quetzal::coalescence::newick_with_distance_to_parent< Space, Time > Class Template Reference

#include <quetzal/coalescence/policies/distance_to_parent.hpp>

Detailed Description

template<typename Space, typename Time>
class quetzal::coalescence::newick_with_distance_to_parent< Space, Time >

Policy class for coalescing gene copies into a Newick formula.

Policy class for coalescing gene copies into a Newick formula, computing distances (in generations) to parent nodes.

Template Parameters

Space	coordinate type
Time	time type

Classes
class	cell_type
struct	treatment
	Treatment to operate on a DFS on the tree to compute branches length. More...

Public Types
using	coord_type = Space
using	time_type = Time
using	tree_type = quetzal::coalescence::container::Tree< cell_type >
using	forest_type = quetzal::coalescence::container::Forest< coord_type, tree_type >

Public Member Functions
void	ancestral_Wright_Fisher_N (unsigned int value)
	Set the size of the putative ancestral Wright-Fisher population preceding the spatial history.
unsigned int	ancestral_Wright_Fisher_N () const
	Get the size of the putative ancestral Wright-Fisher population preceding the spatial history.
template<typename Generator >
tree_type	find_mrca (forest_type const &forest, time_type const &first_time, Generator &gen) const
	Coalesce the given forest into a discrete time Wright-Fisher model.

Static Public Member Functions
static auto	make_forest (std::map< coord_type, unsigned int > const &sample_counts, time_type const &sampling_time)
	Make a forest respecting the policy from a geographic sample.
static auto	branch ()
	Get the functor interface required to branch a parent node to a child node.
static auto	init ()
	Get the functor interface required to initialize a node.
static std::string	treat (tree_type &tree)
	Visit the whole tree and builds its Newick formula.

Member Typedef Documentation

coord_type

template<typename Space , typename Time >

using quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::coord_type = Space

Geographic coordinate type

forest_type

template<typename Space , typename Time >

using quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::forest_type = quetzal::coalescence::container::Forest<coord_type, tree_type>

The type used to represent a spatial forest of genealogies

time_type

template<typename Space , typename Time >

using quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::time_type = Time

Time type

tree_type

template<typename Space , typename Time >

using quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::tree_type = quetzal::coalescence::container::Tree<cell_type>

The type used to represent a genealogy

Member Function Documentation

ancestral_Wright_Fisher_N() [1/2]

template<typename Space , typename Time >

unsigned int quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::ancestral_Wright_Fisher_N ( ) const

inline

Get the size of the putative ancestral Wright-Fisher population preceding the spatial history.

Returns

The Wright-Fisher population size

ancestral_Wright_Fisher_N() [2/2]

template<typename Space , typename Time >

void quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::ancestral_Wright_Fisher_N ( unsigned int  value )

inline

Set the size of the putative ancestral Wright-Fisher population preceding the spatial history.

Parameters

value

The Wright-Fisher population size

branch()

template<typename Space , typename Time >

static auto quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::branch ( )

inlinestatic

Get the functor interface required to branch a parent node to a child node.

Returns

A functor to forward to quetzal coalescence algorithms.

find_mrca()

template<typename Space , typename Time >

template<typename Generator >

tree_type quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::find_mrca ( forest_type const &  forest, time_type const &  first_time, Generator &  gen  ) const

inline

Coalesce the given forest into a discrete time Wright-Fisher model.

Template Parameters

Generator

The type of random generator.

Parameters

forest	The forest to coalesce.
first_time	The time at which coalescence begins
gen	The random generator

Returns

A single tree with root being the MRCA.

init()

template<typename Space , typename Time >

static auto quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::init ( )

inlinestatic

Get the functor interface required to initialize a node.

Returns

A functor to forward to quetzal coalescence algorithms.

make_forest()

template<typename Space , typename Time >

static auto quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::make_forest ( std::map< coord_type, unsigned int > const &  sample_counts, time_type const &  sampling_time  )

inlinestatic

Make a forest respecting the policy from a geographic sample.

Parameters

sample_counts	A map giving for each deme the number of sampled gene copies
sampling_time	At what time the gene copies are sampled.

Returns

A forest compliant with the policy chosen.

treat()

template<typename Space , typename Time >

static std::string quetzal::coalescence::newick_with_distance_to_parent< Space, Time >::treat ( tree_type &  tree )

inlinestatic

Visit the whole tree and builds its Newick formula.

Parameters

tree	The tree to visit.

Returns

The newick formula of the tree.

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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/policies/distance_to_parent.hpp