A base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc. More...

#include <OpenMS/KERNEL/DimMapper.h>

Inheritance diagram for DimBase:

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Collaboration diagram for DimBase:

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Public Types
using	ValueType = double

using	ValueTypes = std::vector< ValueType >

Public Member Functions
	DimBase ()=delete
	No default c'tor. More...

	DimBase (DIM_UNIT unit)
	Custom c'tor with unit. More...

DimBase &	operator= (const DimBase &rhs)=default
	Assignment operator. More...

virtual	~DimBase () noexcept=default
	D'tor (needs to be virtual; we are holding pointers to base in DimMapper) More...

bool	operator== (const DimBase &rhs) const
	Equality. More...

virtual std::unique_ptr< DimBase >	clone () const =0
	Copy derived objects to avoid slicing when dealing with pointers to DimBase. More...

virtual ValueType	map (const Peak1D &p) const =0

virtual ValueType	map (const Peak2D &p) const =0

virtual ValueType	map (const ChromatogramPeak &p) const =0

virtual ValueType	map (const MSExperiment::ConstAreaIterator &it) const =0

virtual ValueType	map (const MobilityPeak1D &p) const =0

virtual ValueType	map (const MobilityPeak2D &p) const =0

virtual ValueType	map (const MSSpectrum &spec, const Size index) const =0
	obtain value from a certain point in a spectrum More...

virtual ValueType	map (const MSChromatogram &chrom, const Size index) const =0
	obtain value from a certain point in a chromatogram More...

virtual ValueType	map (const Mobilogram &mb, const Size index) const =0
	obtain value from a certain point in a mobilogram More...

virtual ValueTypes	map (const MSSpectrum &spec) const =0

virtual ValueTypes	map (const MSChromatogram &chrom) const =0

virtual ValueType	map (const BaseFeature &bf) const =0

virtual ValueType	map (const PeptideIdentification &pi) const =0

virtual RangeBase	map (const RangeAllType &rm) const =0
	Return the min/max (range) for a certain dimension. More...

virtual RangeBase &	map (RangeAllType &rm) const =0
	Return the min/max (range) for a certain dimension (i.e. a reference to the base class of `rm`) More...

virtual void	setRange (const RangeBase &in, RangeAllType &out) const =0
	Set the min/max (range) in `out` for a certain dimension. More...

virtual void	fromXY (const ValueType in, Peak1D &p) const =0
	set the dimension of a Peak1D More...

virtual void	fromXY (const ValueType in, ChromatogramPeak &p) const =0
	set the dimension of a ChromatogramPeak More...

virtual void	fromXY (const ValueType in, MobilityPeak1D &p) const =0
	set the dimension of a MobilityPeak1D More...

virtual void	fromXY (const ValueType in, MobilityPeak2D &p) const =0
	set the dimension of a MobilityPeak2D More...

std::string_view	getDimName () const
	Name of the dimension, e.g. 'RT [s]'. More...

std::string_view	getDimNameShort () const
	Name of the dimension, e.g. 'RT'. More...

DIM_UNIT	getUnit () const
	The unit of the dimension. More...

String	formattedValue (const ValueType value) const
	Creates a short string representation with "UNIT: value", where value has a predefined precision (see valuePrecision()) More...

String	formattedValue (ValueType value, const String &prefix) const
	like formattedValue() but with a custom unit prefix instead of the default one for the dim, e.g. "myText: 45.32" More...

int	valuePrecision () const
	return the recommended precision for the current unit (2 digits for RT, 8 for m/z, etc) More...

Protected Attributes
DIM_UNIT	unit_
	the unit of this dimension More...

Detailed Description

A base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc.

The reverse (X-Y coordinates to data type, e.g. Peak1D) is also possible using 'from...()' methods

Member Typedef Documentation

◆ ValueType

using ValueType = double

◆ ValueTypes

using ValueTypes = std::vector<ValueType>

Constructor & Destructor Documentation

◆ DimBase() [1/2]

DimBase ( )

delete

No default c'tor.

◆ DimBase() [2/2]

DimBase ( DIM_UNIT unit )

inline

Custom c'tor with unit.

◆ ~DimBase()

virtual ~DimBase ( )

virtualdefaultnoexcept

D'tor (needs to be virtual; we are holding pointers to base in DimMapper)

Member Function Documentation

◆ clone()

virtual std::unique_ptr<DimBase> clone ( ) const

pure virtual

Copy derived objects to avoid slicing when dealing with pointers to DimBase.

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ formattedValue() [1/2]

String formattedValue ( const ValueType value ) const

Creates a short string representation with "UNIT: value", where value has a predefined precision (see valuePrecision())

Parameters

value The value of this Dim to format

Returns: A formatted string, e.g. "RT: 45.32"

◆ formattedValue() [2/2]

String formattedValue	(	ValueType	value,
		const String &	prefix
	)		const

like formattedValue() but with a custom unit prefix instead of the default one for the dim, e.g. "myText: 45.32"

◆ fromXY() [1/4]

virtual void fromXY	(	const ValueType	in,
		ChromatogramPeak &	p
	)		const

pure virtual

set the dimension of a ChromatogramPeak

Implemented in DimIM, DimMZ, DimINT, and DimRT.

◆ fromXY() [2/4]

virtual void fromXY	(	const ValueType	in,
		MobilityPeak1D &	p
	)		const

pure virtual

set the dimension of a MobilityPeak1D

Implemented in DimMZ, DimRT, DimIM, and DimINT.

◆ fromXY() [3/4]

virtual void fromXY	(	const ValueType	in,
		MobilityPeak2D &	p
	)		const

pure virtual

set the dimension of a MobilityPeak2D

Implemented in DimRT, DimIM, DimINT, and DimMZ.

◆ fromXY() [4/4]

virtual void fromXY	(	const ValueType	in,
		Peak1D &	p
	)		const

pure virtual

set the dimension of a Peak1D

Implemented in DimIM, DimRT, DimINT, and DimMZ.

◆ getDimName()

std::string_view getDimName ( ) const

inline

Name of the dimension, e.g. 'RT [s]'.

References OpenMS::DIM_NAMES.

◆ getDimNameShort()

std::string_view getDimNameShort ( ) const

inline

Name of the dimension, e.g. 'RT'.

References OpenMS::DIM_NAMES_SHORT.

◆ getUnit()

DIM_UNIT getUnit ( ) const

inline

The unit of the dimension.

Referenced by Gravitator::setIntensityAsGravity(), and Plot2DWidget::setMapper().

◆ map() [1/15]

virtual ValueType map ( const BaseFeature & bf ) const

pure virtual

Implemented in DimINT, DimMZ, DimRT, and DimIM.

◆ map() [2/15]

virtual ValueType map ( const ChromatogramPeak & p ) const

pure virtual

Implemented in DimINT, DimRT, DimIM, and DimMZ.

◆ map() [3/15]

virtual ValueType map ( const MobilityPeak1D & p ) const

pure virtual

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ map() [4/15]

virtual ValueType map ( const MobilityPeak2D & p ) const

pure virtual

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ map() [5/15]

virtual ValueType map	(	const Mobilogram &	mb,
		const Size	index
	)		const

pure virtual

obtain value from a certain point in a mobilogram

Implemented in DimRT, DimIM, DimINT, and DimMZ.

◆ map() [6/15]

virtual ValueTypes map ( const MSChromatogram & chrom ) const

pure virtual

obtain vector of same length as spec; one element per peak

Exceptions

Exception::InvalidRange if elements do not support the dimension

Implemented in DimINT, DimRT, DimIM, and DimMZ.

◆ map() [7/15]

virtual ValueType map	(	const MSChromatogram &	chrom,
		const Size	index
	)		const

pure virtual

obtain value from a certain point in a chromatogram

Implemented in DimMZ, DimINT, DimRT, and DimIM.

◆ map() [8/15]

virtual ValueType map ( const MSExperiment::ConstAreaIterator & it ) const

pure virtual

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ map() [9/15]

virtual ValueTypes map ( const MSSpectrum & spec ) const

pure virtual

obtain vector of same length as spec; one element per peak

Exceptions

Exception::InvalidRange if elements do not support the dimension

Implemented in DimINT, DimMZ, DimIM, and DimRT.

◆ map() [10/15]

virtual ValueType map	(	const MSSpectrum &	spec,
		const Size	index
	)		const

pure virtual

obtain value from a certain point in a spectrum

Implemented in DimIM, DimRT, DimINT, and DimMZ.

◆ map() [11/15]

virtual ValueType map ( const Peak1D & p ) const

pure virtual

Implemented in DimINT, DimMZ, DimIM, and DimRT.

◆ map() [12/15]

virtual ValueType map ( const Peak2D & p ) const

pure virtual

Implemented in DimINT, DimMZ, DimRT, and DimIM.

◆ map() [13/15]

virtual ValueType map ( const PeptideIdentification & pi ) const

pure virtual

Implemented in DimMZ, DimRT, DimIM, and DimINT.

◆ map() [14/15]

virtual RangeBase map ( const RangeAllType & rm ) const

pure virtual

Return the min/max (range) for a certain dimension.

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ map() [15/15]

virtual RangeBase& map ( RangeAllType & rm ) const

pure virtual

Return the min/max (range) for a certain dimension (i.e. a reference to the base class of rm)

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ operator=()

DimBase& operator= ( const DimBase & rhs )

default

Assignment operator.

◆ operator==()

bool operator== ( const DimBase & rhs ) const

inline

Equality.

◆ setRange()

virtual void setRange	(	const RangeBase &	in,
		RangeAllType &	out
	)		const

pure virtual

Set the min/max (range) in out for a certain dimension.

Implemented in DimIM, DimINT, DimMZ, and DimRT.

◆ valuePrecision()

int valuePrecision ( ) const

return the recommended precision for the current unit (2 digits for RT, 8 for m/z, etc)

Member Data Documentation

◆ unit_

DIM_UNIT unit_

protected

the unit of this dimension

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ValueType

◆ ValueTypes

Constructor & Destructor Documentation

◆ DimBase() [1/2]

◆ DimBase() [2/2]

◆ ~DimBase()

Member Function Documentation

◆ clone()

◆ formattedValue() [1/2]

◆ formattedValue() [2/2]

◆ fromXY() [1/4]

◆ fromXY() [2/4]

◆ fromXY() [3/4]

◆ fromXY() [4/4]

◆ getDimName()

◆ getDimNameShort()

◆ getUnit()

◆ map() [1/15]

◆ map() [2/15]

◆ map() [3/15]

◆ map() [4/15]

◆ map() [5/15]

◆ map() [6/15]

◆ map() [7/15]

◆ map() [8/15]

◆ map() [9/15]

◆ map() [10/15]

◆ map() [11/15]

◆ map() [12/15]

◆ map() [13/15]

◆ map() [14/15]

◆ map() [15/15]

◆ operator=()

◆ operator==()

◆ setRange()

◆ valuePrecision()

Member Data Documentation

◆ unit_