BinnedSpectrum Class Reference

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

#include <OpenMS/KERNEL/BinnedSpectrum.h>

Collaboration diagram for BinnedSpectrum:

Public Types
using	SparseVectorType = Eigen::SparseVector< float, 0, int >
	typedef for the underlying sparse vector More...

Public Member Functions
	BinnedSpectrum ()
	the empty SparseVector More...
	BinnedSpectrum (const PeakSpectrum &ps, float size, bool unit_ppm, UInt spread, float offset)
	detailed constructor More...
	BinnedSpectrum (const BinnedSpectrum &)
	copy constructor More...
virtual	~BinnedSpectrum ()
	destructor More...
BinnedSpectrum &	operator= (const BinnedSpectrum &)
	assignment operator More...
bool	operator== (const BinnedSpectrum &rhs) const
	equality operator More...
bool	operator!= (const BinnedSpectrum &rhs) const
	inequality operator More...
float	getBinIntensity (double mz)
	returns the bin intensity at a given m/z position More...
size_t	getBinIndex (float mz) const
	return the bin index of a given m/z position More...
float	getBinLowerMZ (size_t i) const
	return the lower m/z of a bin given its index More...
float	getBinSize () const
	get the bin size More...
size_t	getBinSpread () const
	get the bin spread More...
const SparseVectorType *	getBins () const
	immutable access to the bin container More...
SparseVectorType *	getBins ()
	mutable access to the bin container More...
float	getOffset () const
	return offset More...
const std::vector< Precursor > &	getPrecursors () const
	immutable access to precursors More...
std::vector< Precursor > &	getPrecursors ()
	mutable access to precursors More...

Static Public Member Functions
static bool	isCompatible (const BinnedSpectrum &a, const BinnedSpectrum &b)
	Check if two BinnedSpectrum objects have equally sized bins and offset. More...

Static Public Attributes
static constexpr const float	DEFAULT_BIN_WIDTH_LOWRES = 1.0005f
static constexpr const float	DEFAULT_BIN_WIDTH_HIRES = 0.02f
static constexpr const float	DEFAULT_BIN_OFFSET_HIRES = 0.0f
	default bin offset for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x) More...
static constexpr const float	DEFAULT_BIN_OFFSET_LOWRES = 0.4f
	default bin offset for low-resolution data (adapted from doi:10.1007/s13361-015-1179-x) More...

Private Member Functions
void	binSpectrum_ (const PeakSpectrum &ps)
	calculate binning of peak spectrum More...

Private Attributes
UInt	bin_spread_ {0}
	the spread to left or right More...
float	bin_size_ {0}
	the size of each bin More...
bool	unit_ppm_ {false}
	absolute bin size or relative bin size More...
float	offset_ {0}
	offset of bin start More...
SparseVectorType *	bins_ {nullptr}
	bins More...
std::vector< Precursor >	precursors_
	precursor information More...

Static Private Attributes
static constexpr const float	MIN_MZ_ = 1.0

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, used to calculate the binned spectrum

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.

Many operations are provided by the underlying SparseVector implementation:

• bin-wise addition (e.g.: c = a.getBins() + b.getBins())
• bin-wise scaling (e.g.: c = a.getBins() * 5f)
• to get the number of filled bins, call: getBins().nonZeros()
• many more... See the Eigen SparseVector implementation for details.

Implementation detail: Eigen SparseVectors need to have the same dimensionality. EmptySparseVector provides an empty SparseVector with compatible dimension to perform all supported operations.

Member Typedef Documentation

SparseVectorType

using SparseVectorType = Eigen::SparseVector<float, 0, int>

typedef for the underlying sparse vector

Constructor & Destructor Documentation

BinnedSpectrum() [1/3]

BinnedSpectrum ( )

inline

the empty SparseVector

default constructor

BinnedSpectrum() [2/3]

BinnedSpectrum	(	const PeakSpectrum &	ps,
		float	size,
		bool	unit_ppm,
		UInt	spread,
		float	offset
	)

detailed constructor

BinnedSpectrum() [3/3]

BinnedSpectrum

(

const BinnedSpectrum &

)

copy constructor

~BinnedSpectrum()

virtual ~BinnedSpectrum ( )

virtual

destructor

Member Function Documentation

binSpectrum_()

void binSpectrum_ ( const PeakSpectrum &  ps )

private

calculate binning of peak spectrum

getBinIndex()

size_t getBinIndex

(

float

mz

)

const

return the bin index of a given m/z position

getBinIntensity()

float getBinIntensity

(

double

mz

)

returns the bin intensity at a given m/z position

getBinLowerMZ()

float getBinLowerMZ ( size_t  i ) const

inline

return the lower m/z of a bin given its index

getBins() [1/2]

SparseVectorType* getBins

(

)

mutable access to the bin container

getBins() [2/2]

const SparseVectorType* getBins

(

)

const

immutable access to the bin container

getBinSize()

float getBinSize ( ) const

inline

get the bin size

getBinSpread()

size_t getBinSpread ( ) const

inline

get the bin spread

getOffset()

float getOffset ( ) const

inline

return offset

getPrecursors() [1/2]

std::vector<Precursor>& getPrecursors

(

)

mutable access to precursors

getPrecursors() [2/2]

const std::vector<Precursor>& getPrecursors

(

)

const

immutable access to precursors

isCompatible()

static bool isCompatible ( const BinnedSpectrum &  a, const BinnedSpectrum &  b  )

static

Check if two BinnedSpectrum objects have equally sized bins and offset.

operator!=()

bool operator!=

(

const BinnedSpectrum &

rhs

)

const

inequality operator

operator=()

BinnedSpectrum& operator=

(

const BinnedSpectrum &

)

assignment operator

operator==()

bool operator==

(

const BinnedSpectrum &

rhs

)

const

equality operator

Member Data Documentation

bin_size_

float bin_size_ {0}

private

the size of each bin

bin_spread_

UInt bin_spread_ {0}

private

the spread to left or right

bins_

SparseVectorType* bins_ {nullptr}

private

bins

DEFAULT_BIN_OFFSET_HIRES

constexpr const float DEFAULT_BIN_OFFSET_HIRES = 0.0f

staticconstexpr

default bin offset for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)

DEFAULT_BIN_OFFSET_LOWRES

constexpr const float DEFAULT_BIN_OFFSET_LOWRES = 0.4f

staticconstexpr

default bin offset for low-resolution data (adapted from doi:10.1007/s13361-015-1179-x)

DEFAULT_BIN_WIDTH_HIRES

constexpr const float DEFAULT_BIN_WIDTH_HIRES = 0.02f

staticconstexpr

DEFAULT_BIN_WIDTH_LOWRES

constexpr const float DEFAULT_BIN_WIDTH_LOWRES = 1.0005f

staticconstexpr

Sensible default values and notes from doi:10.1007/s13361-015-1179-x Low-resolution MS/MS data: bin width = 1.0005
offset = 0.4 spread should be 0

High-resolution MS/MS data: bin width = 0.02
offset = 0.0 spread should be 0 Note: in sum scores, intensities from neighboring bins should be considered with half intensity of each flanking bin.

Todo:

: Weighted intensity spread is currently not implemented(but could replace the spread parameter).

MIN_MZ_

constexpr const float MIN_MZ_ = 1.0

staticconstexprprivate

offset_

float offset_ {0}

private

offset of bin start

precursors_

std::vector<Precursor> precursors_

private

precursor information

unit_ppm_

bool unit_ppm_ {false}

private

absolute bin size or relative bin size