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:

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, 0); // the run ID is only used when writing
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.

A deltaRT of zero returns only the first spectrum at or after RT (or no spectrum if there is none); getMultipleSpectra relies on this first-at-or-after behaviour.

Parameters

[in]	RT	Centre of the RT window (same units as the underlying spectra).
[in]	deltaRT	Half-width of the RT window. A positive value matches spectra in \([RT - \mathrm{deltaRT}, RT + \mathrm{deltaRT}]\); zero matches only the first spectrum at or after RT (spectra are assumed to be stored in RT order).

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".