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OpenMS
2.6.0
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46 #include <boost/shared_ptr.hpp>
129 void setExpectedSize(
Size expectedSpectra,
Size expectedChromatograms)
override;
165 virtual Size getNrSpectraWritten();
170 virtual Size getNrChromatogramsWritten();
196 virtual void doCleanup_();
226 std::vector<std::vector< ConstDataProcessingPtr > >
dps_;
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:88
NoopMSDataWritingConsumer(String filename)
Definition: MSDataWritingConsumer.h:263
DataProcessingPtr additional_dataprocessing_
The dataprocessing to be added to each spectrum/chromatogram.
Definition: MSDataWritingConsumer.h:228
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
A more convenient string class.
Definition: String.h:59
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
MapType::SpectrumType SpectrumType
Definition: MSDataWritingConsumer.h:95
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< std::vector< ConstDataProcessingPtr > > dps_
Vector of data processing objects -> will be filled by writeHeader_.
Definition: MSDataWritingConsumer.h:226
Consumer class that perform no operation.
Definition: MSDataWritingConsumer.h:258
std::ofstream ofs_
File stream (to write mzML)
Definition: MSDataWritingConsumer.h:201
bool started_writing_
Stores whether we have already started writing any data.
Definition: MSDataWritingConsumer.h:204
bool add_dataprocessing_
Whether to add dataprocessing term to the data before writing.
Definition: MSDataWritingConsumer.h:218
boost::shared_ptr< DataProcessing > DataProcessingPtr
Definition: DataProcessing.h:135
Size spectra_expected_
Number of spectra expected.
Definition: MSDataWritingConsumer.h:214
PlainMSDataWritingConsumer(String filename)
Definition: MSDataWritingConsumer.h:248
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void consumeSpectrum(SpectrumType &) override
Consume a spectrum.
Definition: MSDataWritingConsumer.h:265
bool writing_chromatograms_
Stores whether we are currently writing chromatograms.
Definition: MSDataWritingConsumer.h:208
void processSpectrum_(MapType::SpectrumType &) override
Process a spectrum before storing to disk.
Definition: MSDataWritingConsumer.h:271
MapType::ChromatogramType ChromatogramType
Definition: MSDataWritingConsumer.h:96
Internal::MzMLValidator * validator_
Validator that knows about CV terms.
Definition: MSDataWritingConsumer.h:221
Semantically validates MzXML files.
Definition: MzMLValidator.h:48
ExperimentalSettings settings_
Experimental settings to use for the whole file.
Definition: MSDataWritingConsumer.h:224
void consumeChromatogram(ChromatogramType &) override
Consume a chromatogram.
Definition: MSDataWritingConsumer.h:266
void processChromatogram_(MapType::ChromatogramType &) override
Process a chromatogram before storing to disk.
Definition: MSDataWritingConsumer.h:244
Size spectra_written_
Number of spectra written.
Definition: MSDataWritingConsumer.h:210
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
void processSpectrum_(MapType::SpectrumType &) override
Process a spectrum before storing to disk.
Definition: MSDataWritingConsumer.h:243
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
PeakMap MapType
Definition: MSDataWritingConsumer.h:94
Size chromatograms_written_
Number of chromatograms written.
Definition: MSDataWritingConsumer.h:212
The representation of a chromatogram.
Definition: MSChromatogram.h:54
Size chromatograms_expected_
Number of chromatograms expected.
Definition: MSDataWritingConsumer.h:216
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void doCleanup_() override
Cleanup function called by the destructor.
Definition: MSDataWritingConsumer.h:270
void setExperimentalSettings(const ExperimentalSettings &) override
Set experimental settings for the whole file.
Definition: MSDataWritingConsumer.h:264
Handler for mzML file format.
Definition: MzMLHandler.h:116
bool writing_spectra_
Stores whether we are currently writing spectra.
Definition: MSDataWritingConsumer.h:206
void processChromatogram_(MapType::ChromatogramType &) override
Process a chromatogram before storing to disk.
Definition: MSDataWritingConsumer.h:272