SpectrumAccessSqMass Class Reference

An implementation of the Spectrum Access interface using SQL files. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h>

Inheritance diagram for SpectrumAccessSqMass:

Public Types
typedef OpenMS::MSSpectrum	MSSpectrumType
typedef OpenMS::MSChromatogram	MSChromatogramType

Public Member Functions
	SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler)
	Constructor. More...
	SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler, const std::vector< int > &indices)
	SpectrumAccessSqMass (const SpectrumAccessSqMass &sp, const std::vector< int > &indices)
	~SpectrumAccessSqMass () override
	Destructor. More...
	SpectrumAccessSqMass (const SpectrumAccessSqMass &rhs)
	Copy constructor. More...
boost::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	Light clone operator (actual data will not get copied) More...
OpenSwath::SpectrumPtr	getSpectrumById (int) override
	Return a pointer to a spectrum at the given id. More...
OpenSwath::SpectrumMeta	getSpectrumMetaById (int) const override
	Returns the meta information for a spectrum. More...
void	getAllSpectra (std::vector< OpenSwath::SpectrumPtr > &spectra, std::vector< OpenSwath::SpectrumMeta > &spectra_meta) const
	Load all spectra from the underlying sqMass file into memory. More...
std::vector< std::size_t >	getSpectraByRT (double, double) const override
	Return a vector of ids of spectra that are within RT +/- deltaRT. More...
size_t	getNrSpectra () const override
	Returns the number of spectra available. More...
OpenSwath::ChromatogramPtr	getChromatogramById (int) override
	Return a pointer to a chromatogram at the given id. More...
size_t	getNrChromatograms () const override
	Returns the number of chromatograms available. More...
std::string	getChromatogramNativeID (int) const override
	Returns the native id of the chromatogram at the given id. More...
Public Member Functions inherited from ISpectrumAccess
virtual	~ISpectrumAccess ()
	Destructor. More...

Private Attributes
OpenMS::Internal::MzMLSqliteHandler	handler_
	Access to underlying sqMass file. More...
std::vector< int >	sidx_
	Optional subset of spectral indices. More...

Detailed Description

An implementation of the Spectrum Access interface using SQL files.

The interface takes an MzMLSqliteHandler object to access spectra and chromatograms from a sqlite file (sqMass). Currently access to individual spectra and chromatograms are not supported due to large overhead of opening a DB connection and performing a single query.

Instead, the users should use getAllSpectra which returns all available spectra together.

The interface allows to be constructed in a way as to only provide access to a subset of spectra / chromatograms by supplying a set of indices which are then used to provide a transparent interface to any consumer who will get access to the described subset of spectra / chromatograms. This can be useful to provide a specific interface to MS1 or MS2 spectra only or to different DIA / SWATH-MS windows.

Parallel access is supported through this interface as it is read-only and sqlite3 supports multiple parallel read threads as long as they use a different db connection.

Sample usage:

// Obtain swath_map with boundaries first
std::vector<int> indices = sql_mass_reader.readSpectraForWindow(swath_map);
OpenMS::Internal::MzMLSqliteHandler handler(file);
OpenSwath::SpectrumAccessPtr sptr(new OpenMS::SpectrumAccessSqMass(handler, indices));
swath_maps[k].sptr = sptr;

Member Typedef Documentation

MSChromatogramType

typedef OpenMS::MSChromatogram MSChromatogramType

MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

SpectrumAccessSqMass() [1/4]

SpectrumAccessSqMass

(

const OpenMS::Internal::MzMLSqliteHandler &

handler

)

Constructor.

SpectrumAccessSqMass() [2/4]

SpectrumAccessSqMass	(	const OpenMS::Internal::MzMLSqliteHandler &	handler,
		const std::vector< int > &	indices
	)

SpectrumAccessSqMass() [3/4]

SpectrumAccessSqMass	(	const SpectrumAccessSqMass &	sp,
		const std::vector< int > &	indices
	)

~SpectrumAccessSqMass()

~SpectrumAccessSqMass ( )

override

Destructor.

SpectrumAccessSqMass() [4/4]

SpectrumAccessSqMass

(

const SpectrumAccessSqMass &

rhs

)

Copy constructor.

Member Function Documentation

getAllSpectra()

void getAllSpectra	(	std::vector< OpenSwath::SpectrumPtr > &	spectra,
		std::vector< OpenSwath::SpectrumMeta > &	spectra_meta
	)		const

Load all spectra from the underlying sqMass file into memory.

getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int  id )

overridevirtual

Return a pointer to a chromatogram at the given id.

Implements ISpectrumAccess.

getChromatogramNativeID()

std::string getChromatogramNativeID ( int  id ) const

overridevirtual

Returns the native id of the chromatogram at the given id.

Implements ISpectrumAccess.

getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Returns the number of chromatograms available.

Implements ISpectrumAccess.

getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Returns the number of spectra available.

Implements ISpectrumAccess.

getSpectraByRT()

std::vector<std::size_t> getSpectraByRT ( double  RT, double  deltaRT  ) const

overridevirtual

Return a vector of ids of spectra that are within RT +/- deltaRT.

Implements ISpectrumAccess.

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Return a pointer to a spectrum at the given id.

Implements ISpectrumAccess.

getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id ) const

overridevirtual

Returns the meta information for a spectrum.

Implements ISpectrumAccess.

lightClone()

boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone ( ) const

overridevirtual

Light clone operator (actual data will not get copied)

Implements ISpectrumAccess.

Member Data Documentation

handler_

OpenMS::Internal::MzMLSqliteHandler handler_

private

Access to underlying sqMass file.

sidx_

std::vector<int> sidx_

private

Optional subset of spectral indices.