SwathFile Class Reference

File adapter for Swath files. More...

#include <OpenMS/FORMAT/SwathFile.h>

Inheritance diagram for SwathFile:

Collaboration diagram for SwathFile:

Public Member Functions
std::vector< OpenSwath::SwathMap >	loadSplit (StringList file_list, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
	Loads a Swath run from a list of split mzML files. More...
std::vector< OpenSwath::SwathMap >	loadMzML (const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal", Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
	Loads a Swath run from a single mzML file. More...
std::vector< OpenSwath::SwathMap >	loadMzXML (String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
	Loads a Swath run from a single mzXML file. More...
std::vector< OpenSwath::SwathMap >	loadSqMass (String file, boost::shared_ptr< ExperimentalSettings > &)
	Loads a Swath run from a single sqMass file. 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
OpenSwath::SpectrumAccessPtr	doCacheFile_ (const String &in, const String &tmp, const String &tmp_fname, boost::shared_ptr< PeakMap > experiment_metadata)
	Cache a file to disk. More...
boost::shared_ptr< PeakMap >	populateMetaData_ (const String &file)
	Only read the meta data from a file and use it to populate exp_meta. More...
void	countScansInSwath_ (const std::vector< MSSpectrum > &exp, std::vector< int > &swath_counter, int &nr_ms1_spectra, std::vector< OpenSwath::SwathMap > &known_window_boundaries)
	Counts the number of scans in a full Swath file (e.g. concatenated non-split file) 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 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

countScansInSwath_()

void countScansInSwath_ ( const std::vector< MSSpectrum > &  exp, std::vector< int > &  swath_counter, int &  nr_ms1_spectra, std::vector< OpenSwath::SwathMap > &  known_window_boundaries  )

protected

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

doCacheFile_()

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

protected

Cache a file to disk.

loadMzML()

std::vector<OpenSwath::SwathMap> loadMzML	(	const String &	file,
		const String &	tmp,
		boost::shared_ptr< ExperimentalSettings > &	exp_meta,
		const 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)

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

loadMzXML()

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

Loads a Swath run from a single mzXML file.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

loadSplit()

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

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

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

loadSqMass()

std::vector<OpenSwath::SwathMap> loadSqMass	(	String	file,
		boost::shared_ptr< ExperimentalSettings > &
	)

Loads a Swath run from a single sqMass file.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

populateMetaData_()

boost::shared_ptr< PeakMap > populateMetaData_ ( const String &  file )

protected

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