OpenSwath::ISpectrumAccess implementation backed by an on-disk OpenMS::CachedmzML cache. More...

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

Inheritance diagram for SpectrumAccessOpenMSCached:

Collaboration diagram for SpectrumAccessOpenMSCached:

Public Types
typedef OpenMS::PeakMap	MSExperimentType

typedef OpenMS::MSSpectrum	MSSpectrumType

Public Member Functions
	SpectrumAccessOpenMSCached (const std::string &filename)
	Open the cached .mzML pair at `filename`.

	~SpectrumAccessOpenMSCached () override
	Destructor; the inherited OpenMS::CachedmzML destructor closes the side-car stream.

	SpectrumAccessOpenMSCached (const SpectrumAccessOpenMSCached &rhs)
	Copy constructor.

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
	Read one spectrum from the side-car file.

OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Return the RT and MS level of one spectrum.

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 in the loaded metadata.

SpectrumSettings	getSpectraMetaInfo (int id) const
	Return the full SpectrumSettings of one spectrum.

OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Read one chromatogram from the side-car file.

size_t	getNrChromatograms () const override
	Number of chromatograms in the loaded metadata.

ChromatogramSettings	getChromatogramMetaInfo (int id) const
	Return the ChromatogramSettings of one chromatogram.

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)

Public Member Functions inherited from CachedmzML
	CachedmzML ()
	Default constructor.

	CachedmzML (const std::string &filename)
	Construct and load metadata + side-car index from `filename` in one step.

	CachedmzML (const CachedmzML &rhs)
	Copy constructor.

	~CachedmzML ()
	Destructor.

MSSpectrum	getSpectrum (Size id)
	Read one spectrum from the side-car file.

MSChromatogram	getChromatogram (Size id)
	Read one chromatogram from the side-car file.

size_t	getNrSpectra () const
	Number of spectra in the loaded experiment.

size_t	getNrChromatograms () const
	Number of chromatograms in the loaded experiment.

const MSExperiment &	getMetaData () const
	Experiment-level metadata loaded from the .mzML file.

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

Static Public Member Functions inherited from CachedmzML
static void	store (const std::string &filename, const PeakMap &map)
	Write `map` to disk as a cached .mzML pair.

static void	load (const std::string &filename, CachedmzML &map)
	Load a cached .mzML pair into `map`.

Protected Member Functions inherited from CachedmzML
void	load_ (const std::string &filename)

Protected Attributes inherited from CachedmzML
MSExperiment	meta_ms_experiment_
	Meta data.

std::ifstream	ifs_
	Internal filestream.

std::string	filename_
	Name of the mzML file.

std::string	filename_cached_
	Name of the cached mzML file.

std::vector< std::streampos >	spectra_index_
	Indices.

std::vector< std::streampos >	chrom_index_

Detailed Description

OpenSwath::ISpectrumAccess implementation backed by an on-disk OpenMS::CachedmzML cache.

Combines the in-memory index of OpenMS::CachedmzML with the OpenSWATH spectrum-access interface: spectrum and chromatogram metadata are served from the in-memory MSExperiment, and the binary payloads are read on demand from the side-car .mzML.cached file.

Note: This implementation is not thread-safe: a single file stream is maintained and seeked per request, so concurrent calls would race on the stream position. Callers must serialise access externally.

Member Typedef Documentation

◆ MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

◆ MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

◆ SpectrumAccessOpenMSCached() [1/2]

SpectrumAccessOpenMSCached ( const std::string & filename )

explicit

Open the cached .mzML pair at filename.

Delegates to OpenMS::CachedmzML's filename constructor: the metadata is loaded from filename and the side-car index for filename + ".cached" is built; subsequent accessor calls read the payloads from that side-car on demand.

Parameters

[in] filename Path to the .mzML metadata file; the side-car is expected next to it at filename + ".cached".

Exceptions

Exception::FileNotFound	when either file cannot be opened.
Exception::ParseError	when the metadata cannot be parsed or the side-car index cannot be built.

◆ ~SpectrumAccessOpenMSCached()

~SpectrumAccessOpenMSCached ( )

override

Destructor; the inherited OpenMS::CachedmzML destructor closes the side-car stream.

◆ SpectrumAccessOpenMSCached() [2/2]

SpectrumAccessOpenMSCached ( const SpectrumAccessOpenMSCached & rhs )

Copy constructor.

Each copy keeps its own file handle on the .mzML.cached side-car (a fresh stream is opened on the same path by the inherited OpenMS::CachedmzML copy constructor). The in-memory metadata and side-car index are duplicated; the spectrum and chromatogram binary payloads are not.

Parameters

[in] rhs Source accessor to copy.

Member Function Documentation

◆ getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int id )

overridevirtual

Read one chromatogram from the side-car file.

Parameters

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

Returns: Decoded chromatogram.

Exceptions

Exception::ParseError when seekg on the side-car stream fails.

Implements ISpectrumAccess.

◆ getChromatogramMetaInfo()

ChromatogramSettings getChromatogramMetaInfo ( int id ) const

Return the ChromatogramSettings of one chromatogram.

Parameters

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

Returns: Copy of the stored ChromatogramSettings.

◆ 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 from the stored metadata.

Implements ISpectrumAccess.

◆ getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Number of chromatograms in the loaded metadata.

Implements ISpectrumAccess.

◆ getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Number of spectra in the loaded metadata.

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].

Walks the metadata MSExperiment forward from the first spectrum with RT >= RT - deltaRT.

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 metadata for spectra inside the window.

Implements ISpectrumAccess.

◆ getSpectraMetaInfo()

SpectrumSettings getSpectraMetaInfo ( int id ) const

Return the full SpectrumSettings of one spectrum.

Unlike getSpectrumMetaById (which returns only RT and ms_level), this returns the full per-spectrum metadata read at construction time.

Parameters

[in] id Spectrum index. No bounds check is performed.

Returns: Copy of the stored SpectrumSettings for that spectrum.

◆ getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int id )

overridevirtual

Read one spectrum from the side-car file.

Parameters

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

Returns: Decoded spectrum.

Exceptions

Exception::ParseError when seekg on the side-car stream fails (e.g. an overflow on a 32-bit system reading a > 2 GB cache file).

Implements ISpectrumAccess.

◆ getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int id ) const

overridevirtual

Return the RT and MS level of one spectrum.

Only RT and ms_level are filled on the returned SpectrumMeta; for the full spectrum settings use getSpectraMetaInfo.

Parameters

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

Returns: SpectrumMeta carrying only RT and ms_level.

Implements ISpectrumAccess.

◆ lightClone()

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

overridevirtual

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

Equivalent to copy-constructing through SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached&); the clone reads payloads lazily from its own stream on the same side-car file.

Returns: Shared pointer to the cloned accessor.

Implements ISpectrumAccess.

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ MSExperimentType

◆ MSSpectrumType

Constructor & Destructor Documentation

◆ SpectrumAccessOpenMSCached() [1/2]

◆ ~SpectrumAccessOpenMSCached()

◆ SpectrumAccessOpenMSCached() [2/2]

Member Function Documentation

◆ getChromatogramById()

◆ getChromatogramMetaInfo()

◆ getChromatogramNativeID()

◆ getNrChromatograms()

◆ getNrSpectra()

◆ getSpectraByRT()

◆ getSpectraMetaInfo()

◆ getSpectrumById()

◆ getSpectrumMetaById()

◆ lightClone()