OpenMS: RegularSwathFileConsumer Class Reference

| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | List of all members
RegularSwathFileConsumer Class Reference

In-memory implementation of FullSwathFileConsumer. More...

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

Inheritance 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::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

In-memory implementation of FullSwathFileConsumer.

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

## Member Typedef Documentation

## ◆ ChromatogramType

typedef MapType::ChromatogramType ChromatogramType

## ◆ MapType

typedef PeakMap MapType

## ◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

## Constructor & Destructor Documentation

## ◆ RegularSwathFileConsumer() [1/2]

RegularSwathFileConsumer | ( |  | ) |

inline

## ◆ RegularSwathFileConsumer() [2/2]

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

inline

## Member Function Documentation

## ◆ addMS1Map_()

void addMS1Map_ | ( |  | ) |

inlineprotected

## ◆ addNewSwathMap_()

void addNewSwathMap_ | ( |  | ) |

inlineprotected

## ◆ 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.

## ◆ 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.