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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::MSExperiment< Peak1DMSExperimentType
 
typedef OpenMS::MSSpectrum< Peak1DMSSpectrumType
 
typedef OpenMS::MSChromatogram< ChromatogramPeakMSChromatogramType
 

Public Member Functions

 SpectrumAccessOpenMS (boost::shared_ptr< MSExperimentType > ms_experiment)
 Constructor. More...
 
 ~SpectrumAccessOpenMS ()
 Destructor. More...
 
 SpectrumAccessOpenMS (const SpectrumAccessOpenMS &rhs)
 Copy constructor. More...
 
boost::shared_ptr< OpenSwath::ISpectrumAccesslightClone () const
 Light clone operator (actual data will not get copied) More...
 
OpenSwath::SpectrumPtr getSpectrumById (int id)
 Return a pointer to a spectrum at the given id. More...
 
OpenSwath::SpectrumMeta getSpectrumMetaById (int id) const
 Returns the meta information for a spectrum. More...
 
std::vector< std::size_t > getSpectraByRT (double RT, double deltaRT) const
 Return a vector of ids of spectra that are within RT +/- deltaRT. More...
 
size_t getNrSpectra () const
 Returns the number of spectra available. More...
 
SpectrumSettings getSpectraMetaInfo (int id) const
 
OpenSwath::ChromatogramPtr getChromatogramById (int id)
 Return a pointer to a chromatogram at the given id. More...
 
size_t getNrChromatograms () const
 Returns the number of chromatograms available. More...
 
ChromatogramSettings getChromatogramMetaInfo (int id) const
 
std::string getChromatogramNativeID (int id) const
 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

Constructor & Destructor Documentation

SpectrumAccessOpenMS ( boost::shared_ptr< MSExperimentType ms_experiment)
explicit

Constructor.

Destructor.

Copy constructor.

Member Function Documentation

OpenSwath::ChromatogramPtr getChromatogramById ( int  id)
virtual

Return a pointer to a chromatogram at the given id.

Implements ISpectrumAccess.

ChromatogramSettings getChromatogramMetaInfo ( int  id) const
std::string getChromatogramNativeID ( int  id) const
virtual

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

Implements ISpectrumAccess.

size_t getNrChromatograms ( ) const
virtual

Returns the number of chromatograms available.

Implements ISpectrumAccess.

size_t getNrSpectra ( ) const
virtual

Returns the number of spectra available.

Implements ISpectrumAccess.

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

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

Implements ISpectrumAccess.

SpectrumSettings getSpectraMetaInfo ( int  id) const
OpenSwath::SpectrumPtr getSpectrumById ( int  id)
virtual

Return a pointer to a spectrum at the given id.

Implements ISpectrumAccess.

OpenSwath::SpectrumMeta getSpectrumMetaById ( int  id) const
virtual

Returns the meta information for a spectrum.

Implements ISpectrumAccess.

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

Light clone operator (actual data will not get copied)

Implements ISpectrumAccess.

Member Data Documentation

boost::shared_ptr<MSExperimentType> ms_experiment_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11