta, Interfaces::IMSDataConsumer *plugin_consumer)
	Passes every spectrum to `plugin_consumer`; throws Exception::IllegalArgument if it modifies one.

std::shared_ptr< IMSExperimentRandomAccess >	openOnDisc_ (const std::string &file)
	Opens `file` with the random-access backend for its type (see loadOnDisc(const std::string&, ...))

OpenSwath::SpectrumAccessPtr	doCacheFile_ (const std::string &in, const std::string &tmp, const std::string &tmp_fname, const std::shared_ptr< PeakMap > &experiment_metadata)
	Cache a file to disk.

std::shared_ptr< PeakMap >	populateMetaData_ (const std::string &file)
	Only read the meta data from a file and use it to populate exp_meta.

void	countScansInSwath_ (const std::vector< MSSpectrum > &exp, std::vector< int > &swath_counter, int &nr_ms1_spectra, std::vector< OpenSwath::SwathMap > &known_window_boundaries, double TOLERANCE=1e-6)
	Counts the number of scans in a full Swath file (e.g. concatenated non-split file)

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

This class can load SWATH files in different storage versions. The most convenient file is a single MzML file which contains one experiment. However, also the loading of a list of files is supported (loadSplit) where it is assumed that each individual file only contains scans from one precursor isolation window (one SWATH). Finally, experimental support for mzXML is available but needs to be selected with a specific compile flag (this is not for everyday use).

Member Function Documentation

◆ buildOnDiscMaps_()

std::vector< OpenSwath::SwathMap > buildOnDiscMaps_	(	const std::shared_ptr< IMSExperimentRandomAccess > &	experiment,
		const PeakMap &	metadata,
		const std::vector< Size > &	indices
	)

protected

SpectrumAccessOnDisc maps for the spectra indices of experiment (metadata: all spectra without peaks)

◆ countScansInSwath_()

void countScansInSwath_	(	const std::vector< MSSpectrum > &	exp,
		std::vector< int > &	swath_counter,
		int &	nr_ms1_spectra,
		std::vector< OpenSwath::SwathMap > &	known_window_boundaries,
		double	TOLERANCE = `1e-6`
	)

protected

Counts the number of scans in a full Swath file (e.g. concatenated non-split file)

◆ doCacheFile_()

OpenSwath::SpectrumAccessPtr doCacheFile_	(	const std::string &	in,
		const std::string &	tmp,
		const std::string &	tmp_fname,
		const std::shared_ptr< PeakMap > &	experiment_metadata
	)

protected

Cache a file to disk.

◆ loadFromMSExperiment()

std::vector< OpenSwath::SwathMap > loadFromMSExperiment	(	const std::shared_ptr< PeakMap > &	exp,
		const std::string &	tmp,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		const std::string &	readoptions = `"normal"`
	)

Loads a Swath run from a pre-loaded in-memory MSExperiment.

Used when the input format does not have a streaming reader (e.g. Thermo .raw via openms-thermo-bridge), so the full experiment has already been materialized. Avoids the round-trip through a temporary mzML file.

Parameters

[in]	exp	The pre-loaded experiment (must contain all spectra and metadata)
[in]	tmp	Temporary directory (used only for readoptions=="cache")
[out]	exp_meta	ExperimentalSettings extracted from `exp`
[in]	readoptions	"normal" (in-memory) or "cache" (disk-cached)

Returns: Swath maps for MS2 and MS1

◆ loadFromMSExperimentByFAIMSCV()

std::vector< FAIMSSwathMapGroup > loadFromMSExperimentByFAIMSCV	(	PeakMap &&	exp,
		const std::string &	tmp,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		const std::string &	readoptions = `"normal"`
	)

Partition a pre-loaded experiment once by FAIMS CV and convert each group to SWATH maps.

This is the FAIMS-aware adapter for in-memory inputs such as Thermo RAW data loaded through ThermoRawFile. It reuses IMDataConverter::splitByFAIMSCV() for CV assignment and loadFromMSExperiment() for the existing SWATH-window conversion. No FAIMS-specific state is added to OpenSwath::SwathMap; the CV is carried by the enclosing FAIMSSwathMapGroup.

The input experiment is consumed. For non-FAIMS data, one group with a NaN CV is returned. For single-CV FAIMS data, one group with that CV is returned. Multi-CV input produces one group per exact compensation voltage.

Parameters

[in,out]	exp	Pre-loaded experiment; spectra are moved into per-CV groups
[in]	tmp	Temporary directory (used only for readoptions=="cache")
[out]	exp_meta	Experimental metadata copied before `exp` is consumed
[in]	readoptions	"normal" (in-memory) or "cache" (disk-cached)

Returns: FAIMS CV groups containing ordinary OpenSWATH maps

◆ loadMzML()

std::vector< OpenSwath::SwathMap > loadMzML	(	const std::string &	file,
		const std::string &	tmp,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		const std::string &	readoptions = `"normal"`,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

Loads a Swath run from a single mzML file.

Using the plugin_consumer, you can provide a custom consumer which will be chained into the process of loading the data and making it available (depending on readoptions). This is useful if you want to modify the data a priori or extract some other information using MSDataTransformingConsumer (for example). Make sure it leaves the data intact, such that the returned SwathMaps are actually useful.

Parameters

[in]	file	Input filename
[in]	tmp	Temporary directory (for cached data)
[out]	exp_meta	Experimental metadata from mzML file
[in]	readoptions	How are spectra accessed after reading - tradeoff between memory usage and time (disk caching)
[in]	plugin_consumer	An intermediate custom consumer

Returns: Swath maps for MS2 and MS1 (unless readoptions == split, which returns no data)

◆ loadMzXML()

std::vector< OpenSwath::SwathMap > loadMzXML	(	const std::string &	file,
		const std::string &	tmp,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		const std::string &	readoptions = `"normal"`
	)

Loads a Swath run from a single mzXML file.

◆ loadOnDisc() [1/2]

std::vector< OpenSwath::SwathMap > loadOnDisc	(	const std::shared_ptr< IMSExperimentRandomAccess > &	experiment,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

SWATH maps that read the spectra on access from a random-access experiment ("onDisc")

The SWATH windows are determined from the spectrum metadata as for the other read options; each map is a SpectrumAccessOnDisc view with its own handle (clone()) on experiment.

Parameters

[in]	experiment	Open random-access experiment
[out]	exp_meta	Run metadata
[in]	plugin_consumer	Optional consumer that observes every spectrum once. The maps read the spectra again, so it must not modify them.

Returns: Swath maps for MS2 and MS1

Exceptions

Exception::NullPointer	if `experiment` is null
Exception::IllegalArgument	if `experiment` has no meta data (e.g. opened with skipMetaData), if the input has more than one FAIMS compensation voltage (use loadOnDiscByFAIMSCV()) or if `plugin_consumer` modifies a spectrum

◆ loadOnDisc() [2/2]

std::vector< OpenSwath::SwathMap > loadOnDisc	(	const std::string &	file,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

Loads a Swath run with readoptions "onDisc": the file is indexed once and the spectra are read on access.

The random-access backend is chosen by file type: OnDiscMSExperiment for indexed mzML, OnDiscThermoRawExperiment for Thermo .raw (requires WITH_THERMO_RAW; centroided, as with the other read options). Nothing is loaded or cached up front; the spectra and SWATH windows are the same as with the other read options. See loadOnDisc(const std::shared_ptr<IMSExperimentRandomAccess>&, ...).

Parameters

[in]	file	Indexed mzML or Thermo .raw file
[out]	exp_meta	Run metadata
[in]	plugin_consumer	Optional consumer that observes every spectrum once (it must not modify them)

Returns: Swath maps for MS2 and MS1

Exceptions

Exception::InvalidValue	if the file type has no random-access backend
Exception::ParseError	if an mzML file is not indexed
Exception::IllegalArgument	if the input has more than one FAIMS compensation voltage or if `plugin_consumer` modifies a spectrum

◆ loadOnDiscByFAIMSCV() [1/2]

std::vector< FAIMSSwathMapGroup > loadOnDiscByFAIMSCV	(	const std::shared_ptr< IMSExperimentRandomAccess > &	experiment,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

Like loadOnDisc(), but partitions MS1 and MS2 spectra by FAIMS compensation voltage first.

The assignment follows IMDataConverter::splitByFAIMSCV(): a spectrum with drift time unit FAIMS_COMPENSATION_VOLTAGE goes to the CV in its drift time, an MS2+ spectrum without a CV to the most recent CV before it, other spectra are skipped. SWATH windows are then determined within each CV. Without FAIMS data, one group with CV NaN holds all spectra.

Parameters

[in]	experiment	Open random-access experiment
[out]	exp_meta	Run metadata
[in]	plugin_consumer	Optional consumer that observes every spectrum once (it must not modify them)

Returns: SWATH maps per FAIMS compensation voltage, in ascending CV order

Exceptions

Exception::NullPointer	if `experiment` is null
Exception::IllegalArgument	if `experiment` has no meta data (e.g. opened with skipMetaData) or if `plugin_consumer` modifies a spectrum

◆ loadOnDiscByFAIMSCV() [2/2]

std::vector< FAIMSSwathMapGroup > loadOnDiscByFAIMSCV	(	const std::string &	file,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

loadOnDiscByFAIMSCV() on a file; the backend is chosen as in loadOnDisc(const std::string&, ...)

◆ loadSplit()

std::vector< OpenSwath::SwathMap > loadSplit	(	StringList	file_list,
		const std::string &	tmp,
		std::shared_ptr< ExperimentalSettings > &	exp_meta,
		const std::string &	readoptions = `"normal"`
	)

Loads a Swath run from a list of split mzML files.

◆ loadSqMass()

std::vector< OpenSwath::SwathMap > loadSqMass	(	const std::string &	file,
		std::shared_ptr< ExperimentalSettings > &
	)

Loads a Swath run from a single sqMass file.

◆ openOnDisc_()

std::shared_ptr< IMSExperimentRandomAccess > openOnDisc_ ( const std::string & file )

protected

Opens file with the random-access backend for its type (see loadOnDisc(const std::string&, ...))

◆ passOnDiscToPlugin_()

void passOnDiscToPlugin_	(	IMSExperimentRandomAccess &	experiment,
		const PeakMap &	metadata,
		ExperimentalSettings &	exp_meta,
		Interfaces::IMSDataConsumer *	plugin_consumer
	)

protected

Passes every spectrum to plugin_consumer; throws Exception::IllegalArgument if it modifies one.

◆ populateMetaData_()

std::shared_ptr< PeakMap > populateMetaData_ ( const std::string & file )

protected

Only read the meta data from a file and use it to populate exp_meta.

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ buildOnDiscMaps_()

◆ countScansInSwath_()

◆ doCacheFile_()

◆ loadFromMSExperiment()

◆ loadFromMSExperimentByFAIMSCV()

◆ loadMzML()

◆ loadMzXML()

◆ loadOnDisc() [1/2]

◆ loadOnDisc() [2/2]

◆ loadOnDiscByFAIMSCV() [1/2]

◆ loadOnDiscByFAIMSCV() [2/2]

◆ loadSplit()

◆ loadSqMass()

◆ openOnDisc_()

◆ passOnDiscToPlugin_()

◆ populateMetaData_()