IsotopeWaveletTransform< PeakType >::TransSpectrum Class Reference

Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletTransform.h>

Public Member Functions
	TransSpectrum ()
	TransSpectrum (const MSSpectrum *reference)
virtual	~TransSpectrum ()
virtual void	destroy ()
double	getRT () const
double	getMZ (const UInt i) const
double	getRefIntensity (const UInt i) const
double	getTransIntensity (const UInt i) const
void	setTransIntensity (const UInt i, const double intens)
Size	size () const
const MSSpectrum *	getRefSpectrum ()
const MSSpectrum *	getRefSpectrum () const
MSSpectrum::const_iterator	MZBegin (const double mz) const
MSSpectrum::const_iterator	MZEnd (const double mz) const
MSSpectrum::const_iterator	end () const
MSSpectrum::const_iterator	begin () const

Protected Attributes
const MSSpectrum *	reference_
	The reference spectrum. More...
std::vector< float > *	trans_intens_
	The intensities of the transform. More...

Friends
class	IsotopeWaveletTransform

Detailed Description

template<typename PeakType>
class OpenMS::IsotopeWaveletTransform< PeakType >::TransSpectrum

Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations.

Constructor & Destructor Documentation

TransSpectrum() [1/2]

TransSpectrum ( )

inline

Default constructor

TransSpectrum() [2/2]

TransSpectrum ( const MSSpectrum *  reference )

inline

Copy constructor

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_, and IsotopeWaveletTransform< PeakType >::TransSpectrum::trans_intens_.

~TransSpectrum()

virtual ~TransSpectrum ( )

inlinevirtual

Destructor

References IsotopeWaveletTransform< PeakType >::TransSpectrum::trans_intens_.

Member Function Documentation

begin()

MSSpectrum::const_iterator begin ( ) const

inline

Attention: iterations will only performed over the reference spectrum. You will have to use the "distance"-function in order to get the corresponding entry of the transform.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

destroy()

virtual void destroy ( )

inlinevirtual

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_, and IsotopeWaveletTransform< PeakType >::TransSpectrum::trans_intens_.

end()

MSSpectrum::const_iterator end ( ) const

inline

Attention: iterations will only performed over the reference spectrum. You will have to use the "distance"-function in order to get the corresponding entry of the transform.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_().

getMZ()

double getMZ ( const UInt  i ) const

inline

Returns the mass-over-charge ratio at index i.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

Referenced by IsotopeWaveletTransform< PeakType >::scoreThis_().

getRefIntensity()

double getRefIntensity ( const UInt  i ) const

inline

Returns the reference (non-transformed) intensity at index i.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

getRefSpectrum() [1/2]

const MSSpectrum* getRefSpectrum ( )

inline

Returns a pointer to the reference spectrum.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

getRefSpectrum() [2/2]

const MSSpectrum* getRefSpectrum ( ) const

inline

Returns a pointer to the reference spectrum.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

getRT()

double getRT ( ) const

inline

Returns the RT value (not the index) of the associated scan.

References MSSpectrum::getRT(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

getTransIntensity()

double getTransIntensity ( const UInt  i ) const

inline

Returns the transformed intensity at index i.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::trans_intens_.

Referenced by IsotopeWaveletTransform< PeakType >::getAvIntens_(), IsotopeWaveletTransform< PeakType >::getSdIntens_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

MZBegin()

MSSpectrum::const_iterator MZBegin ( const double  mz ) const

inline

Attention: iterations will only performed over the reference spectrum. You will have to use the "distance"-function in order to get the corresponding entry of the transform.

References MSSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

MZEnd()

MSSpectrum::const_iterator MZEnd ( const double  mz ) const

inline

Attention: iterations will only performed over the reference spectrum. You will have to use the "distance"-function in order to get the corresponding entry of the transform.

References MSSpectrum::MZEnd(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::reference_.

setTransIntensity()

void setTransIntensity ( const UInt  i, const double  intens  )

inline

Stores the intensity value i of the transform at position i.

size()

Size size ( ) const

inline

Returns the size of spectra.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::trans_intens_.

Referenced by IsotopeWaveletTransform< PeakType >::getAvIntens_(), IsotopeWaveletTransform< PeakType >::getSdIntens_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

Friends And Related Function Documentation

IsotopeWaveletTransform

friend class IsotopeWaveletTransform

friend

Member Data Documentation

reference_

const MSSpectrum* reference_

protected

The reference spectrum.

Referenced by IsotopeWaveletTransform< PeakType >::TransSpectrum::begin(), IsotopeWaveletTransform< PeakType >::TransSpectrum::destroy(), IsotopeWaveletTransform< PeakType >::TransSpectrum::end(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getMZ(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRefIntensity(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRefSpectrum(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRT(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZEnd(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::TransSpectrum().

trans_intens_

std::vector<float>* trans_intens_

protected

The intensities of the transform.

Referenced by IsotopeWaveletTransform< PeakType >::TransSpectrum::destroy(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), IsotopeWaveletTransform< PeakType >::TransSpectrum::size(), IsotopeWaveletTransform< PeakType >::TransSpectrum::TransSpectrum(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::~TransSpectrum().