MzMLSwathFileConsumer Class Reference

On-disk mzML implementation of FullSwathFileConsumer. More...

#include <OpenMS/FORMAT/DATAACCESS/SwathFileConsumer.h>

Inheritance diagram for MzMLSwathFileConsumer:

Collaboration diagram for MzMLSwathFileConsumer:

Public Types
typedef PeakMap	MapType
typedef MapType::SpectrumType	SpectrumType
typedef MapType::ChromatogramType	ChromatogramType
Public Types inherited from FullSwathFileConsumer
typedef PeakMap	MapType
typedef MapType::SpectrumType	SpectrumType
typedef MapType::ChromatogramType	ChromatogramType
Public Types inherited from IMSDataConsumer
typedef MSSpectrum	SpectrumType
typedef MSChromatogram	ChromatogramType

Public Member Functions
	MzMLSwathFileConsumer (const String &cachedir, const String &basename, Size nr_ms1_spectra, const std::vector< int > &nr_ms2_spectra)
	MzMLSwathFileConsumer (std::vector< OpenSwath::SwathMap > known_window_boundaries, const String &cachedir, const String &basename, Size nr_ms1_spectra, const std::vector< int > &nr_ms2_spectra)
	~MzMLSwathFileConsumer () override
Public Member Functions inherited from FullSwathFileConsumer
	FullSwathFileConsumer ()
	FullSwathFileConsumer (std::vector< OpenSwath::SwathMap > swath_boundaries)
	Constructor. More...
	~FullSwathFileConsumer () override
void	setExpectedSize (Size, Size) override
	Set expected size of spectra and chromatograms to be consumed. More...
void	setExperimentalSettings (const ExperimentalSettings &exp) override
	Set experimental settings (meta-data) of the data to be consumed. More...
void	retrieveSwathMaps (std::vector< OpenSwath::SwathMap > &maps)
	Populate the vector of swath maps after consuming all spectra. More...
void	consumeChromatogram (MapType::ChromatogramType &) override
	Consume a chromatogram -> should not happen when dealing with SWATH maps. More...
void	consumeSpectrum (MapType::SpectrumType &s) override
	* Consume a spectrum which may belong either to an MS1 scan or one of n MS2 (SWATH) scans More...
Public Member Functions inherited from IMSDataConsumer
virtual	~IMSDataConsumer ()

Protected Member Functions
void	deleteSetNull_ ()
void	addNewSwathMap_ ()
void	consumeSwathSpectrum_ (MapType::SpectrumType &s, size_t swath_nr) override
	Consume an MS2 spectrum belonging to SWATH "swath_nr". More...
void	addMS1Map_ ()
void	consumeMS1Spectrum_ (MapType::SpectrumType &s) override
	Consume an MS1 spectrum. More...
void	ensureMapsAreFilled_ () override
	Callback function after the reading is complete. More...

Protected Attributes
PlainMSDataWritingConsumer *	ms1_consumer_
std::vector< PlainMSDataWritingConsumer * >	swath_consumers_
String	cachedir_
String	basename_
int	nr_ms1_spectra_
std::vector< int >	nr_ms2_spectra_
Protected Attributes inherited from FullSwathFileConsumer
std::vector< OpenSwath::SwathMap >	swath_map_boundaries_
	A list of Swath map identifiers (lower/upper boundary and center) More...
std::vector< boost::shared_ptr< PeakMap > >	swath_maps_
	A list of SWATH maps and the MS1 map. More...
boost::shared_ptr< PeakMap >	ms1_map_
PeakMap	settings_
	The Experimental settings. More...
bool	consuming_possible_
	Whether further spectra can still be consumed. More...
bool	use_external_boundaries_
	Whether to use external input for SWATH boundaries. More...
size_t	correct_window_counter_
	How many windows were correctly annotated (non-zero window limits) More...

Detailed Description

On-disk mzML implementation of FullSwathFileConsumer.

Writes all spectra immediately to disk to an mzML file location using the PlainMSDataWritingConsumer. Internally, it handles n+1 (n SWATH + 1 MS1 map) objects of MSDataCachedConsumer which can consume the spectra and write them to disk immediately.

Warning: no swathmaps (MS1 nor MS2) will be available when calling retrieveSwathMaps() for downstream use.

Member Typedef Documentation

ChromatogramType

typedef MapType::ChromatogramType ChromatogramType

MapType

typedef PeakMap MapType

SpectrumType

typedef MapType::SpectrumType SpectrumType

Constructor & Destructor Documentation

MzMLSwathFileConsumer() [1/2]

MzMLSwathFileConsumer ( const String &  cachedir, const String &  basename, Size  nr_ms1_spectra, const std::vector< int > &  nr_ms2_spectra  )

inline

MzMLSwathFileConsumer() [2/2]

MzMLSwathFileConsumer ( std::vector< OpenSwath::SwathMap >  known_window_boundaries, const String &  cachedir, const String &  basename, Size  nr_ms1_spectra, const std::vector< int > &  nr_ms2_spectra  )

inline

~MzMLSwathFileConsumer()

~MzMLSwathFileConsumer ( )

inlineoverride

Member Function Documentation

addMS1Map_()

void addMS1Map_ ( )

inlineprotected

addNewSwathMap_()

void addNewSwathMap_ ( )

inlineprotected

References MzMLHandler::getOptions(), PeakFileOptions::setCompression(), and MSDataWritingConsumer::setExpectedSize().

consumeMS1Spectrum_()

void consumeMS1Spectrum_ ( MapType::SpectrumType &  s )

inlineoverrideprotectedvirtual

Consume an MS1 spectrum.

This function should handle an MS1 spectrum.

Implements FullSwathFileConsumer.

consumeSwathSpectrum_()

void consumeSwathSpectrum_ ( MapType::SpectrumType &  s, size_t  swath_nr  )

inlineoverrideprotectedvirtual

Consume an MS2 spectrum belonging to SWATH "swath_nr".

This function should handle a spectrum belonging to a specific SWATH (indicated by swath_nr).

Implements FullSwathFileConsumer.

References MSSpectrum::clear().

deleteSetNull_()

void deleteSetNull_ ( )

inlineprotected

ensureMapsAreFilled_()

void ensureMapsAreFilled_ ( )

inlineoverrideprotectedvirtual

Callback function after the reading is complete.

Has to ensure that swath_maps_ and ms1_map_ are correctly populated.

Implements FullSwathFileConsumer.

Member Data Documentation

basename_

String basename_

protected

cachedir_

String cachedir_

protected

ms1_consumer_

PlainMSDataWritingConsumer* ms1_consumer_

protected

nr_ms1_spectra_

int nr_ms1_spectra_

protected

nr_ms2_spectra_

std::vector<int> nr_ms2_spectra_

protected

swath_consumers_

std::vector<PlainMSDataWritingConsumer*> swath_consumers_

protected