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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>

Collaboration diagram for IsotopeWaveletTransform< PeakType >::TransSpectrum:
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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().