| OpenMS 2.5.0

Public Member Functions | Protected Attributes | Friends | List of all members
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 | ( |  | ) |

inline virtual

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 | ( |  | ) |

inline virtual

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().