Sqlite handler for storing spectra and chromatograms in sqMass format. More...

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

Collaboration diagram for MzMLSqliteHandler:

Public Member Functions
	MzMLSqliteHandler (const String &filename, const UInt64 run_id)
	Constructor of sqMass file. More...

Functions for writing files
Writing to SQL file starts here
String	filename_

Int	spec_id_

Int	chrom_id_

UInt64	run_id_

bool	use_lossy_compression_

double	linear_abs_mass_acc_

double	write_full_meta_

int	sql_batch_size_

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	writeRunLevelInformation (const MSExperiment &exp, bool write_full_meta)
	Write the run-level information for an experiment into tables. More...

void	createIndices_ ()

Functions for reading files
Reading of SQL file starts here
void	readExperiment (MSExperiment &exp, bool meta_only=false) const
	Read an experiment into an MSExperiment structure. More...

UInt64	getRunID () const

void	readSpectra (std::vector< MSSpectrum > &exp, const std::vector< int > &indices, bool meta_only=false) const
	Read an set of spectra (potentially restricted to a subset) More...

void	readChromatograms (std::vector< MSChromatogram > &exp, const std::vector< int > &indices, bool meta_only=false) const
	Read an set of chromatograms (potentially restricted to a subset) More...

Size	getNrSpectra () const
	Get number of spectra in the file. More...

Size	getNrChromatograms () const
	Get number of chromatograms in the file. More...

void	setConfig (bool write_full_meta, bool use_lossy_compression, double linear_abs_mass_acc, int sql_batch_size=500)
	Set file configuration. More...

std::vector< size_t >	getSpectraIndicesbyRT (double RT, double deltaRT, const std::vector< int > &indices) const
	Get spectral indices around a specific retention time. More...

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

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

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

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

void	prepareChroms_ (sqlite3 *db, std::vector< MSChromatogram > &chromatograms, const std::vector< int > &indices={}) const

void	prepareSpectra_ (sqlite3 *db, std::vector< MSSpectrum > &spectra, const std::vector< int > &indices={}) const

Detailed Description

Sqlite handler for storing spectra and chromatograms in sqMass format.

Note: Do not use this class directly, rather use SqMassFile.; Due to the performance characteristics of the underlying SQLite database, it is highly recommended to read and write data (spectra/chromatograms) in batch. This is supported in this class and essential for reasonable performance. The current class does support batching SQL statements which can be controlled using setConfig and it is recommended to set the batch size to at least 500. The underlying SQLite database only stores the most essential parameters of a MS experiment, to store the complete meta-data, a zipped representation of the mzML data structure can be written directly into the database (and will be retrieved when converting back).

This class also supports writing data using the lossy numpress compression format.

This class contains the internal data structures and SQL statements for communication with the SQLite database

Constructor & Destructor Documentation

◆ MzMLSqliteHandler()

MzMLSqliteHandler	(	const String &	filename,
		const UInt64	run_id
	)

Constructor of sqMass file.

Parameters

filename	The sqMass filename
run_id	Unique identifier which links the sqMass and OSW file. It is currently only used for storing and ignored when reading an sqMass file.

Member Function Documentation

◆ createIndices_()

void createIndices_ ( )

protected

◆ 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!; Be careful with this function, calling this on an existing file will delete the file!

◆ getNrChromatograms()

Size getNrChromatograms ( ) const

Get number of chromatograms in the file.

Returns: The number of chromatograms

◆ getNrSpectra()

Size getNrSpectra ( ) const

Get number of spectra in the file.

Returns: The number of spectra

◆ getRunID()

UInt64 getRunID ( ) const

extract the RUN::ID from the sqMass file

Exceptions

Exception::SqlOperationFailed more than on run exists

◆ getSpectraIndicesbyRT()

std::vector<size_t> getSpectraIndicesbyRT	(	double	RT,
		double	deltaRT,
		const std::vector< int > &	indices
	)		const

Get spectral indices around a specific retention time.

Parameters

RT	The retention time
deltaRT	Tolerance window around RT (if less or equal than zero, only the first spectrum after RT is returned)
indices	Spectra to consider (if empty, all spectra are considered)

Returns: The indices of the spectra within RT +/- deltaRT

◆ populateChromatogramsWithData_() [1/2]

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

protected

◆ populateChromatogramsWithData_() [2/2]

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

protected

◆ populateSpectraWithData_() [1/2]

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

protected

◆ populateSpectraWithData_() [2/2]

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

protected

◆ prepareChroms_()

void prepareChroms_	(	sqlite3 *	db,
		std::vector< MSChromatogram > &	chromatograms,
		const std::vector< int > &	indices = `{}`
	)		const

protected

◆ prepareSpectra_()

void prepareSpectra_	(	sqlite3 *	db,
		std::vector< MSSpectrum > &	spectra,
		const std::vector< int > &	indices = `{}`
	)		const

protected

◆ readChromatograms()

void readChromatograms	(	std::vector< MSChromatogram > &	exp,
		const std::vector< int > &	indices,
		bool	meta_only = `false`
	)		const

Read an set of chromatograms (potentially restricted to a subset)

Parameters

exp	The result
indices	A list of indices restricting the resulting chromatograms only to those specified here
meta_only	Only read the meta data

◆ readExperiment()

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

Read an experiment into an MSExperiment structure.

Parameters

exp	The result data structure
meta_only	Only read the meta data

◆ readSpectra()

void readSpectra	(	std::vector< MSSpectrum > &	exp,
		const std::vector< int > &	indices,
		bool	meta_only = `false`
	)		const

Read an set of spectra (potentially restricted to a subset)

Parameters

exp	The result
indices	A list of indices restricting the resulting spectra only to those specified here
meta_only	Only read the meta data

◆ setConfig()

void setConfig	(	bool	write_full_meta,
		bool	use_lossy_compression,
		double	linear_abs_mass_acc,
		int	sql_batch_size = `500`
	)

inline

Set file configuration.

Parameters

write_full_meta	Whether to write a complete mzML meta data structure into the RUN_EXTRA field (allows complete recovery of the input file)
use_lossy_compression	Whether to use lossy compression (ms numpress)
linear_abs_mass_acc	Accepted loss in mass accuracy (absolute m/z, in Th)
sql_batch_size	Batch size of SQL insert statements

◆ writeChromatograms()

void writeChromatograms ( const std::vector< MSChromatogram > & chroms )

Writes a set of chromatograms to disk.

Parameters

chroms The chromatograms to write

◆ writeExperiment()

void writeExperiment ( const MSExperiment & exp )

Write an experiment to disk.

Parameters

exp	The data to write

◆ writeRunLevelInformation()

void writeRunLevelInformation	(	const MSExperiment &	exp,
		bool	write_full_meta
	)

Write the run-level information for an experiment into tables.

Note: This is a low level function, do not call this function unless you know what you are doing!

Parameters

exp	The result data structure
write_full_meta	Add full meta information into sql tables

◆ writeSpectra()

void writeSpectra ( const std::vector< MSSpectrum > & spectra )

Writes a set of spectra to disk.

Parameters

spectra The spectra to write

Member Data Documentation

◆ chrom_id_

Int chrom_id_

protected

◆ filename_

String filename_

protected

◆ linear_abs_mass_acc_

double linear_abs_mass_acc_

protected

◆ run_id_

UInt64 run_id_

protected

◆ spec_id_

Int spec_id_

protected

◆ sql_batch_size_

int sql_batch_size_

protected

◆ use_lossy_compression_

bool use_lossy_compression_

protected

◆ write_full_meta_

double write_full_meta_

protected

Public Member Functions

Functions for writing files

Writing to SQL file starts here

Functions for reading files

Reading of SQL file starts here

Detailed Description

Constructor & Destructor Documentation

◆ MzMLSqliteHandler()

Member Function Documentation

◆ createIndices_()

◆ createTables()

◆ getNrChromatograms()

◆ getNrSpectra()

◆ getRunID()

◆ getSpectraIndicesbyRT()

◆ populateChromatogramsWithData_() [1/2]

◆ populateChromatogramsWithData_() [2/2]

◆ populateSpectraWithData_() [1/2]

◆ populateSpectraWithData_() [2/2]

◆ prepareChroms_()

◆ prepareSpectra_()

◆ readChromatograms()

◆ readExperiment()

◆ readSpectra()

◆ setConfig()

◆ writeChromatograms()

◆ writeExperiment()

◆ writeRunLevelInformation()

◆ writeSpectra()

Member Data Documentation

◆ chrom_id_

◆ filename_

◆ linear_abs_mass_acc_

◆ run_id_

◆ spec_id_

◆ sql_batch_size_

◆ use_lossy_compression_

◆ write_full_meta_