SplineInterpolatedPeaks Class Reference

Data structure for spline interpolation of MS1 spectra and chromatograms. More...

#include <OpenMS/PROCESSING/MISC/SplineInterpolatedPeaks.h>

Collaboration diagram for SplineInterpolatedPeaks:

Classes
class	Navigator
	iterator class for access of spline packages More...

Public Member Functions
	SplineInterpolatedPeaks (const std::vector< double > &pos, const std::vector< double > &intensity)
	constructor taking two vectors (and an optional scaling factor for the m/z (or RT) step width) More...
	SplineInterpolatedPeaks (const MSSpectrum &raw_spectrum)
	constructor taking an MSSpectrum (and an optional scaling factor for the m/z step width) More...
	SplineInterpolatedPeaks (const MSChromatogram &raw_chromatogram)
	constructor taking an MSChromatogram (and an optional scaling factor for the RT step width) More...
	~SplineInterpolatedPeaks ()
	destructor More...
double	getPosMin () const
	returns the minimum m/z (or RT) of the spectrum More...
double	getPosMax () const
	returns the maximum m/z (or RT) of the spectrum More...
size_t	size () const
	Get number of spline packages found during initialization. More...
SplineInterpolatedPeaks::Navigator	getNavigator (double scaling=0.7)
	returns an iterator for access of spline packages More...

Private Member Functions
	SplineInterpolatedPeaks ()
	hide default C'tor More...
void	init_ (const std::vector< double > &pos, const std::vector< double > &intensity)
	section common for all constructors More...

Private Attributes
double	pos_min_
	m/z (or RT) limits of the spectrum More...
double	pos_max_
std::vector< SplinePackage >	packages_
	set of spline packages each interpolating in a certain m/z (or RT) range More...

Detailed Description

Data structure for spline interpolation of MS1 spectra and chromatograms.

The data structure consists of a set of splines, each interpolating the MS1 spectrum (or chromatogram) in a certain m/z (or RT) range. Between these splines no raw data points exist and the intensity is identical to zero.

A spline on non-equi-distant input data is not well supported in regions without data points. Hence, a spline tends to swing wildly in these regions and cannot be used for reliable interpolation. We assume that in m/z (or RT) regions without data points, the spectrum (or chromatogram) is identical to zero.

See also

SplinePackage

MSSpectrum

MSChromatogram

Constructor & Destructor Documentation

SplineInterpolatedPeaks() [1/4]

SplineInterpolatedPeaks	(	const std::vector< double > &	pos,
		const std::vector< double > &	intensity
	)

constructor taking two vectors (and an optional scaling factor for the m/z (or RT) step width)

Note

Vectors are assumed to be sorted by m/z (or RT)!

SplineInterpolatedPeaks() [2/4]

SplineInterpolatedPeaks

(

const MSSpectrum &

raw_spectrum

)

constructor taking an MSSpectrum (and an optional scaling factor for the m/z step width)

SplineInterpolatedPeaks() [3/4]

SplineInterpolatedPeaks

(

const MSChromatogram &

raw_chromatogram

)

constructor taking an MSChromatogram (and an optional scaling factor for the RT step width)

~SplineInterpolatedPeaks()

~SplineInterpolatedPeaks

(

)

destructor

SplineInterpolatedPeaks() [4/4]

SplineInterpolatedPeaks ( )

private

hide default C'tor

Member Function Documentation

getNavigator()

SplineInterpolatedPeaks::Navigator getNavigator

(

double

scaling = 0.7

)

returns an iterator for access of spline packages

Will throw an exception if no packages were found during construction. Check using getSplineCount().

Make sure that the underlying SplineInterpolatedPeaks does not run out-of-scope since the Navigator relies on its data.

Parameters

scaling

step width scaling parameter

Exceptions

Exception::InvalidSize

if packages is empty

Referenced by SpectraMerger::averageProfileSpectra_().

getPosMax()

double getPosMax

(

)

const

returns the maximum m/z (or RT) of the spectrum

Referenced by SpectraMerger::averageProfileSpectra_().

getPosMin()

double getPosMin

(

)

const

returns the minimum m/z (or RT) of the spectrum

Referenced by SpectraMerger::averageProfileSpectra_().

init_()

void init_ ( const std::vector< double > &  pos, const std::vector< double > &  intensity  )

private

section common for all constructors

size()

size_t size

(

)

const

Get number of spline packages found during initialization.

Note that this function should be called right after the C'tor to ensure the spectrum has some usable data to work on. In case there are no packages, a subsequent call to getNavigator() will throw an exception.

Member Data Documentation

packages_

std::vector<SplinePackage> packages_

private

set of spline packages each interpolating in a certain m/z (or RT) range

pos_max_

double pos_max_

private

pos_min_

double pos_min_

private

m/z (or RT) limits of the spectrum