MzMLSqliteHandler Class Reference

Sqlite handler for storing spectra and chromatograms. More...

#include <OpenMS/FORMAT/HANDLERS/MzMLSqliteHandler.h>

Public Member Functions
	MzMLSqliteHandler (String filename)

Protected Attributes
String	filename_
Base64	base64coder_
	Decoder/Encoder for Base64-data in MzML. More...
MSNumpressCoder	numpress_coder_
Int	spec_id_
Int	chrom_id_

Functions for reading files
----------------------------------- Reading of SQL file starts here -----------------------------------
void	readExperiment (MSExperiment &exp, bool meta_only=false)
	Read an experiment into an MSExperiment structure. More...
void	populateChromatogramsWithData_ (sqlite3 *db, std::vector< MSChromatogram > &chromatograms)
void	populateSpectraWithData_ (sqlite3 *db, std::vector< MSSpectrum > &spectra)
void	prepareChroms_ (sqlite3 *db, std::vector< MSChromatogram > &chromatograms)
void	prepareSpectra_ (sqlite3 *db, std::vector< MSSpectrum > &spectra)

Functions for writing files
----------------------------------- Writing to SQL file starts here -----------------------------------
void	writeExperiment (const MSExperiment &exp)
	Write an experiment to disk. More...
void	createTables ()
	Create data tables for a new file. More...
void	writeSpectra (const std::vector< MSSpectrum > &spectra)
	Writes a set of spectra to disk. More...
void	writeChromatograms (const std::vector< MSChromatogram > &chroms)
	Writes a set of chromatograms to disk. More...
void	executeBlobBind_ (sqlite3 *db, String &prepare_statement, std::vector< String > &data)
void	executeSql_ (sqlite3 *db, const std::stringstream &statement)

Detailed Description

Sqlite handler for storing spectra and chromatograms.

Note

Do not use this class directly, rather use SqMassFile.

This class writes spectra and chromatograms from a cache to make writing substantially faster. It is thus recommended to provide many spectra / chromatograms together to the writing function or else performance suffers.

Constructor & Destructor Documentation

MzMLSqliteHandler()

MzMLSqliteHandler

(

String

filename

)

Member Function Documentation

createTables()

void createTables

(

)

Create data tables for a new file.

Note

It is required to call this function first before writing any data to disk, otherwise the tables will not be set up!

executeBlobBind_()

void executeBlobBind_ ( sqlite3 *  db, String &  prepare_statement, std::vector< String > &  data  )

protected

executeSql_()

void executeSql_ ( sqlite3 *  db, const std::stringstream &  statement  )

protected

populateChromatogramsWithData_()

void populateChromatogramsWithData_ ( sqlite3 *  db, std::vector< MSChromatogram > &  chromatograms  )

protected

populateSpectraWithData_()

void populateSpectraWithData_ ( sqlite3 *  db, std::vector< MSSpectrum > &  spectra  )

protected

prepareChroms_()

void prepareChroms_ ( sqlite3 *  db, std::vector< MSChromatogram > &  chromatograms  )

protected

prepareSpectra_()

void prepareSpectra_ ( sqlite3 *  db, std::vector< MSSpectrum > &  spectra  )

protected

readExperiment()

void readExperiment	(	MSExperiment &	exp,
		bool	meta_only = false
	)

Read an experiment into an MSExperiment structure.

Parameters

exp	The result data structure
meta_only	Only read the meta data

writeChromatograms()

void writeChromatograms

(

const std::vector< MSChromatogram > &

chroms

)

Writes a set of chromatograms to disk.

Parameters

chromatograms

The chromatograms to write

writeExperiment()

void writeExperiment

(

const MSExperiment &

exp

)

Write an experiment to disk.

Parameters

exp	The data to write

writeSpectra()

void writeSpectra

(

const std::vector< MSSpectrum > &

spectra

)

Writes a set of spectra to disk.

Parameters

spectra

The spectra to write

Member Data Documentation

base64coder_

Base64 base64coder_

protected

Decoder/Encoder for Base64-data in MzML.

chrom_id_

Int chrom_id_

protected

filename_

String filename_

protected

numpress_coder_

MSNumpressCoder numpress_coder_

protected

spec_id_

Int spec_id_

protected