Represents a distribution of isotopes restricted to the first K elements. More...

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSIsotopeDistribution.h>

Classes
struct	Peak
	Structure that represents an isotope peak - pair of mass and abundance. More...

Public Types
typedef double	mass_type
	Type of isotope mass. More...

typedef double	abundance_type
	Type of isotope abundance. More...

typedef unsigned int	nominal_mass_type
	Type of isotope nominal mass. More...

typedef Peak	peak_type
	Type of isotope peak. More...

typedef std::vector< peak_type >	peaks_container
	Type of container to store peaks. More...

typedef peaks_container::iterator	peaks_iterator
	Type of iterator over container with peaks. More...

typedef peaks_container::const_iterator	const_peaks_iterator
	Type of const iterator over container with peaks. More...

typedef peaks_container::size_type	size_type
	Type of peaks container's size. More...

typedef std::vector< mass_type >	masses_container
	Type of container with isotope masses. More...

typedef masses_container::iterator	masses_iterator
	Type of iterator over container with isotope masses. More...

typedef masses_container::const_iterator	const_masses_iterator
	Type of const iterator over container with isotope masses. More...

typedef std::vector< abundance_type >	abundances_container
	Type of container with isotope abundances. More...

typedef abundances_container::iterator	abundances_iterator
	Type of iterator over container with isotope abundances. More...

typedef abundances_container::const_iterator	const_abundances_iterator
	Type of const iterator over container with isotope abundances. More...

Public Member Functions
	IMSIsotopeDistribution (nominal_mass_type nominalMass=0)
	Constructor with nominal mass. More...

	IMSIsotopeDistribution (mass_type mass)
	Constructor with single isotope. More...

	IMSIsotopeDistribution (const peaks_container &peaks, nominal_mass_type nominalMass=0)
	Constructor with isotopes and nominal mass. More...

	IMSIsotopeDistribution (const IMSIsotopeDistribution &distribution)
	Copy constructor. More...

	~IMSIsotopeDistribution ()
	Destructor. More...

size_type	size () const

IMSIsotopeDistribution &	operator= (const IMSIsotopeDistribution &distribution)

bool	operator== (const IMSIsotopeDistribution &distribution) const

bool	operator!= (const IMSIsotopeDistribution &distribution) const

IMSIsotopeDistribution &	operator*= (const IMSIsotopeDistribution &distribution)

IMSIsotopeDistribution &	operator*= (unsigned int pow)

mass_type	getMass (size_type i) const

abundance_type	getAbundance (size_type i) const

mass_type	getAverageMass () const

nominal_mass_type	getNominalMass () const

void	setNominalMass (nominal_mass_type nominalMass)

masses_container	getMasses () const

abundances_container	getAbundances () const

void	normalize ()

bool	empty () const

Static Public Attributes
static abundance_type	ABUNDANCES_SUM_ERROR
	Error to be allowed for isotope distribution. More...

static size_type	SIZE
	Length of isotope distribution. More...

Private Member Functions
void	setMinimumSize_ ()
	Sets peaks/isotopes container minimum size. More...

Private Attributes
peaks_container	peaks_
	Container for isotopes. More...

nominal_mass_type	nominal_mass_
	Nominal mass of distribution. More...

Detailed Description

Represents a distribution of isotopes restricted to the first K elements.

Represents a distribution of isotopes of chemical elements as a list of peaks each as a pair of mass and abundance. IsotopeDistribution unlike IsotopeSpecies has one abundance per a nominal mass. Here is an example in the format (mass; abundance %) for molecule H2O (values are taken randomly):

IsotopeDistribution (18.00221; 99.03 %) (19.00334; 0.8 %) (20.00476; 0.17 %)
IsotopeSpecies (18.00197; 98.012 %) (18.00989; 1.018 %) (19.00312; 0.683 %) (19.00531; 0.117 %) (20.00413; 0.134 %) (20.00831; 0.036 %)

To the sake of faster computations distribution is restricted to the first K elements, where K can be set by adjusting size SIZE of distribution.

Note: For the elements most abundant in living beings (CHNOPS) this restriction is negligible, since abundances decrease dramatically in isotopes order and are usually of no interest starting from +10 isotope.

IsotopeDistribution implements folding with other distribution using an algorithm described in details in paper: Boecker et al. "Decomposing metabolic isotope patterns" WABI 2006. doi: 10.1007/11851561_2

Folding with itself is done using Russian Multiplication Scheme.

Author: Anton Pervukhin Anton.nosp@m..Per.nosp@m.vukhi.nosp@m.n@Ce.nosp@m.BiTec.nosp@m..Uni.nosp@m.-Biel.nosp@m.efel.nosp@m.d.DE

Member Typedef Documentation

◆ abundance_type

typedef double abundance_type

Type of isotope abundance.

◆ abundances_container

typedef std::vector<abundance_type> abundances_container

Type of container with isotope abundances.

◆ abundances_iterator

typedef abundances_container::iterator abundances_iterator

Type of iterator over container with isotope abundances.

◆ const_abundances_iterator

typedef abundances_container::const_iterator const_abundances_iterator

Type of const iterator over container with isotope abundances.

◆ const_masses_iterator

typedef masses_container::const_iterator const_masses_iterator

Type of const iterator over container with isotope masses.

◆ const_peaks_iterator

typedef peaks_container::const_iterator const_peaks_iterator

Type of const iterator over container with peaks.

◆ mass_type

typedef double mass_type

Type of isotope mass.

◆ masses_container

typedef std::vector<mass_type> masses_container

Type of container with isotope masses.

◆ masses_iterator

typedef masses_container::iterator masses_iterator

Type of iterator over container with isotope masses.

◆ nominal_mass_type

typedef unsigned int nominal_mass_type

Type of isotope nominal mass.

◆ peak_type

typedef Peak peak_type

Type of isotope peak.

◆ peaks_container

typedef std::vector<peak_type> peaks_container

Type of container to store peaks.

◆ peaks_iterator

typedef peaks_container::iterator peaks_iterator

Type of iterator over container with peaks.

◆ size_type

typedef peaks_container::size_type size_type

Type of peaks container's size.

Constructor & Destructor Documentation

◆ IMSIsotopeDistribution() [1/4]

IMSIsotopeDistribution ( nominal_mass_type nominalMass = 0 )

inlineexplicit

Constructor with nominal mass.

◆ IMSIsotopeDistribution() [2/4]

IMSIsotopeDistribution ( mass_type mass )

inlineexplicit

Constructor with single isotope.

◆ IMSIsotopeDistribution() [3/4]

IMSIsotopeDistribution	(	const peaks_container &	peaks,
		nominal_mass_type	nominalMass = `0`
	)

inline

Constructor with isotopes and nominal mass.

◆ IMSIsotopeDistribution() [4/4]

IMSIsotopeDistribution ( const IMSIsotopeDistribution & distribution )

inline

Copy constructor.

◆ ~IMSIsotopeDistribution()

~IMSIsotopeDistribution ( )

inline

Destructor.

Member Function Documentation

◆ empty()

bool empty ( ) const

inline

Returns true if the distribution has no peaks, false - otherwise.

Returns: True if the distribution has no peaks, false - otherwise.

◆ getAbundance()

abundance_type getAbundance ( size_type i ) const

inline

Gets an abundance of isotope i.

Parameters

i	An index of isotope.

Returns: An abundance of isotope i.

◆ getAbundances()

abundances_container getAbundances ( ) const

Gets abundances of isotopes.

Returns: Abundances of isotopes.

◆ getAverageMass()

mass_type getAverageMass ( ) const

Gets an average mass of all isotopes.

Returns: An average mass of all isotopes.

◆ getMass()

mass_type getMass ( size_type i ) const

inline

Gets a mass of isotope i.

Parameters

i	An index of isotope.

Returns: Mass of isotope i.

◆ getMasses()

masses_container getMasses ( ) const

Gets masses of isotopes.

Returns: Masses of isotopes.

◆ getNominalMass()

nominal_mass_type getNominalMass ( ) const

inline

Gets a nominal mass of distribution.

Returns: The nominal mass of the distribution.

◆ normalize()

void normalize ( )

Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error ABUNDANCES_SUM_ERROR allowed.

◆ operator!=()

bool operator!= ( const IMSIsotopeDistribution & distribution ) const

Inequality operator. Returns true, if a given distribution is unequal to this one, false - otherwise.

Returns: true, if a given distribution is unequal to this distribution, false - otherwise

◆ operator*=() [1/2]

IMSIsotopeDistribution& operator*= ( const IMSIsotopeDistribution & distribution )

Operator for folding this distribution with a given distribution.

Note: Operator is unary, so result is stored in this object itself.

Parameters

distribution Distribution to be folded with this one.

Returns: Reference to this object.

See also: IsotopeDistribution& operator *=(unsigned int)

◆ operator*=() [2/2]

IMSIsotopeDistribution& operator*= ( unsigned int pow )

Operator for folding this distribution with itself pow times.

Note: Operator is unary, so result is stored in this object itself.

Parameters

pow	Number of times this distribution is to be folded with itself.

Returns: Reference to this object.

See also: IsotopeDistribution& operator *=(const IsotopeDistribution&)

◆ operator=()

IMSIsotopeDistribution& operator= ( const IMSIsotopeDistribution & distribution )

Assignment operator.

Parameters

distribution Isotope distribution to be assigned to this one.

Returns: Reference to this object.

◆ operator==()

bool operator== ( const IMSIsotopeDistribution & distribution ) const

Equality operator. Returns true, if a given distribution is equal to this one, false - otherwise.

Returns: true, if a given distribution is equal to this distribution, false - otherwise

◆ setMinimumSize_()

void setMinimumSize_ ( )

private

Sets peaks/isotopes container minimum size.

◆ setNominalMass()

void setNominalMass ( nominal_mass_type nominalMass )

inline

Sets a nominal mass for distribution.

Parameters

nominalMass The new nominal mass for the distribution.

References OpenSwath::normalize().

◆ size()

size_type size ( ) const

inline

Gets size of isotope distribution.

Note: Size is not smaller than predefined SIZE.

Returns: Size of isotope distribution.

References KDTree::operator!=(), and KDTree::operator==().

Member Data Documentation

◆ ABUNDANCES_SUM_ERROR

abundance_type ABUNDANCES_SUM_ERROR

static

Error to be allowed for isotope distribution.

◆ nominal_mass_

nominal_mass_type nominal_mass_

private

Nominal mass of distribution.

◆ peaks_

peaks_container peaks_

private

Container for isotopes.

◆ SIZE

size_type SIZE

static

Length of isotope distribution.

Classes

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ abundance_type

◆ abundances_container

◆ abundances_iterator

◆ const_abundances_iterator

◆ const_masses_iterator

◆ const_peaks_iterator

◆ mass_type

◆ masses_container

◆ masses_iterator

◆ nominal_mass_type

◆ peak_type

◆ peaks_container

◆ peaks_iterator

◆ size_type

Constructor & Destructor Documentation

◆ IMSIsotopeDistribution() [1/4]

◆ IMSIsotopeDistribution() [2/4]

◆ IMSIsotopeDistribution() [3/4]

◆ IMSIsotopeDistribution() [4/4]

◆ ~IMSIsotopeDistribution()

Member Function Documentation

◆ empty()

◆ getAbundance()

◆ getAbundances()

◆ getAverageMass()

◆ getMass()

◆ getMasses()

◆ getNominalMass()

◆ normalize()

◆ operator!=()

◆ operator*=() [1/2]

◆ operator*=() [2/2]

◆ operator=()

◆ operator==()

◆ setMinimumSize_()

◆ setNominalMass()

◆ size()

Member Data Documentation

◆ ABUNDANCES_SUM_ERROR

◆ nominal_mass_

◆ peaks_

◆ SIZE