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.
	~SqMassFile ()
	Default destructor.

Read / Write a complete mass spectrometric experiment
SqMassConfig	config_
void	load (const String &filename, MapType &map) const
void	store (const String &filename, const MapType &map) const
	Store an MSExperiment in sqMass format.
void	transform (const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false) const
void	convertToXICParquet (const String &filename_in, const String &xic_filename, UInt64 run_id=0, const String &source_file="", const OpenSwath::LightTargetedExperiment &transition_exp=OpenSwath::LightTargetedExperiment()) const
	Convert an sqMass file containing chromatogram data to an XIC Parquet file.
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 {-1}	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 {false}	use lossy numpress compression
bool	write_full_meta {true}	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

convertToXICParquet()

void convertToXICParquet	(	const String &	filename_in,
		const String &	xic_filename,
		UInt64	run_id = 0,
		const String &	source_file = "",
		const OpenSwath::LightTargetedExperiment &	transition_exp = OpenSwath::LightTargetedExperiment()
	)		const

Convert an sqMass file containing chromatogram data to an XIC Parquet file.

This is a convenience function that will stream chromatograms from the input sqMass file into an OpenMS Parquet writer (MSChromatogramParquetConsumer) and write them to disk.

Note: The transition/precursor metadata passed to the underlying Parquet consumer is optional from the API perspective, but the writer expects chromatogram native IDs to have matching transition/precursor metadata in many cases. If required metadata for a chromatogram (precursor or transition) is missing the writer will throw an exception and the conversion will fail. Therefore it is recommended to provide a populated transition experiment when possible.

Parameters

[in]	filename_in	Path to the input sqMass file.
[in]	xic_filename	Path to the output .xic Parquet file.
[in]	run_id	Run identifier to store with each chromatogram (default 0).
[in]	source_file	Source filename to store in the parquet file (if empty, filename_in is used).
[in]	transition_exp	Optional transition/precursor metadata (LightTargetedExperiment) used to annotate chromatograms. If left empty, no transition metadata will be available to the writer and conversion may fail for chromatograms that require such metadata. Prefer supplying a populated transition experiment when available.

Exceptions

Exception::InvalidValue	If a chromatogram refers to a precursor or transition for which no matching metadata entry exists, or if Arrow/Parquet operations fail while assembling/writing the table.
Exception::FileNotWritable	If the output parquet file cannot be opened for writing.
Exception::NotImplemented	If Parquet support was not compiled in.
Exception::BaseException	Other OpenMS exceptions propagated from the writer/encoding layers may also be thrown.

load()

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

setConfig()

void setConfig ( const SqMassConfig &  config )

inline

store()

void store	(	const String &	filename,
		const 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