quetzal::format::newick Namespace Reference

Generic components for parsing or generating Newick strings. More...

Namespaces
namespace	extended
	Generic components for parsing or generating extended Newick strings.

Classes
class	Formatter
	Generic algorithm to generate the Newick formula of a tree. More...
class	generator
	Generate the Newick formula from an external (custom) tree class. More...
struct	PAUP
	Allow nested comments. More...
struct	PHYLIP
	Requires that an unrooted tree begin with a trifurcation; it will not "uproot" a rooted tree. More...
struct	remove_comments_of_depth
	Template class. More...
struct	remove_comments_of_depth< 0 >
	Do not remove anything. More...
struct	remove_comments_of_depth< 1 >
	Remove all comments substrings contained between square brackets. More...
struct	remove_comments_of_depth< 2 >
	Remove all comments substrings contained between square brackets of depth 2. More...
struct	single_function_argument
struct	single_function_argument< std::function< Ret(Arg)> >
struct	single_function_argument_impl
struct	TreeAlign
	Set a root node branch length to zero. Remove all nested comments. More...

Concepts
concept	Formattable
	Concept for label name.

Typedefs
template<typename P1 >
using	single_function_argument_t = typename single_function_argument_impl< P1 >::type

Functions
template<class P1 , class P2 , class F1 , class F2 , class Policy = PAUP>
	Formatter (P1 &&, P2 &&, F1 &&, F2 &&) -> Formatter< single_function_argument_t< P1 >, P1, P2, F1, F2, Policy >
template<class P1 , class P2 , class F1 , class F2 , class Policy = PAUP>
auto	make_formatter (P1 &&has_parent, P2 &&has_children, F1 &&label, F2 &&branch_length, Policy policy=Policy())
	to use for template lambda [](const auto& s) {} e.g. make_formatter<Node>`
template<class T , std::predicate< T > P1, std::predicate< T > P2, Formattable< T > F1, Formattable< T > F2, class Policy >
auto	make_formatter (P1 &&has_parent, P2 &&has_children, F1 &&label, F2 &&branch_length, Policy policy=Policy())
	Can still specify type manually if you want, to use for template lambda [](const auto& s) {} e.g. make_formatter<Node>`.
template<typename Flavor >
std::string	generate_from (quetzal::coalescence::k_ary_tree< boost::no_property, boost::no_property > const &graph, typename quetzal::coalescence::k_ary_tree< boost::no_property, boost::no_property >::vertex_descriptor root, Flavor flavor)
template<typename Flavor >
std::string	generate_from (quetzal::coalescence::binary_tree< boost::no_property, boost::no_property > const &graph, typename quetzal::coalescence::binary_tree< boost::no_property, boost::no_property >::vertex_descriptor root, Flavor flavor)
template<class VertexProperty , class EdgeProperty , typename Flavor > requires (!std::is_same_v<VertexProperty, boost::no_property> && !std::is_same_v<VertexProperty, boost::no_property>)
std::string	generate_from (quetzal::coalescence::binary_tree< VertexProperty, EdgeProperty > const &graph, typename quetzal::coalescence::binary_tree< VertexProperty, EdgeProperty >::vertex_descriptor root, Flavor flavor)
template<class VertexProperty , class EdgeProperty , typename Flavor > requires (!std::is_same_v<VertexProperty, boost::no_property> && !std::is_same_v<VertexProperty, boost::no_property>)
std::string	generate_from (const quetzal::coalescence::k_ary_tree< VertexProperty, EdgeProperty > &graph, typename quetzal::coalescence::binary_tree< VertexProperty, EdgeProperty >::vertex_descriptor root, Flavor flavor)
	Generate a Newick string from a k-ary tree with properties.
template<class P1 , class P2 , class F1 , class F2 , class Policy = PAUP>
	generator (P1, P2, F1, F2, Policy pol={}) -> generator< detail::single_function_argument_t< P1 >, P1, P2, F1, F2, Policy >
	User-defined deduction guide where the node/graph type T is deduced from P1.
template<class VertexProperty = quetzal::format::newick::ast::node::vertex_property, class EdgeProperty = quetzal::format::newick::ast::node::edge_property>
std::tuple< quetzal::coalescence::k_ary_tree< VertexProperty, EdgeProperty >, typename quetzal::coalescence::k_ary_tree< VertexProperty, EdgeProperty >::vertex_descriptor >	to_k_ary_tree (quetzal::format::newick::ast::node ast_root)
	Converts a standard Newick AST to a quetzal Tree graph.
template<class VertexProperty = quetzal::format::newick::ast::node::vertex_property, class EdgeProperty = quetzal::format::newick::ast::node::edge_property>
std::tuple< quetzal::coalescence::k_ary_tree< VertexProperty, EdgeProperty >, typename quetzal::coalescence::k_ary_tree< VertexProperty, EdgeProperty >::vertex_descriptor >	to_k_ary_tree (const std::string &newick)
	Converts a standard Newick string to a quetzal Tree graph.

Detailed Description

Generic components for parsing or generating Newick strings.

• 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

generator()

template<class P1 , class P2 , class F1 , class F2 , class Policy = PAUP>

quetzal::format::newick::generator	(	P1	,
		P2	,
		F1	,
		F2	,
		Policy	pol = {}
	)		-> generator< detail::single_function_argument_t< P1 >, P1, P2, F1, F2, Policy >

User-defined deduction guide where the node/graph type T is deduced from P1.

Remarks

Template deduction guides are patterns associated with a template class that tell the compiler how to translate a set of constructor arguments (and their types) into template parameters for the class.