SqMassFile Class Reference

An class that uses on-disk SQLite database to read and write spectra and chromatograms. More...

#include <OpenMS/FORMAT/SqMassFile.h>

Collaboration diagram for SqMassFile:

Classes
struct	SqMassConfig
	Configuration class for SqMassFile. More...

Public Types
typedef MSExperiment	MapType

Public Member Functions
Constructors and Destructor
	SqMassFile ()
	Default constructor. More...
	~SqMassFile ()
	Default destructor. More...

Read / Write a complete mass spectrometric experiment
SqMassConfig	config_
void	load (const String &filename, MapType &map) const
void	store (const String &filename, MapType &map) const
	Store an MSExperiment in sqMass format. More...
void	transform (const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false) const
void	setConfig (const SqMassConfig &config)

Detailed Description

An class that uses on-disk SQLite database to read and write spectra and chromatograms.

This class provides functions to read and write spectra and chromatograms to disk using a SQLite database and store them in sqMass format. This allows users to access, select and filter spectra and chromatograms on-demand even in a large collection of data.

Spectra and chromatograms with precursor information will additionally load/store the metavalue 'peptide_sequence' from the first precursor (if any).

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Class Documentation

OpenMS::SqMassFile::SqMassConfig

struct OpenMS::SqMassFile::SqMassConfig

Configuration class for SqMassFile.

Contains configuration options for SQLite file

Collaboration diagram for SqMassFile::SqMassConfig:

Class Members
double	linear_fp_mass_acc	desired mass accuracy for numpress linear encoding (-1 no effect, use 0.0001 for 0.2 ppm accuracy @ 500 m/z)
bool	use_lossy_numpress	use lossy numpress compression
bool	write_full_meta	write full meta data

Member Typedef Documentation

MapType

typedef MSExperiment MapType

Constructor & Destructor Documentation

SqMassFile()

SqMassFile

(

)

Default constructor.

~SqMassFile()

~SqMassFile

(

)

Default destructor.

Member Function Documentation

load()

void load	(	const String &	filename,
		MapType &	map
	)		const

setConfig()

void setConfig ( const SqMassConfig &  config )

inline

store()

void store	(	const String &	filename,
		MapType &	map
	)		const

Store an MSExperiment in sqMass format.

If you want a specific RUN::ID in the sqMass file, make sure to populate MSExperiment::setSqlRunID(UInt64 id) before.

transform()

void transform	(	const String &	filename_in,
		Interfaces::IMSDataConsumer *	consumer,
		bool	skip_full_count = false,
		bool	skip_first_pass = false
	)		const

Member Data Documentation

config_

SqMassConfig config_

protected