SpectrumAccessOpenMSInMemory Class Reference

OpenSwath::ISpectrumAccess implementation that holds the complete spectrum / chromatogram payload in memory. More...

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

Inheritance diagram for SpectrumAccessOpenMSInMemory:

Collaboration diagram for SpectrumAccessOpenMSInMemory:

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

Public Member Functions
	SpectrumAccessOpenMSInMemory (OpenSwath::ISpectrumAccess &origin)
	Construct by reading every spectrum and chromatogram from origin into memory.
	~SpectrumAccessOpenMSInMemory () override
	Destructor.
	SpectrumAccessOpenMSInMemory (const SpectrumAccessOpenMSInMemory &rhs)
	Copy constructor (light copy).
std::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	Return a clone of this accessor as a new OpenSwath::ISpectrumAccess.
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Look up one spectrum by index.
OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Look up one spectrum's metadata by index.
std::vector< std::size_t >	getSpectraByRT (double RT, double deltaRT) const override
	Indices of cached spectra whose RT lies in [RT - deltaRT, RT + deltaRT].
size_t	getNrSpectra () const override
	Number of spectra cached in memory.
OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Look up one chromatogram by index.
size_t	getNrChromatograms () const override
	Number of chromatograms cached in memory.
std::string	getChromatogramNativeID (int id) const override
	Native id of one cached chromatogram.
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
std::vector< OpenSwath::SpectrumPtr >	spectra_
	Spectrum payloads captured at construction; shared with light clones.
std::vector< OpenSwath::SpectrumMeta >	spectra_meta_
	Parallel metadata cache (native id, RT, MS level) keyed on the same index.
std::vector< OpenSwath::ChromatogramPtr >	chromatograms_
	Chromatogram payloads captured at construction; shared with light clones.
std::vector< std::string >	chromatogram_ids_
	Parallel chromatogram native-id cache keyed on the same index.

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 that holds the complete spectrum / chromatogram payload in memory.

Constructed from any other OpenSwath::ISpectrumAccess (file-backed, on-disk cached, etc.); every spectrum and chromatogram is read through the source's interface during construction and cached locally, so subsequent accesses do not touch the disk again. The view exposes exactly the same data as the source. After construction the source is no longer referenced.

OpenSwath::ISpectrumAccess * data_access;
fillData(data_access); // assume data_access now points at some data
OpenSwath::ISpectrumAccess * in_memory_data_access = new SpectrumAccessOpenMSInMemory(*data_access);

After this snippet, data_access still serves the original data (its backing store is opaque to the caller), while in_memory_data_access serves the same data with the guarantee that it is held in memory and not re-read from disk.

Member Typedef Documentation

MSChromatogramType

typedef OpenMS::MSChromatogram MSChromatogramType

MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

SpectrumAccessOpenMSInMemory() [1/2]

SpectrumAccessOpenMSInMemory ( OpenSwath::ISpectrumAccess &  origin )

explicit

Construct by reading every spectrum and chromatogram from origin into memory.

After construction the accessor exposes the same spectra and chromatograms as origin, served entirely from memory; origin itself is no longer referenced.

Parameters

[in]

origin

Source accessor; read once during construction and not retained.

~SpectrumAccessOpenMSInMemory()

~SpectrumAccessOpenMSInMemory ( )

override

Destructor.

SpectrumAccessOpenMSInMemory() [2/2]

SpectrumAccessOpenMSInMemory

(

const SpectrumAccessOpenMSInMemory &

rhs

)

Copy constructor (light copy).

The copy shares the underlying spectrum / chromatogram payloads with rhs; only the per-element handles are duplicated. No data is re-read from the original source.

Parameters

[in]

rhs

Source accessor to copy.

Member Function Documentation

getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int  id )

overridevirtual

Look up one chromatogram by index.

Parameters

[in]

id

Chromatogram index in [0, getNrChromatograms()). Out-of-range access is a programming error (checked in debug builds).

Returns

Cached ChromatogramPtr for the requested chromatogram.

Implements ISpectrumAccess.

getChromatogramNativeID()

std::string getChromatogramNativeID ( int  id ) const

overridevirtual

Native id of one cached chromatogram.

Parameters

[in]

id

Chromatogram index in [0, getNrChromatograms()). Out-of-range access is a programming error (checked in debug builds).

Returns

Native-id string captured at construction time.

Implements ISpectrumAccess.

getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Number of chromatograms cached in memory.

Implements ISpectrumAccess.

getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Number of spectra cached in memory.

Implements ISpectrumAccess.

getSpectraByRT()

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

overridevirtual

Indices of cached spectra whose RT lies in [RT - deltaRT, RT + deltaRT].

Relies on the cached metadata being sorted by RT (inherited from the source); the lookup is logarithmic in the number of spectra.

Parameters

[in]	RT	Centre of the RT window.
[in]	deltaRT	Half-width of the RT window. Must be non-negative; a negative value is a programming error (checked in debug builds).

Returns

Indices into the in-memory view of spectra whose RT falls in the window.

Implements ISpectrumAccess.

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Look up one spectrum by index.

Parameters

[in]

id

Spectrum index in [0, getNrSpectra()). Out-of-range access is a programming error (checked in debug builds).

Returns

Cached SpectrumPtr for the requested spectrum.

Implements ISpectrumAccess.

getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id ) const

overridevirtual

Look up one spectrum's metadata by index.

Parameters

[in]

id

Spectrum index in [0, getNrSpectra()). Out-of-range access is a programming error (checked in debug builds).

Returns

Cached SpectrumMeta for the requested spectrum.

Implements ISpectrumAccess.

lightClone()

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

overridevirtual

Return a clone of this accessor as a new OpenSwath::ISpectrumAccess.

The clone shares this accessor's spectrum / chromatogram payloads, so it is cheap to create and safe to hand to another thread without re-reading the source.

Returns

Shared pointer to the cloned accessor.

Implements ISpectrumAccess.

Member Data Documentation

chromatogram_ids_

std::vector< std::string > chromatogram_ids_

private

Parallel chromatogram native-id cache keyed on the same index.

chromatograms_

std::vector< OpenSwath::ChromatogramPtr > chromatograms_

private

Chromatogram payloads captured at construction; shared with light clones.

spectra_

std::vector< OpenSwath::SpectrumPtr > spectra_

private

Spectrum payloads captured at construction; shared with light clones.

spectra_meta_

std::vector< OpenSwath::SpectrumMeta > spectra_meta_

private

Parallel metadata cache (native id, RT, MS level) keyed on the same index.