quetzal::coalescence Namespace Reference

Simulation of coalescent trees. More...

Namespaces
namespace	algorithm
	Generic algorithms for manipulating abstract coalescent trees.
namespace	container
	Generic data structures for manipulating abstract coalescent trees.
namespace	detail
namespace	occupancy_spectrum
	How to simulate occupancy spectrums (coalescence merging configurations) when required by coalescence::algorithm::simultaneous_multiple_merge.

Classes
class	binary_tree
class	binary_tree< no_property, EdgeProperty >
	A binary tree class with information attached to vertices. More...
class	binary_tree< no_property, no_property >
	A binary tree class with no information attached to either vertices nor edges. More...
class	binary_tree< VertexProperty, EdgeProperty >
	A binary tree class with information attached to vertices. More...
class	binary_tree< VertexProperty, no_property >
	A binary tree class with information attached to vertices. More...
class	k_ary_tree
class	k_ary_tree< no_property, EdgeProperty >
	A k-ary tree class with information attached to edges. More...
class	k_ary_tree< no_property, no_property >
	A k-ary tree class with no information attached to either vertices nor edges. More...
class	k_ary_tree< VertexProperty, EdgeProperty >
	A k-ary tree class with information attached to vertices. More...
class	k_ary_tree< VertexProperty, no_property >
	A k-ary tree class with information attached to vertices. More...
class	network
class	network< no_property, EdgeProperty >
	A network class with information attached to edges. More...
class	network< no_property, no_property >
	A network class with no information attached to either vertices nor edges. More...
class	network< VertexProperty, EdgeProperty >
	A network class with information attached to vertices. More...
class	network< VertexProperty, no_property >
	A network class with information attached to vertices. More...
class	newick_with_distance_to_parent
	Policy class for coalescing gene copies into a Newick formula. More...
class	newick_with_distance_to_parent_and_leaf_name

Typedefs
using	no_property = boost::no_property

Functions
template<typename Vertex = boost::no_property, typename Edge = boost::no_property, typename Generator >
std::pair< quetzal::coalescence::binary_tree< Vertex, Edge >, typename quetzal::coalescence::binary_tree< Vertex, Edge >::vertex_descriptor >	get_random_binary_tree (int n_leaves, Generator &rng)
	Generate a random binary tree.
template<typename Vertex = boost::no_property, typename Edge = boost::no_property, typename Generator >
std::pair< quetzal::coalescence::k_ary_tree< Vertex, Edge >, typename quetzal::coalescence::k_ary_tree< Vertex, Edge >::vertex_descriptor >	get_random_k_ary_tree (int n_leaves, Generator &rng)
	Generate a random k-ary tree.

Detailed Description

Simulation of coalescent trees.

• This program is free software; you can redistribute it and/or modify /// it under the terms of the GNU General Public License as published by /// the Free Software Foundation; either version 2 of the License, or /// (at your option) any later version. /// ///

Function Documentation

get_random_binary_tree()

template<typename Vertex = boost::no_property, typename Edge = boost::no_property, typename Generator >

std::pair< quetzal::coalescence::binary_tree< Vertex, Edge >, typename quetzal::coalescence::binary_tree< Vertex, Edge >::vertex_descriptor > quetzal::coalescence::get_random_binary_tree	(	int	n_leaves,
		Generator &	rng
	)

Generate a random binary tree.

Template Parameters

Generator

Random Number Generator

Parameters

n_leaves	Number of leaves in the binary tree
rng	The random number generator

Returns

A binary tree with its root vertex descriptor

get_random_k_ary_tree()

template<typename Vertex = boost::no_property, typename Edge = boost::no_property, typename Generator >

std::pair< quetzal::coalescence::k_ary_tree< Vertex, Edge >, typename quetzal::coalescence::k_ary_tree< Vertex, Edge >::vertex_descriptor > quetzal::coalescence::get_random_k_ary_tree	(	int	n_leaves,
		Generator &	rng
	)

Generate a random k-ary tree.

Template Parameters

Generator

Random Number Generator

Parameters

n_leaves	Number of leaves in the k-ary tree
rng	The random number generator

Returns

A k-ary tree with its root vertex descriptor