SpectrumAccessOpenMSCached Class Reference

An implementation of the Spectrum Access interface using on-disk caching. 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 String &filename)
	Constructor, opens the file stream. More...
	~SpectrumAccessOpenMSCached () override
	Destructor. More...
	SpectrumAccessOpenMSCached (const SpectrumAccessOpenMSCached &rhs)
	Copy constructor. More...
boost::shared_ptr< OpenSwath::ISpectrumAccess >	lightClone () const override
	Light clone operator (actual data will not get copied) More...
OpenSwath::SpectrumPtr	getSpectrumById (int id) override
	Return a pointer to a spectrum at the given id. More...
OpenSwath::SpectrumMeta	getSpectrumMetaById (int id) const override
	Returns the meta information for a spectrum. More...
std::vector< std::size_t >	getSpectraByRT (double RT, double deltaRT) const override
	Return a vector of ids of spectra that are within RT +/- deltaRT. More...
size_t	getNrSpectra () const override
	Returns the number of spectra available. More...
SpectrumSettings	getSpectraMetaInfo (int id) const
OpenSwath::ChromatogramPtr	getChromatogramById (int id) override
	Return a pointer to a chromatogram at the given id. More...
size_t	getNrChromatograms () const override
	Returns the number of chromatograms available. More...
ChromatogramSettings	getChromatogramMetaInfo (int id) const
std::string	getChromatogramNativeID (int id) const override
	Returns the native id of the chromatogram at the given id. More...
Public Member Functions inherited from ISpectrumAccess
virtual	~ISpectrumAccess ()
	Destructor. More...
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. More...
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. 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

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 More...
Static Public Member Functions inherited from CachedmzML
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...
Protected Member Functions inherited from CachedmzML
void	load_ (const String &filename)
Protected Attributes inherited from CachedmzML
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_

Detailed Description

An implementation of the Spectrum Access interface using on-disk caching.

This class implements the OpenSWATH Spectrum Access interface (ISpectrumAccess) using the CachedmzML class which is able to read and write a cached mzML file.

Note

This implementation is not thread-safe since it keeps internally a single file access pointer which it moves when accessing a specific data item. The caller is responsible to ensure that access is performed atomically.

Member Typedef Documentation

MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

SpectrumAccessOpenMSCached() [1/2]

SpectrumAccessOpenMSCached ( const String &  filename )

explicit

Constructor, opens the file stream.

Parameters

filename

The filename of the .mzML file (it is assumed a second file .mzML.cached exists).

Exceptions

Exception::FileNotFound	is thrown if the file is not found
Exception::ParseError	is thrown if the file cannot be parsed

~SpectrumAccessOpenMSCached()

~SpectrumAccessOpenMSCached ( )

override

Destructor.

SpectrumAccessOpenMSCached() [2/2]

SpectrumAccessOpenMSCached

(

const SpectrumAccessOpenMSCached &

rhs

)

Copy constructor.

Member Function Documentation

getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById ( int  id )

overridevirtual

Return a pointer to a chromatogram at the given id.

Implements ISpectrumAccess.

getChromatogramMetaInfo()

ChromatogramSettings getChromatogramMetaInfo

(

int

id

)

const

getChromatogramNativeID()

std::string getChromatogramNativeID ( int  id ) const

overridevirtual

Returns the native id of the chromatogram at the given id.

Implements ISpectrumAccess.

getNrChromatograms()

size_t getNrChromatograms ( ) const

overridevirtual

Returns the number of chromatograms available.

Implements ISpectrumAccess.

getNrSpectra()

size_t getNrSpectra ( ) const

overridevirtual

Returns the number of spectra available.

Implements ISpectrumAccess.

getSpectraByRT()

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

overridevirtual

Return a vector of ids of spectra that are within RT +/- deltaRT.

Implements ISpectrumAccess.

getSpectraMetaInfo()

SpectrumSettings getSpectraMetaInfo

(

int

id

)

const

getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById ( int  id )

overridevirtual

Return a pointer to a spectrum at the given id.

Implements ISpectrumAccess.

getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id ) const

overridevirtual

Returns the meta information for a spectrum.

Implements ISpectrumAccess.

lightClone()

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

overridevirtual

Light clone operator (actual data will not get copied)

Implements ISpectrumAccess.