SpectrumAccessSqMass Class Reference

OpenSwath::ISpectrumAccess implementation backed by an sqMass (SQLite) spectrum store. 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)
	Construct from an sqMass handler exposing every spectrum it contains.
	SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler, const std::vector< int > &indices)
	Construct from an sqMass handler exposing only the spectra at the given indices.
	SpectrumAccessSqMass (const SpectrumAccessSqMass &sp, const std::vector< int > &indices)
	Construct a narrower view of an existing accessor.
	~SpectrumAccessSqMass () override
	Destructor.
	SpectrumAccessSqMass (const SpectrumAccessSqMass &rhs)
	Copy constructor.
std::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	Return a copy of this accessor as a new OpenSwath::ISpectrumAccess pointer.
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Load one spectrum by index in the visible view.
OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Load metadata (native id, RT, MS level) for one spectrum.
void	getAllSpectra (std::vector< OpenSwath::SpectrumPtr > &spectra, std::vector< OpenSwath::SpectrumMeta > &spectra_meta) const
	Batch-load every spectrum in the visible view into memory.
std::vector< std::size_t >	getSpectraByRT (double RT, double deltaRT) const override
	Indices into the visible view of spectra whose RT lies within an absolute window.
size_t	getNrSpectra () const override
	Number of spectra in the visible view.
OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Not supported on sqMass.
size_t	getNrChromatograms () const override
	Number of chromatograms in the underlying sqMass file.
std::string	getChromatogramNativeID (int id) const override
	Not supported on sqMass.
Public Member Functions inherited from ISpectrumAccess
virtual	~ISpectrumAccess ()
	Destructor.
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.
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_
	Handler for the underlying sqMass file (copied by value into each accessor / clone)
std::vector< int >	sidx_
	Optional subset of absolute spectrum indices; empty means "all spectra in the file are visible".

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

Detailed Description

OpenSwath::ISpectrumAccess implementation backed by an sqMass (SQLite) spectrum store.

Wraps an OpenMS::Internal::MzMLSqliteHandler to expose its spectra through the OpenSWATH spectrum-access interface. Optionally restricts the visible set to a subset of spectra via a vector of indices, so the same on-disk store can back several views (e.g. one per SWATH window, or MS1-only / MS2-only).

Subsetting

Three constructors are provided:

• (handler) — expose every spectrum in handler.
• (handler, indices) — expose only the spectra at the given indices.
• (parent, indices) — narrow an existing SpectrumAccessSqMass further; indices are interpreted against the parent's already-filtered view. Out-of-range entries throw Exception::IllegalArgument.

All getXxxById methods honour the subset: id i refers to the i-th element of the visible view, not the i-th row of the underlying SQLite table.

Performance and concurrency

Per-spectrum access (getSpectrumById / getSpectrumMetaById) is implemented but each call performs one OpenMS::Internal::MzMLSqliteHandler::readSpectra invocation and incurs the per-query SQLite overhead. Callers that need many spectra should prefer getAllSpectra, which issues a single batched read.

The class is read-only and SQLite supports parallel reads from independent connections, so cloning via lightClone gives a clone safe to use from another thread.

Chromatogram support

Spectrum-side operations are fully supported. On the chromatogram side, only the count getNrChromatograms is implemented; both getChromatogramById and getChromatogramNativeID throw Exception::NotImplemented. Use a different accessor (e.g. read via OpenMS::Internal::MzMLSqliteHandler directly) for chromatogram payloads.

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

)

Construct from an sqMass handler exposing every spectrum it contains.

Parameters

[in]

handler

Read-only handler to the underlying sqMass file.

SpectrumAccessSqMass() [2/4]

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

Construct from an sqMass handler exposing only the spectra at the given indices.

Parameters

[in]	handler	Read-only handler to the underlying sqMass file.
[in]	indices	Absolute spectrum indices to expose; an empty vector falls back to "all spectra" semantics.

SpectrumAccessSqMass() [3/4]

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

Construct a narrower view of an existing accessor.

If sp already has a subset configured, indices are interpreted against that subset (i.e. indices[k] is a position within sp's already-visible view, not within the raw sqMass file).

Parameters

[in]	sp	Parent accessor.
[in]	indices	Indices into sp's already-filtered view; empty inherits sp's subset unchanged.

Exceptions

Exception::IllegalArgument

If any entry of indices is out of range of sp's subset.

~SpectrumAccessSqMass()

~SpectrumAccessSqMass ( )

override

Destructor.

SpectrumAccessSqMass() [4/4]

SpectrumAccessSqMass

(

const SpectrumAccessSqMass &

rhs

)

Copy constructor.

Duplicates the OpenMS::Internal::MzMLSqliteHandler value and the optional subset-index vector; no shared mutable state remains between the copy and the original.

Parameters

[in]

rhs

Source accessor to copy.

Member Function Documentation

getAllSpectra()

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

Batch-load every spectrum in the visible view into memory.

Preferred over repeated getSpectrumById calls — issues a single batched read.

Parameters

[out]	spectra	Receives one SpectrumPtr per visible spectrum.
[out]	spectra_meta	Receives the parallel metadata records.

getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int  id )

overridevirtual

Not supported on sqMass.

Parameters

[in]

id

Ignored.

Returns

Never returns normally.

Exceptions

Exception::NotImplemented

Always — sqMass-backed access does not implement per-chromatogram payload retrieval. Use a different accessor for chromatogram payloads.

Implements ISpectrumAccess.

getChromatogramNativeID()

std::string getChromatogramNativeID ( int  id ) const

overridevirtual

Not supported on sqMass.

Parameters

[in]

id

Ignored.

Returns

Never returns normally.

Exceptions

Exception::NotImplemented

Always — sqMass-backed access does not expose chromatogram native ids.

Implements ISpectrumAccess.

getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Number of chromatograms in the underlying sqMass file.

The count is supported even though per-chromatogram payload / native-id access is not.

Returns

Total chromatogram count.

Implements ISpectrumAccess.

getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Number of spectra in the visible view.

Returns

Subset size when a subset is configured, otherwise the total spectrum count of the underlying sqMass file.

Implements ISpectrumAccess.

getSpectraByRT()

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

overridevirtual

Indices into the visible view of spectra whose RT lies within an absolute window.

Parameters

[in]	RT	Centre of the RT window (same units as the underlying spectra).
[in]	deltaRT	Half-width of the RT window; matches spectra in \([RT - \mathrm{deltaRT}, RT + \mathrm{deltaRT}]\).

Returns

Indices into the visible view (already remapped through the subset, if any).

Note

Aborts via OPENMS_PRECONDITION if deltaRT is negative.

Implements ISpectrumAccess.

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Load one spectrum by index in the visible view.

Issues a single OpenMS::Internal::MzMLSqliteHandler::readSpectra call per invocation, so the SQLite per-query overhead applies to each call.

Parameters

[in]

id

Spectrum index in the visible view (0-based; honours the optional subset).

Returns

Pointer to the loaded spectrum.

Warning

Prefer getAllSpectra when many spectra are needed; per-call cost is dominated by the SQLite query overhead.

Implements ISpectrumAccess.

getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id ) const

overridevirtual

Load metadata (native id, RT, MS level) for one spectrum.

Same per-call cost trade-off as getSpectrumById.

Parameters

[in]

id

Spectrum index in the visible view (0-based).

Returns

Metadata record for the requested spectrum.

Implements ISpectrumAccess.

lightClone()

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

overridevirtual

Return a copy of this accessor as a new OpenSwath::ISpectrumAccess pointer.

The clone uses an independent OpenMS::Internal::MzMLSqliteHandler value, so it is safe to use from another thread (SQLite supports parallel reads from independent connections).

Returns

Shared pointer to a new accessor with the same visible view as this one.

Implements ISpectrumAccess.

Member Data Documentation

handler_

OpenMS::Internal::MzMLSqliteHandler handler_

private

Handler for the underlying sqMass file (copied by value into each accessor / clone)

sidx_

std::vector<int> sidx_

private

Optional subset of absolute spectrum indices; empty means "all spectra in the file are visible".