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:

Collaboration 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...
SpectrumPtr	getSpectrumById (int id, double drift_start, double drift_end)
	Return pointer to a spectrum at the given id, the spectrum will be filtered by drift time. More...
SpectrumSequence	getMultipleSpectra (double RT, int nr_spectra_to_fetch)
SpectrumSequence	getMultipleSpectra (double RT, int nr_spectra_to_fetch, double drift_start, double drift_end)

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

Additional Inherited Members
Static Public Member Functions inherited from ISpectrumAccess
static SpectrumPtr	filterByDrift (const SpectrumPtr &input, double drift_start, double drift_end)
	filters a spectrum by drift time, spectrum pointer returned is a copy 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.