MSDataSqlConsumer Class Reference

A data consumer that inserts MS data into a SQLite database. More...

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

Inheritance diagram for MSDataSqlConsumer:

Collaboration diagram for MSDataSqlConsumer:

Public Member Functions
	MSDataSqlConsumer (const String &sql_filename, UInt64 run_id, int buffer_size=500, bool full_meta=true, bool lossy_compression=false, double linear_mass_acc=1e-4)
	Constructor. More...
	~MSDataSqlConsumer () override
	Destructor. More...
void	flush ()
	Flushes the data for good. More...
void	consumeSpectrum (SpectrumType &s) override
	Write a spectrum to the output file. More...
void	consumeChromatogram (ChromatogramType &c) override
	Write a chromatogram to the output file. More...
void	setExpectedSize (Size, Size) override
	Set expected size of spectra and chromatograms to be consumed. More...
void	setExperimentalSettings (const ExperimentalSettings &) override
	Set experimental settings (meta-data) of the data to be consumed. More...
Public Member Functions inherited from IMSDataConsumer
virtual	~IMSDataConsumer ()

Protected Attributes
String	filename_
OpenMS::Internal::MzMLSqliteHandler *	handler_
size_t	flush_after_
bool	full_meta_
std::vector< SpectrumType >	spectra_
std::vector< ChromatogramType >	chromatograms_
MSExperiment	peak_meta_

Private Types
typedef MSExperiment	MapType
typedef MapType::SpectrumType	SpectrumType
typedef MapType::ChromatogramType	ChromatogramType

Additional Inherited Members
Public Types inherited from IMSDataConsumer
typedef MSSpectrum	SpectrumType
typedef MSChromatogram	ChromatogramType

Detailed Description

A data consumer that inserts MS data into a SQLite database.

Consumes spectra and chromatograms and inserts them into an file-based SQL database using SQLite. As SQLite is highly inefficient when inserting one spectrum/chromatogram at a time, the consumer collects the data in an internal buffer and then flushes them all together to disk.

It uses MzMLSqliteHandler internally to write batches of data to disk.

Member Typedef Documentation

ChromatogramType

typedef MapType::ChromatogramType ChromatogramType

private

MapType

typedef MSExperiment MapType

private

SpectrumType

typedef MapType::SpectrumType SpectrumType

private

Constructor & Destructor Documentation

MSDataSqlConsumer()

MSDataSqlConsumer	(	const String &	sql_filename,
		UInt64	run_id,
		int	buffer_size = 500,
		bool	full_meta = true,
		bool	lossy_compression = false,
		double	linear_mass_acc = 1e-4
	)

Constructor.

Opens the SQLite file and writes the tables.

Parameters

sql_filename	The filename of the SQLite database
run_id	Unique identifier which links the sqMass and OSW file
buffer_size	How large the internal buffer size should be (defaults to 500 spectra / chromatograms)
full_meta	Whether to write the full meta-data in the SQLite header
lossy_compression	Whether to use lossy compression (numpress)
linear_mass_acc	Desired mass accuracy for RT or m/z space (absolute value)

~MSDataSqlConsumer()

~MSDataSqlConsumer ( )

override

Destructor.

Flushes the data for good.

Member Function Documentation

consumeChromatogram()

void consumeChromatogram ( ChromatogramType &  c )

overridevirtual

Write a chromatogram to the output file.

Implements IMSDataConsumer.

consumeSpectrum()

void consumeSpectrum ( SpectrumType &  s )

overridevirtual

Write a spectrum to the output file.

Implements IMSDataConsumer.

flush()

void flush

(

)

Flushes the data for good.

After calling this function, no more data is held in the buffer but the class is still able to receive new data.

setExpectedSize()

void setExpectedSize ( Size  expectedSpectra, Size  expectedChromatograms  )

overridevirtual

Set expected size of spectra and chromatograms to be consumed.

Some implementations might care about the number of spectra and chromatograms to be consumed and need to be informed about this (usually before consuming starts).

Note

Calling this method is optional but good practice.

Parameters

expectedSpectra	Number of spectra expected
expectedChromatograms	Number of chromatograms expected

Implements IMSDataConsumer.

setExperimentalSettings()

void setExperimentalSettings ( const ExperimentalSettings &  exp )

overridevirtual

Set experimental settings (meta-data) of the data to be consumed.

Some implementations might need to know about the meta-data (or the context) of the spectra and chromatograms to be consumed. This method allows them learn this.

Note

Calling this method is optional but good practice.

Parameters

exp	Experimental settings meta data for the data to be consumed

Implements IMSDataConsumer.

Member Data Documentation

chromatograms_

std::vector<ChromatogramType> chromatograms_

protected

filename_

String filename_

protected

flush_after_

size_t flush_after_

protected

full_meta_

bool full_meta_

protected

handler_

OpenMS::Internal::MzMLSqliteHandler* handler_

protected

peak_meta_

MSExperiment peak_meta_

protected

spectra_

std::vector<SpectrumType> spectra_

protected