OpenMS  2.5.0
Public Types | Public Member Functions | Private Attributes | List of all members
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:
ISpectrumAccess

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::ISpectrumAccesslightClone () 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...
 

Private Attributes

boost::shared_ptr< MSExperimentTypems_experiment_
 

Detailed Description

An implementation of the OpenSWATH Spectrum Access interface using OpenMS.

Member Typedef Documentation

◆ MSChromatogramType

◆ MSExperimentType

◆ MSSpectrumType

Constructor & Destructor Documentation

◆ SpectrumAccessOpenMS() [1/2]

SpectrumAccessOpenMS ( boost::shared_ptr< MSExperimentType ms_experiment)
explicit

Constructor.

◆ ~SpectrumAccessOpenMS()

~SpectrumAccessOpenMS ( )
override

Destructor.

◆ SpectrumAccessOpenMS() [2/2]

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