RegularSwathFileConsumer Class Reference

In-memory implementation of FullSwathFileConsumer. More...

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

Inheritance diagram for RegularSwathFileConsumer:
Collaboration diagram for RegularSwathFileConsumer:

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

 RegularSwathFileConsumer ()
 RegularSwathFileConsumer (std::vector< OpenSwath::SwathMap > known_window_boundaries)
- 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 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...

Additional Inherited Members

- Protected Attributes inherited from FullSwathFileConsumer
std::vector< OpenSwath::SwathMapswath_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< PeakMapms1_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

In-memory implementation of FullSwathFileConsumer.

Keeps all the spectra in memory by just appending them to an MSExperiment.

Member Typedef Documentation

◆ ChromatogramType

◆ MapType

typedef PeakMap MapType

◆ SpectrumType

Constructor & Destructor Documentation

◆ RegularSwathFileConsumer() [1/2]

◆ RegularSwathFileConsumer() [2/2]

RegularSwathFileConsumer ( std::vector< OpenSwath::SwathMap known_window_boundaries)

Member Function Documentation

◆ addMS1Map_()

void addMS1Map_ ( )

◆ addNewSwathMap_()

void addNewSwathMap_ ( )

◆ consumeMS1Spectrum_()

void consumeMS1Spectrum_ ( MapType::SpectrumType s)

Consume an MS1 spectrum.

This function should handle an MS1 spectrum.

Implements FullSwathFileConsumer.

◆ consumeSwathSpectrum_()

void consumeSwathSpectrum_ ( MapType::SpectrumType s,
size_t  swath_nr 

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.

◆ ensureMapsAreFilled_()

void ensureMapsAreFilled_ ( )

Callback function after the reading is complete.

Has to ensure that swath_maps_ and ms1_map_ are correctly populated.

Implements FullSwathFileConsumer.