CachedmzML Class Reference

An class that uses on-disk caching to read and write spectra and chromatograms. More...

#include <OpenMS/FORMAT/CachedMzML.h>

Inheritance diagram for CachedmzML:

Constructors and Destructor
MSExperiment	meta_ms_experiment_
	Meta data. More...
std::ifstream	ifs_
	Internal filestream. More...
String	filename_
	Name of the mzML file. More...
String	filename_cached_
	Name of the cached mzML file. More...
std::vector< std::streampos >	spectra_index_
	Indices. More...
std::vector< std::streampos >	chrom_index_
	CachedmzML ()
	Default constructor. More...
	CachedmzML (const String &filename)
	CachedmzML (const CachedmzML &rhs)
	Copy constructor. More...
	~CachedmzML ()
	Default destructor. More...
MSSpectrum	getSpectrum (Size id)
MSChromatogram	getChromatogram (Size id)
size_t	getNrSpectra () const
size_t	getNrChromatograms () const
const MSExperiment &	getMetaData () const
static void	store (const String &filename, const PeakMap &map)
	Stores a map in a cached MzML file. More...
static void	load (const String &filename, CachedmzML &map)
	Loads a map from a cached MzML file. More...
void	load_ (const String &filename)

Detailed Description

An class that uses on-disk caching to read and write spectra and chromatograms.

This class provides functions to read and write spectra and chromatograms to disk using a time-efficient format. Reading the data items from disk can be very fast and done in random order (once the in-memory index is built for the file).

Constructor & Destructor Documentation

CachedmzML() [1/3]

CachedmzML

(

)

Default constructor.

CachedmzML() [2/3]

CachedmzML

(

const String &

filename

)

CachedmzML() [3/3]

CachedmzML

(

const CachedmzML &

rhs

)

Copy constructor.

~CachedmzML()

~CachedmzML

(

)

Default destructor.

Member Function Documentation

getChromatogram()

MSChromatogram getChromatogram

(

Size

id

)

getMetaData()

const MSExperiment& getMetaData ( ) const

inline

getNrChromatograms()

size_t getNrChromatograms

(

)

const

getNrSpectra()

size_t getNrSpectra

(

)

const

getSpectrum()

MSSpectrum getSpectrum

(

Size

id

)

load()

static void load ( const String &  filename, CachedmzML &  map  )

static

Loads a map from a cached MzML file.

filename The data location (ends in .mzML, expects an adjacent .mzML.cached file) map A CachedmzML result object

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

load_()

void load_ ( const String &  filename )

protected

store()

static void store ( const String &  filename, const PeakMap &  map  )

static

Stores a map in a cached MzML file.

filename The data location (ends in .mzML) map has to be an MSExperiment or have the same interface.

Exceptions

Exception::UnableToCreateFile

is thrown if the file could not be created

Member Data Documentation

chrom_index_

std::vector<std::streampos> chrom_index_

protected

filename_

String filename_

protected

Name of the mzML file.

filename_cached_

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.