IMSExperimentRandomAccess Class Reference

Random access to the spectra and chromatograms of an MS run that stays on disk. More...

#include <OpenMS/KERNEL/IMSExperimentRandomAccess.h>

Inheritance diagram for IMSExperimentRandomAccess:

Public Member Functions
virtual	~IMSExperimentRandomAccess ()
virtual Size	getNrSpectra () const =0
	Number of spectra.
virtual Size	getNrChromatograms () const =0
	Number of chromatograms.
Size	size () const
	Alias for getNrSpectra()
bool	empty () const
	True if there are no spectra.
virtual MSSpectrum	getSpectrum (Size index)=0
	The spectrum with index index, including peaks and metadata.
virtual MSSpectrum	getSpectrumMetadata (Size index)=0
	The spectrum with index index without peaks and data arrays.
virtual MSSpectrum	getSpectrumPeaks (Size index)
	Peaks and data arrays of spectrum index; other metadata may be missing.
virtual double	getSpectrumRT (Size index) const =0
	Retention time (in seconds) of spectrum index, from the index.
virtual UInt	getSpectrumMSLevel (Size index) const =0
	MS level of spectrum index, from the index.
virtual bool	isSortedByRT () const =0
	True if the spectra are sorted by ascending retention time.
virtual Size	findFirstRT (double rt) const
	Index of the first spectrum with retention time >= rt.
virtual MSChromatogram	getChromatogram (Size index)=0
	The chromatogram with index index.
virtual std::shared_ptr< const ExperimentalSettings >	getExperimentalSettings () const =0
	Run-level metadata (instrument, source files, sample, ...)
virtual std::unique_ptr< IMSExperimentRandomAccess >	clone () const =0
	A new instance on the same data with its own file handle (for another thread).

Protected Member Functions
	IMSExperimentRandomAccess ()=default
	IMSExperimentRandomAccess (const IMSExperimentRandomAccess &)=default
IMSExperimentRandomAccess &	operator= (const IMSExperimentRandomAccess &)=default

Detailed Description

Random access to the spectra and chromatograms of an MS run that stays on disk.

Backends keep a small index in memory (e.g. retention time and MS level of every spectrum) and decode spectra on request. Implemented by OnDiscMSExperiment (indexed mzML) and OnDiscThermoRawExperiment (Thermo RAW); further formats (e.g. Bruker TDF, imzML) can be added the same way. Algorithms that only need random access, such as the OpenSWATH adapter SpectrumAccessOnDisc, are written against this interface.

Note

An instance is not thread-safe, as it typically holds one file handle. Give each thread its own clone(); clones share the immutable index.

Constructor & Destructor Documentation

~IMSExperimentRandomAccess()

virtual ~IMSExperimentRandomAccess ( )

virtual

IMSExperimentRandomAccess() [1/2]

IMSExperimentRandomAccess ( )

protecteddefault

IMSExperimentRandomAccess() [2/2]

IMSExperimentRandomAccess ( const IMSExperimentRandomAccess &  )

protecteddefault

Member Function Documentation

clone()

virtual std::unique_ptr< IMSExperimentRandomAccess > clone ( ) const

pure virtual

A new instance on the same data with its own file handle (for another thread).

Cheap: the index is shared, not copied.

Implemented in OnDiscMSExperiment.

empty()

bool empty ( ) const

inline

True if there are no spectra.

findFirstRT()

virtual Size findFirstRT ( double  rt ) const

virtual

Index of the first spectrum with retention time >= rt.

Binary search if the spectra are sorted by retention time, linear search otherwise.

Parameters

[in]

rt

Retention time in seconds

Returns

the index, or getNrSpectra() if there is no such spectrum

getChromatogram()

virtual MSChromatogram getChromatogram ( Size  index )

pure virtual

The chromatogram with index index.

Parameters

[in]

index

Chromatogram index (0 <= index < getNrChromatograms())

Implemented in OnDiscMSExperiment.

getExperimentalSettings()

virtual std::shared_ptr< const ExperimentalSettings > getExperimentalSettings ( ) const

pure virtual

Run-level metadata (instrument, source files, sample, ...)

Implemented in OnDiscMSExperiment.

getNrChromatograms()

virtual Size getNrChromatograms ( ) const

pure virtual

Number of chromatograms.

Implemented in OnDiscMSExperiment.

getNrSpectra()

virtual Size getNrSpectra ( ) const

pure virtual

Number of spectra.

Implemented in OnDiscMSExperiment.

getSpectrum()

virtual MSSpectrum getSpectrum ( Size  index )

pure virtual

The spectrum with index index, including peaks and metadata.

Parameters

[in]

index

Spectrum index (0 <= index < getNrSpectra())

Exceptions

Exception::IndexOverflow

if index is out of range (backend dependent)

Implemented in OnDiscMSExperiment.

getSpectrumMetadata()

virtual MSSpectrum getSpectrumMetadata ( Size  index )

pure virtual

The spectrum with index index without peaks and data arrays.

Parameters

[in]

index

Spectrum index (0 <= index < getNrSpectra())

Implemented in OnDiscMSExperiment.

getSpectrumMSLevel()

virtual UInt getSpectrumMSLevel ( Size  index ) const

pure virtual

MS level of spectrum index, from the index.

Implemented in OnDiscMSExperiment.

getSpectrumPeaks()

virtual MSSpectrum getSpectrumPeaks ( Size  index )

virtual

Peaks and data arrays of spectrum index; other metadata may be missing.

Backends can skip decoding metadata that consumers of peak data alone (e.g. OpenSWATH) do not need. The default returns getSpectrum().

Parameters

[in]

index

Spectrum index (0 <= index < getNrSpectra())

getSpectrumRT()

virtual double getSpectrumRT ( Size  index ) const

pure virtual

Retention time (in seconds) of spectrum index, from the index.

Implemented in OnDiscMSExperiment.

isSortedByRT()

virtual bool isSortedByRT ( ) const

pure virtual

True if the spectra are sorted by ascending retention time.

Implemented in OnDiscMSExperiment.

operator=()

IMSExperimentRandomAccess & operator= ( const IMSExperimentRandomAccess &  )

protecteddefault

size()

Size size ( ) const

inline

Alias for getNrSpectra()