quetzal::coalescence::occupancy_spectrum::OccupancySpectrum Class Reference

#include <quetzal/coalescence/occupancy_spectrum/OccupancySpectrum.hpp>

Detailed Description

An occupancy spectrum as defined in Becheler & Knowles, 2020.

To understand the implementation of occupancy spectrum concept as applied to the coalescent, it is useful to consider the coalescence process as an urn and balls experiment where \(n\) balls (lineages) are randomly assigned to \(m\) urns (parents), each urn having an assignment probability of \(m−1\)⁠. If an urn contains \(r\) balls at the end of a random experiment, \(r\) is said to be the occupancy number of the urn (see Johnson and Kotz, 1977).

The number of urns having the same occupancy number \(r\) is denoted \(M_r\) and the term occupancy spectrum refers to the vector \(M_0, M_1,\dots , M_n\)⁠.

This is an useful abstraction to separate modules that are responsible for randomely producing spectrums (coalescence::occupancy_spectrum::generation_policy) from modules that consume them (coalescence::algorithm::simultaneous_multiple_merge).

Public Types
using	value_type = typename occupancy_spectrum_type::value_type
using	iterator = typename occupancy_spectrum_type::iterator
using	const_iterator = typename occupancy_spectrum_type::const_iterator

Public Member Functions
	OccupancySpectrum (std::vector< int > const &v, int k, int N)
	Constructor by copy.
	OccupancySpectrum (std::vector< int > &&v, int k, int N)
	Move constructor.
	OccupancySpectrum ()=delete
	Deleted default constructor.
	OccupancySpectrum (const OccupancySpectrum &other)=default
	Default copy constructor.
	OccupancySpectrum (OccupancySpectrum &&other) noexcept
	Move constructor.
OccupancySpectrum &	operator= (const OccupancySpectrum &other)
	Copy assignment operator.
OccupancySpectrum &	operator= (OccupancySpectrum &&other)
	Move assignment operator.
iterator	begin ()
	returns iterator to the beginning of the spectrum
iterator	end ()
	returns iterator to the end of the spectrum
const_iterator	begin () const
	returns iterator to the beginning of the spectrum
const_iterator	end () const
	returns iterator to the end of the spectrum
const_iterator	cbegin () const
	returns iterator to the beginning of the spectrum
const_iterator	cend () const
	returns iterator to the end of the spectrum
void	erase (iterator first, iterator last)
	erase a range of elements of the spectrum.
bool	empty () const
	Returns whether the spectrum is empty (i.e. whether its size is 0).

Constructor & Destructor Documentation

OccupancySpectrum() [1/5]

quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::OccupancySpectrum ( std::vector< int > const &  v, int  k, int  N  )

inline

Constructor by copy.

Parameters

v	A vector of occupancy numbers
N	the number of urns (parents) of the random experience
k	the number of balls (coalescing lineages) of the random experience

OccupancySpectrum() [2/5]

quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::OccupancySpectrum ( std::vector< int > &&  v, int  k, int  N  )

inline

Move constructor.

Parameters

v	A vector of occupancy numbers
N	the number of urns (parents) of the random experience
k	the number of balls (coalescing lineages) of the random experience

OccupancySpectrum() [3/5]

quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::OccupancySpectrum ( )

delete

Deleted default constructor.

Remarks

this would break class invariants as there is no good way to initialize by default

OccupancySpectrum() [4/5]

quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::OccupancySpectrum ( const OccupancySpectrum &  other )

default

Default copy constructor.

Parameters

other

An occupancy spectrum to copy content from

OccupancySpectrum() [5/5]

quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::OccupancySpectrum ( OccupancySpectrum &&  other )

inlinenoexcept

Move constructor.

Parameters

other

An occupancy spectrum to move content from

Member Function Documentation

operator=()

OccupancySpectrum & quetzal::coalescence::occupancy_spectrum::OccupancySpectrum::operator= ( OccupancySpectrum &&  other )

inline

Move assignment operator.

Parameters

other

the spectrum to move data from

Remarks

other will be emptied and can not be reused.

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The documentation for this class was generated from the following file:

• /home/runner/work/quetzal-CoaTL/quetzal-CoaTL/src/include/quetzal/coalescence/occupancy_spectrum/OccupancySpectrum.hpp