MzMLSqliteSwathHandler Class Reference

Read-only accessor for SWATH/DIA spectrum indices stored in an sqMass file. More...

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

Collaboration diagram for MzMLSqliteSwathHandler:

Public Member Functions
	MzMLSqliteSwathHandler (const std::string &filename)
	Construct from the path of an sqMass file.
std::vector< OpenSwath::SwathMap >	readSwathWindows ()
	Read the SWATH window boundaries from the file.
std::vector< int >	readMS1Spectra ()
	Read the indices of every MS1 spectrum.
std::vector< int >	readSpectraForWindow (const OpenSwath::SwathMap &swath_map)
	Read the indices of every spectrum that belongs to a given SWATH window.

Protected Attributes
std::string	filename_
	Path of the sqMass file passed in at construction time.
Int	spec_id_
	Next spectrum id used when appending spectra to the database; lets multiple append passes coexist on the same file.
Int	chrom_id_
	Next chromatogram id used when appending chromatograms to the database; lets multiple append passes coexist on the same file.

Detailed Description

Read-only accessor for SWATH/DIA spectrum indices stored in an sqMass file.

Exposes three lookups against a single sqMass file:

• readSwathWindows – the SWATH window definitions (precursor isolation centre and lower/upper offsets),
• readMS1Spectra – the spectrum indices of all MS1 scans,
• readSpectraForWindow – the spectrum indices that belong to a given SWATH window, identified by its centre m/z.

Internal helper class used by the OpenSWATH I/O stack; not part of the stable public API.

Constructor & Destructor Documentation

MzMLSqliteSwathHandler()

MzMLSqliteSwathHandler ( const std::string &  filename )

inline

Construct from the path of an sqMass file.

The file is not opened by the constructor; each accessor opens its own connection on demand.

Parameters

[in]

filename

Path of the sqMass file to read.

Member Function Documentation

readMS1Spectra()

std::vector< int > readMS1Spectra

(

)

Read the indices of every MS1 spectrum.

Returns

Spectrum indices for the MS1 scans in the file's natural order.

Exceptions

Exception::SqlOperationFailed	if the sqMass file cannot be opened.
Exception::IllegalArgument	if preparing the SQL query fails.

readSpectraForWindow()

std::vector< int > readSpectraForWindow

(

const OpenSwath::SwathMap &

swath_map

)

Read the indices of every spectrum that belongs to a given SWATH window.

The window is identified by swath_map's center value; spectra whose precursor isolation centre lies within a small fixed tolerance (0.01 m/z) of swath_map.center are returned.

Note

Only swath_map.center is consulted; the lower and upper fields are ignored.

Parameters

[in]

swath_map

SWATH window to look up; only its center is used.

Returns

Spectrum indices that fall into the window, in the file's natural order.

Exceptions

Exception::SqlOperationFailed	if the sqMass file cannot be opened.
Exception::IllegalArgument	if preparing the SQL query fails.

readSwathWindows()

std::vector< OpenSwath::SwathMap > readSwathWindows

(

)

Read the SWATH window boundaries from the file.

Returns one SwathMap entry per distinct precursor isolation centre present at MS level 2; center, lower and upper are filled. Other SwathMap fields are left at their default values.

Returns

SWATH window definitions in the file's natural order.

Exceptions

Exception::SqlOperationFailed	if the sqMass file cannot be opened.
Exception::IllegalArgument	if preparing the SQL query fails.

Member Data Documentation

chrom_id_

Int chrom_id_

protected

Next chromatogram id used when appending chromatograms to the database; lets multiple append passes coexist on the same file.

filename_

std::string filename_

protected

Path of the sqMass file passed in at construction time.

spec_id_

Int spec_id_

protected

Next spectrum id used when appending spectra to the database; lets multiple append passes coexist on the same file.