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

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

Collaboration diagram for BinnedSpectrum:

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

using	SparseVectorIndexType = Eigen::SparseVector< float >::Index
	typedef for the index into the sparse vector More...

using	SparseVectorIteratorType = Eigen::SparseVector< float >::InnerIterator
	typedef for the index into the sparse vector More...

Public Member Functions
	BinnedSpectrum ()
	default constructor More...

	BinnedSpectrum (const PeakSpectrum &ps, float size, bool unit_ppm, UInt spread, float offset)
	detailed constructor More...

	BinnedSpectrum (const BinnedSpectrum &)=default
	copy constructor More...

virtual	~BinnedSpectrum ()
	destructor More...

BinnedSpectrum &	operator= (const BinnedSpectrum &)=default
	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...

SparseVectorIndexType	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...

static const SparseVectorType	EmptySparseVector
	the empty SparseVector More...

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

Private Attributes
UInt	bin_spread_
	the spread to left or right More...

float	bin_size_
	the size of each bin More...

bool	unit_ppm_
	absolute bin size or relative bin size More...

float	offset_
	offset of bin start More...

SparseVectorType	bins_
	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

◆ SparseVectorIndexType

using SparseVectorIndexType = Eigen::SparseVector<float>::Index

typedef for the index into the sparse vector

◆ SparseVectorIteratorType

using SparseVectorIteratorType = Eigen::SparseVector<float>::InnerIterator

typedef for the index into the sparse vector

◆ SparseVectorType

using SparseVectorType = Eigen::SparseVector<float>

typedef for the underlying sparse vector

Constructor & Destructor Documentation

◆ BinnedSpectrum() [1/3]

BinnedSpectrum ( )

inline

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 & )

default

copy constructor

◆ ~BinnedSpectrum()

virtual ~BinnedSpectrum ( )

virtual

destructor

Member Function Documentation

◆ binSpectrum_()

void binSpectrum_ ( const PeakSpectrum & ps )

private

calculate binning of peak spectrum

◆ getBinIndex()

SparseVectorIndexType getBinIndex ( float mz ) const

inline

return the bin index of a given m/z position

◆ getBinIntensity()

float getBinIntensity ( double mz )

inline

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 & )

default

assignment operator

◆ operator==()

bool operator== ( const BinnedSpectrum & rhs ) const

equality operator

Member Data Documentation

◆ bin_size_

float bin_size_

private

the size of each bin

◆ bin_spread_

UInt bin_spread_

private

the spread to left or right

◆ bins_

SparseVectorType bins_

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)

Referenced by TOPPGNPSExport::main_().

◆ 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).

◆ EmptySparseVector

const SparseVectorType EmptySparseVector

static

the empty SparseVector

◆ MIN_MZ_

constexpr const float MIN_MZ_ = 1.0

staticconstexprprivate

◆ offset_

float offset_

private

offset of bin start

◆ precursors_

std::vector<Precursor> precursors_

private

precursor information

◆ unit_ppm_

bool unit_ppm_

private

absolute bin size or relative bin size

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ SparseVectorIndexType

◆ SparseVectorIteratorType

◆ SparseVectorType

Constructor & Destructor Documentation

◆ BinnedSpectrum() [1/3]

◆ BinnedSpectrum() [2/3]

◆ BinnedSpectrum() [3/3]

◆ ~BinnedSpectrum()

Member Function Documentation

◆ binSpectrum_()

◆ getBinIndex()

◆ getBinIntensity()

◆ getBinLowerMZ()

◆ getBins() [1/2]

◆ getBins() [2/2]

◆ getBinSize()

◆ getBinSpread()

◆ getOffset()

◆ getPrecursors() [1/2]

◆ getPrecursors() [2/2]

◆ isCompatible()

◆ operator!=()

◆ operator=()

◆ operator==()

Member Data Documentation

◆ bin_size_

◆ bin_spread_

◆ bins_

◆ DEFAULT_BIN_OFFSET_HIRES

◆ DEFAULT_BIN_OFFSET_LOWRES

◆ DEFAULT_BIN_WIDTH_HIRES

◆ DEFAULT_BIN_WIDTH_LOWRES

◆ EmptySparseVector

◆ MIN_MZ_

◆ offset_

◆ precursors_

◆ unit_ppm_