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

Classes
class	cell_type
	Inner class defining what data type the tree stores. More...
struct	treatment

Public Types
using	coord_type = Space
	Geographic coordinate type.
using	time_type = Time
	Time type.
using	tree_type = quetzal::coalescence::container::Tree< cell_type >
	The type used to represent a genealogy.
using	forest_type = quetzal::coalescence::container::Forest< coord_type, tree_type >
	The type used to represent a spatial forest of genealogies.

Public Member Functions
void	ancestral_Wright_Fisher_N (unsigned int value)
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.
std::string	treat (tree_type &tree) const
	Visit the whole tree and builds its Newick formula.

Static Public Member Functions
template<typename F >
static auto	make_forest (std::map< coord_type, unsigned int > const &sample_counts, time_type const &sampling_time, F get_name)
	Make a forest respecting the policy from a geographic sample.
template<typename T , typename F1 , typename F2 >
static auto	make_forest (std::vector< T > sample, time_type const &sampling_time, F1 get_location, F2 get_name)
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.

Member Function Documentation

branch()

template<typename Space , typename Time >

static auto quetzal::coalescence::newick_with_distance_to_parent_and_leaf_name< 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_and_leaf_name< 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_and_leaf_name< 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 >

template<typename F >

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

inlinestatic

Make a forest respecting the policy from a geographic sample.

Template Parameters

F	the type of functor used to get the name of a tip.

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.
get_name	functor fabricating a name for each tip node and according to two parameters: its deme location and the time of sampling. Signature should be equivalent to std::string f(coord_type const& x, time_type t)

Returns

A forest compliant with the policy chosen.

treat()

template<typename Space , typename Time >

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

inline

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