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 () | |
| void | setExpectedSize (Size, Size) |
| Set expected size of spectra and chromatograms to be consumed. More... | |
| void | setExperimentalSettings (const ExperimentalSettings &exp) |
| 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 &) |
| Consume a chromatogram -> should not happen when dealing with SWATH maps. More... | |
| void | consumeSpectrum (MapType::SpectrumType &s) |
| * 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) |
| Consume an MS2 spectrum belonging to SWATH "swath_nr". More... | |
| void | addMS1Map_ () |
| void | consumeMS1Spectrum_ (MapType::SpectrumType &s) |
| Consume an MS1 spectrum. More... | |
| void | ensureMapsAreFilled_ () |
| 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
◆ MapType
◆ SpectrumType
| typedef MapType::SpectrumType SpectrumType |
Constructor & Destructor Documentation
◆ RegularSwathFileConsumer() [1/2]
|
inline |
◆ RegularSwathFileConsumer() [2/2]
|
inline |
Member Function Documentation
◆ addMS1Map_()
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inlineprotected |
◆ addNewSwathMap_()
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inlineprotected |
◆ consumeMS1Spectrum_()
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inlineprotectedvirtual |
Consume an MS1 spectrum.
This function should handle an MS1 spectrum.
Implements FullSwathFileConsumer.
◆ consumeSwathSpectrum_()
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inlineprotectedvirtual |
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_()
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inlineprotectedvirtual |
Callback function after the reading is complete.
Has to ensure that swath_maps_ and ms1_map_ are correctly populated.
Implements FullSwathFileConsumer.