SpectrumAccessOpenMSInMemory Class Reference

An implementation of the OpenSWATH Spectrum Access interface completely in memory. More...

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

Inheritance diagram for SpectrumAccessOpenMSInMemory:

Collaboration diagram for SpectrumAccessOpenMSInMemory:

Public Types
typedef OpenMS::PeakMap	MSExperimentType
typedef OpenMS::MSSpectrum	MSSpectrumType
typedef OpenMS::MSChromatogram	MSChromatogramType

Public Member Functions
	SpectrumAccessOpenMSInMemory (OpenSwath::ISpectrumAccess &origin)
	Constructor. More...
	~SpectrumAccessOpenMSInMemory () override
	Destructor. More...
	SpectrumAccessOpenMSInMemory (const SpectrumAccessOpenMSInMemory &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...
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...
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)

Private Attributes
std::vector< OpenSwath::SpectrumPtr >	spectra_
std::vector< OpenSwath::SpectrumMeta >	spectra_meta_
std::vector< OpenSwath::ChromatogramPtr >	chromatograms_
std::vector< std::string >	chromatogram_ids_

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...

Detailed Description

An implementation of the OpenSWATH Spectrum Access interface completely in memory.

This implementation of the spectrum access interface ensures that all data is held completely in memory and is quickly accessible. This class can be generated by passing any object implementing the Spectrum Access interface and guarantees to provide the same access to the raw data as the original object with the added benefits (and downside) of keeping all data in system memory.

A possible example

OpenSwath::ISpectrumAccess * data_access;
fillData(data_access); // assume that data_access points to some data
OpenSwath::ISpectrumAccess * in_memory_data_access = SpectrumAccessOpenMSInMemory(data_access);

After executing this code, two variables exist: data_access which provides access to the original data but does so in one of multiple ways which is not transparent to the user. However, in_memory_data_access will provide access to the same data but with the guarantee that the data is available in memory and not read from the disk.

Member Typedef Documentation

MSChromatogramType

typedef OpenMS::MSChromatogram MSChromatogramType

MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

SpectrumAccessOpenMSInMemory() [1/2]

SpectrumAccessOpenMSInMemory ( OpenSwath::ISpectrumAccess &  origin )

explicit

Constructor.

~SpectrumAccessOpenMSInMemory()

~SpectrumAccessOpenMSInMemory ( )

override

Destructor.

SpectrumAccessOpenMSInMemory() [2/2]

SpectrumAccessOpenMSInMemory

(

const SpectrumAccessOpenMSInMemory &

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.

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.

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.

Member Data Documentation

chromatogram_ids_

std::vector< std::string > chromatogram_ids_

private

chromatograms_

std::vector< OpenSwath::ChromatogramPtr > chromatograms_

private

spectra_

std::vector< OpenSwath::SpectrumPtr > spectra_

private

spectra_meta_

std::vector< OpenSwath::SpectrumMeta > spectra_meta_

private