Dimension implementation for retention time values. More...

#include <OpenMS/KERNEL/DimMapper.h>

Inheritance diagram for DimRT:

Collaboration diagram for DimRT:

Public Member Functions
	DimRT ()

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

ValueType	map (const Peak1D &) const override

ValueType	map (const Peak2D &p) const override

ValueType	map (const ChromatogramPeak &p) const override

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

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

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

ValueTypes	map (const MSSpectrum &) const override

ValueTypes	map (const MSChromatogram &chrom) const override

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

ValueType	map (const MobilityPeak1D &) const override

ValueType	map (const MobilityPeak2D &) const override

ValueType	map (const BaseFeature &bf) const override

ValueType	map (const PeptideIdentification &pi) const override

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

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

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

void	fromXY (const ValueType, Peak1D &) const override
	set the RT of a Peak1D (throws) More...

void	fromXY (const ValueType in, ChromatogramPeak &p) const override
	set the RT of a ChromatogramPeak More...

void	fromXY (const ValueType, MobilityPeak1D &) const override
	set the RT of a MobilityPeak1D (throws) More...

void	fromXY (const ValueType, MobilityPeak2D &) const override
	set the RT of a MobilityPeak2D (throws) More...

Public Member Functions inherited from DimBase
	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...

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...

Additional Inherited Members
Public Types inherited from DimBase
using	ValueType = double

using	ValueTypes = std::vector< ValueType >

Protected Attributes inherited from DimBase
DIM_UNIT	unit_
	the unit of this dimension More...

Detailed Description

Dimension implementation for retention time values.

This class implements the DimBase interface for the retention time dimension. It provides methods to access RT values from various data structures and convert between RT values and generic dimension values.

See also: DimBase

Constructor & Destructor Documentation

◆ DimRT()

DimRT ( )

inline

References OpenMS::RT.

Member Function Documentation

◆ clone()

std::unique_ptr<DimBase> clone ( ) const

inlineoverridevirtual

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

Implements DimBase.

◆ fromXY() [1/4]

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

inlineoverridevirtual

set the RT of a ChromatogramPeak

Implements DimBase.

References ChromatogramPeak::setRT().

◆ fromXY() [2/4]

void fromXY	(	const	ValueType,
		MobilityPeak1D &
	)		const

inlineoverridevirtual

set the RT of a MobilityPeak1D (throws)

Implements DimBase.

◆ fromXY() [3/4]

void fromXY	(	const	ValueType,
		MobilityPeak2D &
	)		const

inlineoverridevirtual

set the RT of a MobilityPeak2D (throws)

Implements DimBase.

◆ fromXY() [4/4]

void fromXY	(	const	ValueType,
		Peak1D &
	)		const

inlineoverridevirtual

set the RT of a Peak1D (throws)

Implements DimBase.

◆ map() [1/15]

ValueType map ( const BaseFeature & bf ) const

inlineoverridevirtual

Implements DimBase.

References Peak2D::getRT().

◆ map() [2/15]

ValueType map ( const ChromatogramPeak & p ) const

inlineoverridevirtual

Implements DimBase.

References ChromatogramPeak::getRT().

◆ map() [3/15]

ValueType map ( const MobilityPeak1D & ) const

inlineoverridevirtual

Implements DimBase.

◆ map() [4/15]

ValueType map ( const MobilityPeak2D & ) const

inlineoverridevirtual

Implements DimBase.

◆ map() [5/15]

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

inlineoverridevirtual

obtain value from a certain point in a mobilogram

Implements DimBase.

References Mobilogram::getRT().

◆ map() [6/15]

ValueTypes map ( const MSChromatogram & chrom ) const

inlineoverridevirtual

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

Exceptions

Exception::InvalidRange if elements do not support the dimension

Implements DimBase.

◆ map() [7/15]

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

inlineoverridevirtual

obtain value from a certain point in a chromatogram

Implements DimBase.

◆ map() [8/15]

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

inlineoverridevirtual

Implements DimBase.

References AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::getRT().

◆ map() [9/15]

ValueTypes map ( const MSSpectrum & spec ) const

inlineoverridevirtual

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

Exceptions

Exception::InvalidRange if elements do not support the dimension

Implements DimBase.

◆ map() [10/15]

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

inlineoverridevirtual

obtain value from a certain point in a spectrum

Implements DimBase.

References MSSpectrum::getRT().

◆ map() [11/15]

ValueType map ( const Peak1D & ) const

inlineoverridevirtual

Implements DimBase.

◆ map() [12/15]

ValueType map ( const Peak2D & p ) const

inlineoverridevirtual

Implements DimBase.

References Peak2D::getRT().

◆ map() [13/15]

ValueType map ( const PeptideIdentification & pi ) const

inlineoverridevirtual

Implements DimBase.

References PeptideIdentification::getRT().

◆ map() [14/15]

RangeBase map ( const RangeAllType & rm ) const

inlineoverridevirtual

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

Implements DimBase.

References RangeManager< RangeBases >::getRangeForDim(), and OpenMS::RT.

◆ map() [15/15]

RangeBase& map ( RangeAllType & rm ) const

inlineoverridevirtual

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

Implements DimBase.

References RangeManager< RangeBases >::getRangeForDim(), and OpenMS::RT.

◆ setRange()

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

inlineoverridevirtual

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

Implements DimBase.

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DimRT()

Member Function Documentation

◆ clone()

◆ fromXY() [1/4]

◆ fromXY() [2/4]

◆ fromXY() [3/4]

◆ fromXY() [4/4]

◆ 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]

◆ setRange()