BinnedSpectrum Class Reference

This is a binned representation of a PeakSpectrum. More...

#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>

Classes
class	NoSpectrumIntegrated
	Exception which is thrown if BinnedSpectrum bins are accessed and no PeakSpektrum has been integrated yet i.e. bins_ is empty. More...

Public Types
typedef SparseVector< float >::const_iterator	const_bin_iterator
typedef SparseVector< float >::iterator	bin_iterator

Public Member Functions
	BinnedSpectrum ()
	default constructor More...
	BinnedSpectrum (float size, UInt spread, PeakSpectrum ps)
	detailed constructor More...
	BinnedSpectrum (const BinnedSpectrum &source)
	copy constructor More...
virtual	~BinnedSpectrum ()
	destructor More...
BinnedSpectrum &	operator= (const BinnedSpectrum &source)
	assignment operator More...
BinnedSpectrum &	operator= (const PeakSpectrum &source)
	assignment operator for PeakSpectra More...
bool	operator== (const BinnedSpectrum &rhs) const
	equality operator More...
bool	operator!= (const BinnedSpectrum &rhs) const
	inequality operator More...
bool	operator== (const PeakSpectrum &rhs) const
	equality operator for PeakSpectra More...
bool	operator!= (const PeakSpectrum &rhs) const
	inequality operator for PeakSpectra More...
double	getBinSize () const
	get the BinSize More...
UInt	getBinSpread () const
	get the BinSpread More...
UInt	getBinNumber () const
	get the BinNumber, number of Bins More...
UInt	getFilledBinNumber () const
	get the FilledBinNumber, number of filled Bins More...
const SparseVector< float > &	getBins () const
SparseVector< float > &	getBins ()
const_bin_iterator	begin () const
	returns the const begin iterator of the container More...
const_bin_iterator	end () const
	returns the const end iterator of the container More...
bin_iterator	begin ()
	returns the begin iterator of the container More...
bin_iterator	end ()
	returns the end iterator of the container More...
void	setBinSize (double s)
void	setBinSpread (UInt s)
void	setBinning ()
bool	checkCompliance (const BinnedSpectrum &bs) const
	function to check comparability of two BinnedSpectrum objects, i.e. if they have equal bin size and spread More...
const PeakSpectrum &	getRawSpectrum () const
	Gives access to the underlying raw spectrum. More...

Private Attributes
UInt	bin_spread_
float	bin_size_
SparseVector< float >	bins_
	The computed bins. More...
PeakSpectrum	raw_spec_
	The original raw spectrum. More...

Detailed Description

This is a binned representation of a PeakSpectrum.

Parameters

sz	the size of the bins and
sp	number of neighboring bins to both sides affected by a peak contribution
ps	the peakspectrum, that shall be represented

sz denotes the size of a bin in Th, thereby deciding the number of bins(all of size sz) the spectrum is discretized to. Each bin will represent a certain Th range and the peaks will be put in the respective bins and sum up inside. sp denotes the number of neighboring bins to the left and the number of neighboring bins to the right a peak is also added to. E.g. a BinnedSpectrum with binsize of 0.5 Th will have a peak at 100 Th in bin no. 200, a peak at 100.1 Th will be in bin no. 201. If the binspread is 1, the peak at 100 Th will be added to bin no. 199, 200 and 201. If the binspread is 2, the peak at 100 Th will also be added to bin no. 198 and 202, and so on.

Member Typedef Documentation

bin_iterator

typedef SparseVector<float>::iterator bin_iterator

const_bin_iterator

typedef SparseVector<float>::const_iterator const_bin_iterator

Constructor & Destructor Documentation

BinnedSpectrum() [1/3]

BinnedSpectrum

(

)

default constructor

BinnedSpectrum() [2/3]

BinnedSpectrum	(	float	size,
		UInt	spread,
		PeakSpectrum	ps
	)

detailed constructor

BinnedSpectrum() [3/3]

BinnedSpectrum

(

const BinnedSpectrum &

source

)

copy constructor

~BinnedSpectrum()

virtual ~BinnedSpectrum ( )

virtual

destructor

Member Function Documentation

begin() [1/2]

const_bin_iterator begin ( ) const

inline

returns the const begin iterator of the container

References SparseVector< Value >::begin().

begin() [2/2]

bin_iterator begin ( )

inline

returns the begin iterator of the container

References SparseVector< Value >::begin().

checkCompliance()

bool checkCompliance

(

const BinnedSpectrum &

bs

)

const

function to check comparability of two BinnedSpectrum objects, i.e. if they have equal bin size and spread

end() [1/2]

const_bin_iterator end ( ) const

inline

returns the const end iterator of the container

References SparseVector< Value >::end().

end() [2/2]

bin_iterator end ( )

inline

returns the end iterator of the container

References SparseVector< Value >::end().

getBinNumber()

UInt getBinNumber ( ) const

inline

get the BinNumber, number of Bins

References SparseVector< Value >::size().

getBins() [1/2]

const SparseVector<float>& getBins ( ) const

inline

immutable access to the Bincontainer

Exceptions

NoSpectrumIntegrated

is thrown if no spectrum was integrated

References SparseVector< Value >::empty().

Referenced by BinnedSpectrum::operator=().

getBins() [2/2]

SparseVector<float>& getBins ( )

inline

mutable access to the Bincontainer

Exceptions

NoSpectrumIntegrated

is thrown if no spectrum was integrated

References SparseVector< Value >::empty().

getBinSize()

double getBinSize ( ) const

inline

get the BinSize

Referenced by BinnedSpectrum::operator=(), and BinnedSpectrum::operator==().

getBinSpread()

UInt getBinSpread ( ) const

inline

get the BinSpread

Referenced by BinnedSpectrum::operator=(), and BinnedSpectrum::operator==().

getFilledBinNumber()

UInt getFilledBinNumber ( ) const

inline

get the FilledBinNumber, number of filled Bins

References SparseVector< Value >::nonzero_size().

getRawSpectrum()

const PeakSpectrum& getRawSpectrum

(

)

const

Gives access to the underlying raw spectrum.

operator!=() [1/2]

bool operator!= ( const BinnedSpectrum &  rhs ) const

inline

inequality operator

References KDTree::operator==().

operator!=() [2/2]

bool operator!= ( const PeakSpectrum &  rhs ) const

inline

inequality operator for PeakSpectra

References KDTree::operator==().

operator=() [1/2]

BinnedSpectrum& operator= ( const BinnedSpectrum &  source )

inline

assignment operator

References BinnedSpectrum::getBins(), BinnedSpectrum::getBinSize(), BinnedSpectrum::getBinSpread(), and BinnedSpectrum::raw_spec_.

operator=() [2/2]

BinnedSpectrum& operator= ( const PeakSpectrum &  source )

inline

assignment operator for PeakSpectra

operator==() [1/2]

bool operator== ( const BinnedSpectrum &  rhs ) const

inline

equality operator

References BinnedSpectrum::getBinSize(), BinnedSpectrum::getBinSpread(), and BinnedSpectrum::raw_spec_.

operator==() [2/2]

bool operator== ( const PeakSpectrum &  rhs ) const

inline

equality operator for PeakSpectra

setBinning()

void setBinning

(

)

makes the binning: all Peaks of the containing PeakSpectrum are summed up in the bins corresponding to m/z ranges

Exceptions

NoSpectrumIntegrated

is thrown if no spectrum was integrated before

setBinSize()

void setBinSize ( double  s )

inline

sets the BinSize_ (and re-bins)

Parameters

s	defines the size of the bins

Exceptions

NoSpectrumIntegrated

is thrown if no spectrum is integrated

setBinSpread()

void setBinSpread ( UInt  s )

inline

sets the BinSpread_ (and re-bins)

Parameters

s	defines the binning spread, given as positive integer

Exceptions

NoSpectrumIntegrated

is thrown if no spec was integrated into the instance

Member Data Documentation

bin_size_

float bin_size_

private

bin_spread_

UInt bin_spread_

private

bins_

SparseVector<float> bins_

private

The computed bins.

raw_spec_

PeakSpectrum raw_spec_

private

The original raw spectrum.

Referenced by BinnedSpectrum::operator=(), and BinnedSpectrum::operator==().