Abstract base class which can consume spectra coming from SWATH experiment stored in a single file. More...

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

Inheritance diagram for FullSwathFileConsumer:

Collaboration diagram for FullSwathFileConsumer:

Public Types
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
	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
virtual void	consumeSwathSpectrum_ (MapType::SpectrumType &s, size_t swath_nr)=0
	Consume an MS2 spectrum belonging to SWATH "swath_nr". More...

virtual void	consumeMS1Spectrum_ (MapType::SpectrumType &s)=0
	Consume an MS1 spectrum. More...

virtual void	ensureMapsAreFilled_ ()=0
	Callback function after the reading is complete. More...

Protected Attributes
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

Abstract base class which can consume spectra coming from SWATH experiment stored in a single file.

The class consumes spectra which are coming from a complete SWATH experiment. It will group MS2 spectra by their precursor m/z, assuming that they correspond to the same SWATH window. For example, the spectra could be arranged in the following fashion:

MS1 Spectrum (no precursor)
MS2 Spectrum (precursor = [400,425])
MS2 Spectrum (precursor = [425,450])
[...]
MS2 Spectrum (precursor = [1175,1200])
MS1 Spectrum (no precursor)
MS2 Spectrum (precursor = [400,425])
MS2 Spectrum (precursor = [425,450])
[...]

Base classes are expected to implement functions consuming a spectrum coming from a specific SWATH or an MS1 spectrum and a final function ensureMapsAreFilled_ after which the swath_maps_ vector needs to contain valid pointers to MSExperiment.

In addition it is possible to provide the swath boundaries and the read in spectra will be matched by their precursor m/z to the "center" attribute of the provided Swath maps.

Usage:

FullSwathFileConsumer * dataConsumer;
// assign dataConsumer to an implementation of FullSwathFileConsumer
MzMLFile().transform(file, dataConsumer);
dataConsumer->retrieveSwathMaps(maps);

Member Typedef Documentation

◆ ChromatogramType

typedef MapType::ChromatogramType ChromatogramType

◆ MapType

typedef PeakMap MapType

◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

Constructor & Destructor Documentation

◆ FullSwathFileConsumer() [1/2]

FullSwathFileConsumer ( )

inline

◆ FullSwathFileConsumer() [2/2]

FullSwathFileConsumer ( std::vector< OpenSwath::SwathMap > swath_boundaries )

inline

Constructor.

Parameters

swath_boundaries A vector of SwathMaps of which only the center, lower and upper attributes will be used to infer the expected Swath maps.

◆ ~FullSwathFileConsumer()

~FullSwathFileConsumer ( )

inlineoverride

Member Function Documentation

◆ consumeChromatogram()

void consumeChromatogram ( MapType::ChromatogramType & )

inlineoverridevirtual

Consume a chromatogram -> should not happen when dealing with SWATH maps.

Implements IMSDataConsumer.

◆ consumeMS1Spectrum_()

virtual void consumeMS1Spectrum_ ( MapType::SpectrumType & s )

protectedpure virtual

Consume an MS1 spectrum.

This function should handle an MS1 spectrum.

Implemented in MzMLSwathFileConsumer, CachedSwathFileConsumer, and RegularSwathFileConsumer.

◆ consumeSpectrum()

void consumeSpectrum ( MapType::SpectrumType & s )

inlineoverridevirtual

* Consume a spectrum which may belong either to an MS1 scan or one of n MS2 (SWATH) scans

Implements IMSDataConsumer.

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

◆ consumeSwathSpectrum_()

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

protectedpure virtual

Consume an MS2 spectrum belonging to SWATH "swath_nr".

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

Implemented in MzMLSwathFileConsumer, CachedSwathFileConsumer, and RegularSwathFileConsumer.

◆ ensureMapsAreFilled_()

virtual void ensureMapsAreFilled_ ( )

protectedpure virtual

Callback function after the reading is complete.

Has to ensure that swath_maps_ and ms1_map_ are correctly populated.

Implemented in MzMLSwathFileConsumer, CachedSwathFileConsumer, and RegularSwathFileConsumer.

◆ retrieveSwathMaps()

void retrieveSwathMaps ( std::vector< OpenSwath::SwathMap > & maps )

inline

Populate the vector of swath maps after consuming all spectra.

Will populate the input vector with SwathMap objects which correspond to the MS1 map (if present) and the MS2 maps (SWATH maps). This should be called after all spectra are consumed.

Note: It is not possible to consume any more spectra after calling this function (it contains finalization code and may close file streams).

References SwathMap::center, SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(), SwathMap::lower, SwathMap::ms1, SwathMap::sptr, and SwathMap::upper.

◆ setExpectedSize()

void setExpectedSize	(	Size	expectedSpectra,
		Size	expectedChromatograms
	)

inlineoverridevirtual

Set expected size of spectra and chromatograms to be consumed.

Some implementations might care about the number of spectra and chromatograms to be consumed and need to be informed about this (usually before consuming starts).

Note: Calling this method is optional but good practice.

Parameters

expectedSpectra	Number of spectra expected
expectedChromatograms	Number of chromatograms expected

Implements IMSDataConsumer.

◆ setExperimentalSettings()

void setExperimentalSettings ( const ExperimentalSettings & exp )

inlineoverridevirtual

Set experimental settings (meta-data) of the data to be consumed.

Some implementations might need to know about the meta-data (or the context) of the spectra and chromatograms to be consumed. This method allows them learn this.

Note: Calling this method is optional but good practice.

Parameters

exp	Experimental settings meta data for the data to be consumed

Implements IMSDataConsumer.

Member Data Documentation

◆ consuming_possible_

bool consuming_possible_

protected

Whether further spectra can still be consumed.

◆ correct_window_counter_

size_t correct_window_counter_

protected

How many windows were correctly annotated (non-zero window limits)

◆ ms1_map_

boost::shared_ptr<PeakMap > ms1_map_

protected

◆ settings_

PeakMap settings_

protected

The Experimental settings.

◆ swath_map_boundaries_

std::vector<OpenSwath::SwathMap> swath_map_boundaries_

protected

A list of Swath map identifiers (lower/upper boundary and center)

◆ swath_maps_

std::vector<boost::shared_ptr<PeakMap > > swath_maps_

protected

A list of SWATH maps and the MS1 map.

◆ use_external_boundaries_

bool use_external_boundaries_

protected

Whether to use external input for SWATH boundaries.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ChromatogramType

◆ MapType

◆ SpectrumType

Constructor & Destructor Documentation

◆ FullSwathFileConsumer() [1/2]

◆ FullSwathFileConsumer() [2/2]

◆ ~FullSwathFileConsumer()

Member Function Documentation

◆ consumeChromatogram()

◆ consumeMS1Spectrum_()

◆ consumeSpectrum()

◆ consumeSwathSpectrum_()

◆ ensureMapsAreFilled_()

◆ retrieveSwathMaps()

◆ setExpectedSize()

◆ setExperimentalSettings()

Member Data Documentation

◆ consuming_possible_

◆ correct_window_counter_

◆ ms1_map_

◆ settings_

◆ swath_map_boundaries_

◆ swath_maps_

◆ use_external_boundaries_