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.
typedef double	abundance_type
	Type of isotope abundance.
typedef unsigned int	nominal_mass_type
	Type of isotope nominal mass.
typedef Peak	peak_type
	Type of isotope peak.
typedef std::vector< peak_type >	peaks_container
	Type of container to store peaks.
typedef peaks_container::iterator	peaks_iterator
	Type of iterator over container with peaks.
typedef peaks_container::const_iterator	const_peaks_iterator
	Type of const iterator over container with peaks.
typedef peaks_container::size_type	size_type
	Type of peaks container's size.
typedef std::vector< mass_type >	masses_container
	Type of container with isotope masses.
typedef masses_container::iterator	masses_iterator
	Type of iterator over container with isotope masses.
typedef masses_container::const_iterator	const_masses_iterator
	Type of const iterator over container with isotope masses.
typedef std::vector < abundance_type >	abundances_container
	Type of container with isotope abundances.
typedef abundances_container::iterator	abundances_iterator
	Type of iterator over container with isotope abundances.
typedef abundances_container::const_iterator	const_abundances_iterator
	Type of const iterator over container with isotope abundances.
Public Member Functions
	IMSIsotopeDistribution (nominal_mass_type nominalMass=0)
	Constructor with nominal mass.
	IMSIsotopeDistribution (mass_type mass)
	Constructor with single isotope.
	IMSIsotopeDistribution (const peaks_container &peaks, nominal_mass_type nominalMass=0)
	Constructor with isotopes and nominal mass.
	IMSIsotopeDistribution (const IMSIsotopeDistribution &distribution)
	Copy constructor.
	~IMSIsotopeDistribution ()
	Destructor.
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.
static size_type	SIZE
	Length of isotope distribution.
Private Member Functions
void	setMinimumSize_ ()
	Sets peaks/isotopes container minimum size.
Private Attributes
peaks_container	peaks_
	Container for isotopes.
nominal_mass_type	nominal_mass_
	Nominal mass of distribution.

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.

Folding with itself is done using Russian Multiplication Scheme.

Author:: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE>

Member Typedef Documentation

typedef double abundance_type

Type of isotope abundance.

typedef std::vector<abundance_type> abundances_container

Type of container with isotope abundances.

typedef abundances_container::iterator abundances_iterator

Type of iterator over container with isotope abundances.

typedef abundances_container::const_iterator const_abundances_iterator

Type of const iterator over container with isotope abundances.

typedef masses_container::const_iterator const_masses_iterator

Type of const iterator over container with isotope masses.

typedef peaks_container::const_iterator const_peaks_iterator

Type of const iterator over container with peaks.

typedef double mass_type

Type of isotope mass.

typedef std::vector<mass_type> masses_container

Type of container with isotope masses.

typedef masses_container::iterator masses_iterator

Type of iterator over container with isotope masses.

typedef unsigned int nominal_mass_type

Type of isotope nominal mass.

typedef Peak peak_type

Type of isotope peak.

typedef std::vector<peak_type> peaks_container

Type of container to store peaks.

typedef peaks_container::iterator peaks_iterator

Type of iterator over container with peaks.

typedef peaks_container::size_type size_type

Type of peaks container's size.

Constructor & Destructor Documentation

IMSIsotopeDistribution ( nominal_mass_type nominalMass = 0 ) [inline, explicit]

Constructor with nominal mass.

IMSIsotopeDistribution ( mass_type mass ) [inline, explicit]

Constructor with single isotope.

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

Constructor with isotopes and nominal mass.

IMSIsotopeDistribution ( const IMSIsotopeDistribution & distribution ) [inline]

Copy constructor.

~IMSIsotopeDistribution ( ) [inline]

Destructor.

Member Function Documentation

bool empty ( ) const [inline]

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

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

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.

abundances_container getAbundances ( ) const

Gets abundances of isotopes.

Returns:: Abundances of isotopes.

mass_type getAverageMass ( ) const

Gets an average mass of all isotopes.

Returns:: An average mass of all isotopes.

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.

masses_container getMasses ( ) const

Gets masses of isotopes.

Returns:: Masses of isotopes.

nominal_mass_type getNominalMass ( ) const [inline]

Gets a nominal mass of distribution.

Returns:: The nominal mass of the distribution.

void normalize ( )

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

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

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&)

IMSIsotopeDistribution& operator*= ( const IMSIsotopeDistribution & distribution )

Operator for folding this distributoin 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)

IMSIsotopeDistribution& operator= ( const IMSIsotopeDistribution & distribution )

Assignment operator.

Parameters:

distribution

Isotope distribution to be assigned to this one.

Returns:: Reference to this object.

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

void setMinimumSize_ ( ) [private]

Sets peaks/isotopes container minimum size.

void setNominalMass ( nominal_mass_type nominalMass ) [inline]

Sets a nominal mass for distribution.

Parameters:

nominalMass

The new nominal mass for the distributoin.

size_type size ( ) const [inline]

Gets size of isotope distribution.

Note:: Size is not smaller than predefined SIZE.

Returns:: Size of isotope distribution.

Member Data Documentation

abundance_type ABUNDANCES_SUM_ERROR [static]

Error to be allowed for isotope distribution.

nominal_mass_type nominal_mass_ [private]

Nominal mass of distribution.

peaks_container peaks_ [private]

Container for isotopes.

size_type SIZE [static]

Length of isotope distribution.

IMSIsotopeDistribution Class Reference

Classes

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation