SpectrumAccessOnDisc Class Reference

OpenSwath::ISpectrumAccess on an on-disc experiment (e.g. OnDiscThermoRawExperiment or OnDiscMSExperiment). More...

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

Inheritance diagram for SpectrumAccessOnDisc:

Classes
struct	View

Public Member Functions
	SpectrumAccessOnDisc (std::shared_ptr< IMSExperimentRandomAccess > experiment)
	Expose all spectra of experiment.
	SpectrumAccessOnDisc (std::shared_ptr< IMSExperimentRandomAccess > experiment, std::vector< Size > indices)
	Expose only the spectra of experiment with the given indices.
	SpectrumAccessOnDisc (const SpectrumAccessOnDisc &rhs)
	Copy constructor; clones the experiment (new file handle) and shares the index and subset.
	~SpectrumAccessOnDisc () override
	Destructor.
std::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	A copy that can be used from another thread (see the copy constructor)
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Peaks and data arrays of visible spectrum id (float and integer arrays, named after the array)
OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Retention time and MS level of visible spectrum id.
std::vector< std::size_t >	getSpectraByRT (double RT, double deltaRT) const override
	Visible spectra with RT in [RT - deltaRT, RT + deltaRT].
size_t	getNrSpectra () const override
	Number of visible spectra.
OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Chromatogram id of the experiment.
size_t	getNrChromatograms () const override
	Number of chromatograms of the experiment.
std::string	getChromatogramNativeID (int id) const override
	Native ID of chromatogram id.
Size	getExperimentIndex (int id) const
	Index in the experiment of visible spectrum id.
const IMSExperimentRandomAccess &	getExperiment () const
	The experiment this accessor reads from.
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::shared_ptr< IMSExperimentRandomAccess >	experiment_
std::shared_ptr< const View >	view_

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 on an on-disc experiment (e.g. OnDiscThermoRawExperiment or OnDiscMSExperiment).

Spectra are read from the file on request (IMSExperimentRandomAccess::getSpectrumPeaks()), nothing is cached. The accessor can expose a subset of the spectra, e.g. those of one SWATH window, so that several views share one opened file and its index (as SpectrumAccessSqMass does). The visible spectra are ordered by retention time (ties keep the order of the experiment); id i refers to the i-th visible spectrum.

Chromatograms are those of the experiment (the subset applies to spectra only).

Note

lightClone() and the copy constructor clone the experiment (IMSExperimentRandomAccess::clone()), i.e. open a new handle on the file, and share the index and the subset. Clones can be used concurrently from different threads; a single instance must not.

auto experiment = std::make_shared<OnDiscThermoRawExperiment>();
experiment->openFile("run.raw");
std::vector<Size> window; // spectra of one SWATH window
// ...
OpenSwath::SpectrumAccessPtr sptr = std::make_shared<SpectrumAccessOnDisc>(experiment, window);

---

Class Documentation

OpenMS::SpectrumAccessOnDisc::View

struct OpenMS::SpectrumAccessOnDisc::View

Class Members
vector< Size >	indices	experiment index of each visible spectrum
vector< double >	rts	and its retention time (ascending)

Constructor & Destructor Documentation

SpectrumAccessOnDisc() [1/3]

SpectrumAccessOnDisc ( std::shared_ptr< IMSExperimentRandomAccess >  experiment )

explicit

Expose all spectra of experiment.

Parameters

[in]

experiment

The opened experiment; this accessor uses it, clones open new handles.

SpectrumAccessOnDisc() [2/3]

SpectrumAccessOnDisc	(	std::shared_ptr< IMSExperimentRandomAccess >	experiment,
		std::vector< Size >	indices
	)

Expose only the spectra of experiment with the given indices.

Parameters

[in]	experiment	The opened experiment; this accessor uses it, clones open new handles.
[in]	indices	Spectrum indices of experiment; they are ordered by retention time.

Exceptions

Exception::IndexOverflow

if an index is out of range

SpectrumAccessOnDisc() [3/3]

SpectrumAccessOnDisc

(

const SpectrumAccessOnDisc &

rhs

)

Copy constructor; clones the experiment (new file handle) and shares the index and subset.

~SpectrumAccessOnDisc()

~SpectrumAccessOnDisc ( )

override

Destructor.

Member Function Documentation

getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int  id )

overridevirtual

Chromatogram id of the experiment.

Implements ISpectrumAccess.

getChromatogramNativeID()

std::string getChromatogramNativeID ( int  id ) const

overridevirtual

Native ID of chromatogram id.

Implements ISpectrumAccess.

getExperiment()

const IMSExperimentRandomAccess & getExperiment

(

)

const

The experiment this accessor reads from.

getExperimentIndex()

Size getExperimentIndex

(

int

id

)

const

Index in the experiment of visible spectrum id.

getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Number of chromatograms of the experiment.

Implements ISpectrumAccess.

getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Number of visible spectra.

Implements ISpectrumAccess.

getSpectraByRT()

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

overridevirtual

Visible spectra with RT in [RT - deltaRT, RT + deltaRT].

Returns the first visible spectrum with RT >= RT - deltaRT and all following ones up to RT + deltaRT, as SpectrumAccessOpenMS does (so deltaRT = 0 gives the first spectrum at or after RT).

Implements ISpectrumAccess.

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Peaks and data arrays of visible spectrum id (float and integer arrays, named after the array)

Implements ISpectrumAccess.

getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id ) const

overridevirtual

Retention time and MS level of visible spectrum id.

Implements ISpectrumAccess.

lightClone()

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

overridevirtual

A copy that can be used from another thread (see the copy constructor)

Implements ISpectrumAccess.

Member Data Documentation

experiment_

std::shared_ptr<IMSExperimentRandomAccess> experiment_

private

view_

std::shared_ptr<const View> view_

private