SpectrumAccessOpenMS Class Reference

An implementation of the OpenSWATH Spectrum Access interface using OpenMS. More...

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

Inheritance diagram for SpectrumAccessOpenMS:

Collaboration diagram for SpectrumAccessOpenMS:

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

Public Member Functions
	SpectrumAccessOpenMS (boost::shared_ptr< MSExperimentType > ms_experiment)
	Constructor. More...
	~SpectrumAccessOpenMS () override
	Destructor. More...
	SpectrumAccessOpenMS (const SpectrumAccessOpenMS &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)

Private Attributes
boost::shared_ptr< MSExperimentType >	ms_experiment_

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 using OpenMS.

Member Typedef Documentation

MSChromatogramType

typedef OpenMS::MSChromatogram MSChromatogramType

MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

Constructor & Destructor Documentation

SpectrumAccessOpenMS() [1/2]

SpectrumAccessOpenMS ( boost::shared_ptr< MSExperimentType >  ms_experiment )

explicit

Constructor.

~SpectrumAccessOpenMS()

~SpectrumAccessOpenMS ( )

override

Destructor.

SpectrumAccessOpenMS() [2/2]

SpectrumAccessOpenMS

(

const SpectrumAccessOpenMS &

rhs

)

Copy constructor.

Performs a light copy operation when another SpectrumAccessOpenMS instance is given: only a copy of the pointer to the underlying MSExperiment is stored, so after this, both instances (rhs and *this) will point to the same MSExperiment.

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)

Creates a light clone of the current instance, with the clone pointing to the same underlying MSExperiment.

Implements ISpectrumAccess.

Member Data Documentation

ms_experiment_

boost::shared_ptr<MSExperimentType> ms_experiment_

private