CachedmzML Class Reference

Random-access reader/writer for the OpenMS on-disk cache format. More...

#include <OpenMS/FORMAT/CachedMzML.h>

Inheritance diagram for CachedmzML:

Collaboration diagram for CachedmzML:

Constructors and Destructor
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_
	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.
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.
void	load_ (const std::string &filename)

Detailed Description

Random-access reader/writer for the OpenMS on-disk cache format.

Spectra and chromatograms are split across two files: an .mzML file holding the experiment-level metadata and a side-car .mzML.cached binary file holding the per-spectrum / per-chromatogram payload. After load (or constructing with a filename) the side-car's stream offsets are kept in an in-memory index, so single spectra or chromatograms can be fetched in any order from disk without scanning the full file.

Constructor & Destructor Documentation

CachedmzML() [1/3]

CachedmzML

(

)

Default constructor.

Produces an empty instance with no associated file.

CachedmzML() [2/3]

CachedmzML

(

const std::string &

filename

)

Construct and load metadata + side-car index from filename in one step.

Equivalent to default-constructing and then calling load. See load for the exact behaviour, file layout and exceptions.

Parameters

[in]

filename

Path of the .mzML metadata file; the side-car is expected next to it as filename + ".cached".

CachedmzML() [3/3]

CachedmzML

(

const CachedmzML &

rhs

)

Copy constructor.

Each instance keeps its own file handle on the .mzML.cached side-car, so the copy opens a fresh stream on the same path – the original's stream is not shared.

Parameters

[in]

rhs

Instance to copy.

~CachedmzML()

~CachedmzML

(

)

Destructor.

Closes the open file stream on the .mzML.cached side-car.

Member Function Documentation

getChromatogram()

MSChromatogram getChromatogram

(

Size

id

)

Read one chromatogram from the side-car file.

Parameters

[in]

id

Index of the chromatogram to read; must be smaller than 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.

getMetaData()

const MSExperiment & getMetaData ( ) const

inline

Experiment-level metadata loaded from the .mzML file.

The returned experiment contains instrument and acquisition settings as well as the per-spectrum / per-chromatogram headers. Empty until load has been called.

Returns

Const reference to the loaded metadata experiment.

getNrChromatograms()

size_t getNrChromatograms

(

)

const

Number of chromatograms in the loaded experiment.

Returns

Chromatogram count.

getNrSpectra()

size_t getNrSpectra

(

)

const

Number of spectra in the loaded experiment.

Returns

Spectrum count.

getSpectrum()

MSSpectrum getSpectrum

(

Size

id

)

Read one spectrum from the side-car file.

Seeks the cached stream to the indexed offset for id, parses the binary payload and returns the resulting MSSpectrum. The metadata for the spectrum (instrument settings, native id, ...) is taken from the in-memory experiment loaded at load time.

Parameters

[in]

id

Index of the spectrum to read; must be smaller than 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. a 32-bit-system overflow on a > 2 GB cache file).

load()

static void load ( const std::string &  filename, CachedmzML &  map  )

static

Load a cached .mzML pair into map.

Reads the metadata from filename and builds the in-memory index for the side-car at filename + ".cached"; subsequent calls to getSpectrum / getChromatogram on map fetch the payload from the side-car on demand.

Parameters

[in]	filename	Path of the .mzML metadata file (the side-car is expected next to it as filename + ".cached").
[out]	map	Destination instance; previous contents are replaced.

Exceptions

Exception::FileNotFound	when either file cannot be opened.
Exception::ParseError	when parsing the metadata or building the side-car index fails.

load_()

void load_ ( const std::string &  filename )

protected

store()

static void store ( const std::string &  filename, const PeakMap &  map  )

static

Write map to disk as a cached .mzML pair.

Produces two files: a binary side-car at filename + ".cached" holding the spectrum / chromatogram payload, and an .mzML file at filename holding the metadata.

Parameters

[in]	filename	Path of the metadata file (should end in .mzML); the side-car is written next to it as filename + ".cached".
[in]	map	Experiment to write.

Exceptions

Exception::UnableToCreateFile

when either output file cannot be created.

Member Data Documentation

chrom_index_

std::vector<std::streampos> chrom_index_

protected

filename_

std::string filename_

protected

Name of the mzML file.

filename_cached_

std::string filename_cached_

protected

Name of the cached mzML file.

ifs_

std::ifstream ifs_

protected

Internal filestream.

meta_ms_experiment_

MSExperiment meta_ms_experiment_

protected

Meta data.

spectra_index_

std::vector<std::streampos> spectra_index_

protected

Indices.