MSDataSqlConsumer Class Reference

A data consumer that inserts data into a SQL database. More...

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

Inheritance diagram for MSDataSqlConsumer:

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

Protected Attributes
OpenMS::Internal::MzMLSqliteHandler	sql_writer_
bool	clearData_
size_t	flush_after_
std::vector< SpectrumType >	spectra_
std::vector< ChromatogramType >	chromatograms_

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 data into a SQL 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.

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	(	String	filename,
		bool	clearData = true,
		int	buffer_size = 500
	)

Constructor.

Opens the sqlite file and writes the tables.

Parameters

filename	The filename of the Sqlite database
clearData	Whether to clear the data from memory after writing it
buffer_size	How large the internal buffer size should be (defaults to 500 spectra / chromatograms)

~MSDataSqlConsumer()

~MSDataSqlConsumer

(

)

Destructor.

Flushes the data for good.

Member Function Documentation

consumeChromatogram()

void consumeChromatogram ( ChromatogramType &  c )

virtual

Write a chromatogram to the output file.

Implements IMSDataConsumer.

consumeSpectrum()

void consumeSpectrum ( SpectrumType &  s )

virtual

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  )

virtual

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 )

virtual

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

clearData_

bool clearData_

protected

flush_after_

size_t flush_after_

protected

spectra_

std::vector<SpectrumType> spectra_

protected

sql_writer_

OpenMS::Internal::MzMLSqliteHandler sql_writer_

protected