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, 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 (String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
	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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~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...

Protected Member Functions
OpenSwath::SpectrumAccessPtr	doCacheFile_ (String in, String tmp, String tmp_fname, boost::shared_ptr< PeakMap > experiment_metadata)
	Cache a file to disk. More...

boost::shared_ptr< PeakMap >	populateMetaData_ (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
	)

inlineprotected

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

References SwathMap::center, MSSpectrum::getMSLevel(), SpectrumSettings::getPrecursors(), LOG_DEBUG, SwathMap::lower, and SwathMap::upper.

◆ doCacheFile_()

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

inlineprotected

Cache a file to disk.

References SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(), MzMLFile::load(), MzMLFile::transform(), and CachedmzML::writeMetadata().

◆ loadMzML()

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

inline

Loads a Swath run from a single mzML file.

References LOG_DEBUG, FullSwathFileConsumer::retrieveSwathMaps(), and MzMLFile::transform().

Referenced by SortPairDoubleByFirst().

◆ loadMzXML()

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

inline

Loads a Swath run from a single mzXML file.

References MzXMLFile::getOptions(), MzXMLFile::load(), LOG_DEBUG, FullSwathFileConsumer::retrieveSwathMaps(), PeakFileOptions::setAlwaysAppendData(), PeakFileOptions::setFillData(), and MzXMLFile::transform().

Referenced by SortPairDoubleByFirst().

◆ loadSplit()

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