OpenMS
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On-disk cached implementation of FullSwathFileConsumer. More...
#include <OpenMS/FORMAT/DATAACCESS/SwathFileConsumer.h>
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 | |
CachedSwathFileConsumer (String cachedir, String basename, Size nr_ms1_spectra, std::vector< int > nr_ms2_spectra) | |
CachedSwathFileConsumer (std::vector< OpenSwath::SwathMap > known_window_boundaries, String cachedir, String basename, Size nr_ms1_spectra, std::vector< int > nr_ms2_spectra) | |
~CachedSwathFileConsumer () 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 |
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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... | |
Protected Attributes | |
MSDataCachedConsumer * | ms1_consumer_ |
std::vector< MSDataCachedConsumer * > | 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... | |
On-disk cached implementation of FullSwathFileConsumer.
Writes all spectra immediately to disk in a user-specified caching location using the MSDataCachedConsumer. Internally, it handles n+1 (n SWATH + 1 MS1 map) objects of MSDataCachedConsumer which can consume the spectra and write them to disk immediately.
typedef MapType::SpectrumType SpectrumType |
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References MSDataCachedConsumer::setExpectedSize().
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Consume an MS1 spectrum.
This function should handle an MS1 spectrum.
Implements FullSwathFileConsumer.
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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.
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Callback function after the reading is complete.
Has to ensure that swath_maps_ and ms1_map_ are correctly populated.
Implements FullSwathFileConsumer.
References FileHandler::loadExperiment(), and CachedMzMLHandler::writeMetadata().
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