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>

List of all members.

Public Member Functions
	TransSpectrum ()
	TransSpectrum (const MSSpectrum< PeakType > *reference)
virtual	~TransSpectrum ()
virtual void	destroy ()
DoubleReal	getRT () const
DoubleReal	getMZ (const UInt i) const
DoubleReal	getRefIntensity (const UInt i) const
DoubleReal	getTransIntensity (const UInt i) const
void	setTransIntensity (const UInt i, const DoubleReal intens)
Size	size () const
const MSSpectrum< PeakType > *	getRefSpectrum ()
const MSSpectrum< PeakType > *	getRefSpectrum () const
MSSpectrum< PeakType > ::const_iterator	MZBegin (const DoubleReal mz) const
MSSpectrum< PeakType > ::const_iterator	MZEnd (const DoubleReal mz) const
MSSpectrum< PeakType > ::const_iterator	end () const
MSSpectrum< PeakType > ::const_iterator	begin () const
Protected Attributes
const MSSpectrum< PeakType > *	reference_
std::vector< float > *	trans_intens_
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.

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Constructor & Destructor Documentation

TransSpectrum

(

)

[inline]

Default constructor

TransSpectrum

(

const MSSpectrum< PeakType > *

reference

)

[inline]

Copy constructor

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

virtual ~TransSpectrum

(

)

[inline, virtual]

Destructor

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

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Member Function Documentation

MSSpectrum<PeakType>::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_().

virtual void destroy

(

)

[inline, virtual]

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

Referenced by IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), and FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

MSSpectrum<PeakType>::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_().

DoubleReal getMZ

(

const UInt

i

)

const [inline]

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

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

Referenced by IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

DoubleReal getRefIntensity

(

const UInt

i

)

const [inline]

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

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

Referenced by IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), and FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

const MSSpectrum<PeakType>* getRefSpectrum

(

)

[inline]

Returns a pointer to the reference spectrum.

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

const MSSpectrum<PeakType>* getRefSpectrum

(

)

const [inline]

Returns a pointer to the reference spectrum.

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

DoubleReal getRT

(

)

const [inline]

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

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

DoubleReal 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_(), IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

MSSpectrum<PeakType>::const_iterator MZBegin

(

const DoubleReal

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

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

MSSpectrum<PeakType>::const_iterator MZEnd

(

const DoubleReal

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

void setTransIntensity	(	const UInt	i,
		const DoubleReal	intens
	)			[inline]

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

Size size

(

)

const [inline]

Returns the size of spectra.

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

Referenced by IsotopeWaveletTransform< PeakType >::getAvIntens_(), IsotopeWaveletTransform< PeakType >::getSdIntens_(), IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

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Friends And Related Function Documentation

friend class IsotopeWaveletTransform [friend]

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Member Data Documentation

const MSSpectrum<PeakType>* reference_ [protected]

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().

std::vector<float>* trans_intens_ [protected]

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