A template for a class that maintains a list of paths from all leaf nodes to the rerooted node with the name "0". More...

#include <jade.rerooted_tree.hpp>

Inheritance diagram for jade::basic_rerooted_tree< TValue >:

Collaboration diagram for jade::basic_rerooted_tree< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...

typedef basic_tree_path< value_type >	path_type
	The tree path type. More...

typedef basic_newick_node< value_type >	node_type
	The Newick node type. More...

typedef std::unique_ptr< node_type >	node_ptr_type
	The Newick node pointer type. More...

typedef std::vector< path_type >	vector_type
	The tree path vector type. More...

Public Member Functions
	basic_rerooted_tree ()
	Initialize a new instance of the class. More...

	basic_rerooted_tree (const node_type &node)
	Initialize a new instance of the class. More...

size_t	get_rk () const

path_type	get_overlap (const size_t node1, const size_t node2) const

const path_type &	get_path (const size_t index) const

node_type &	get_tree ()

const node_type &	get_tree () const

void	reset (const node_type &node)
	Resets the tree maintained by this instance. More...

Detailed Description

template<typename TValue>
class jade::basic_rerooted_tree< TValue >

A template for a class that maintains a list of paths from all leaf nodes to the rerooted node with the name "0".

Definition at line 19 of file jade.rerooted_tree.hpp.

Member Typedef Documentation

◆ node_ptr_type

template<typename TValue >

typedef std::unique_ptr<node_type> jade::basic_rerooted_tree< TValue >::node_ptr_type

The Newick node pointer type.

Definition at line 32 of file jade.rerooted_tree.hpp.

◆ node_type

template<typename TValue >

typedef basic_newick_node<value_type> jade::basic_rerooted_tree< TValue >::node_type

The Newick node type.

Definition at line 29 of file jade.rerooted_tree.hpp.

◆ path_type

template<typename TValue >

typedef basic_tree_path<value_type> jade::basic_rerooted_tree< TValue >::path_type

The tree path type.

Definition at line 26 of file jade.rerooted_tree.hpp.

◆ value_type

template<typename TValue >

typedef TValue jade::basic_rerooted_tree< TValue >::value_type

The value type.

Definition at line 23 of file jade.rerooted_tree.hpp.

◆ vector_type

template<typename TValue >

typedef std::vector<path_type> jade::basic_rerooted_tree< TValue >::vector_type

The tree path vector type.

Definition at line 35 of file jade.rerooted_tree.hpp.

Constructor & Destructor Documentation

◆ basic_rerooted_tree() [1/2]

template<typename TValue >

jade::basic_rerooted_tree< TValue >::basic_rerooted_tree ( )

inline

Initialize a new instance of the class.

Definition at line 40 of file jade.rerooted_tree.hpp.

             : _rk       (0)
             , _node_ptr ()
             , _vector   ()
         {
         }

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◆ basic_rerooted_tree() [2/2]

template<typename TValue >

jade::basic_rerooted_tree< TValue >::basic_rerooted_tree ( const node_type & node )

inlineexplicit

Initialize a new instance of the class.

Parameters

node	The node to validate and reroot.

Definition at line 50 of file jade.rerooted_tree.hpp.

             : _rk       (_validate_tree(node))
             , _node_ptr (node.find_name("0")->reroot())
             , _vector   ()
         {
             const auto & tree = *_node_ptr;
  
             //
             // Create a list of tree paths, one for each leaf node.
             //
             _vector.reserve(_rk);
             for (size_t i = 1; i <= _rk; i++)
             {
                 std::ostringstream name_stream;
                 name_stream << i;
  
                 const auto name     = name_stream.str();
                 const auto node_ptr = tree.find_name(name.c_str());
                 _vector.emplace_back(*node_ptr);
             }
         }

Member Function Documentation

◆ get_overlap()

template<typename TValue >

path_type jade::basic_rerooted_tree< TValue >::get_overlap	(	const size_t	node1,
		const size_t	node2
	)		const

inline

Returns: The overlapping path between two nodes and the root node.

Parameters

node1	The first node.
node2	The second node.

Definition at line 84 of file jade.rerooted_tree.hpp.

         {
             return _vector[node1] & _vector[node2];
         }

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◆ get_path()

template<typename TValue >

const path_type& jade::basic_rerooted_tree< TValue >::get_path ( const size_t index ) const

inline

Returns: The tree path for the node with the name that corresponds to the specified index.

Parameters

index The index of the node.

Definition at line 96 of file jade.rerooted_tree.hpp.

         {
             assert(index < _vector.size());
             return _vector[index];
         }

◆ get_rk()

template<typename TValue >

size_t jade::basic_rerooted_tree< TValue >::get_rk ( ) const

inline

Returns: The rooted K value.

Definition at line 76 of file jade.rerooted_tree.hpp.

         {
             return _rk;
         }

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◆ get_tree() [1/2]

template<typename TValue >

node_type& jade::basic_rerooted_tree< TValue >::get_tree ( )

inline

Returns: A reference to the rerooted tree.

Definition at line 107 of file jade.rerooted_tree.hpp.

         {
             return *_node_ptr;
         }

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◆ get_tree() [2/2]

template<typename TValue >

const node_type& jade::basic_rerooted_tree< TValue >::get_tree ( ) const

inline

Returns: A reference to the rerooted tree.

Definition at line 115 of file jade.rerooted_tree.hpp.

         {
             return *_node_ptr;
         }

◆ reset()

template<typename TValue >

void jade::basic_rerooted_tree< TValue >::reset ( const node_type & node )

inline

Resets the tree maintained by this instance.

Parameters

node	The node to validate and reroot.

Definition at line 123 of file jade.rerooted_tree.hpp.

         {
             *this = basic_rerooted_tree(node);
         }

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

jade.rerooted_tree.hpp

Public Types

Public Member Functions

Detailed Description

template<typename TValue> class jade::basic_rerooted_tree< TValue >

Member Typedef Documentation

◆ node_ptr_type

◆ node_type

◆ path_type

◆ value_type

◆ vector_type

Constructor & Destructor Documentation

◆ basic_rerooted_tree() [1/2]

◆ basic_rerooted_tree() [2/2]

Member Function Documentation

◆ get_overlap()

◆ get_path()

◆ get_rk()

◆ get_tree() [1/2]

◆ get_tree() [2/2]

◆ reset()

template<typename TValue>
class jade::basic_rerooted_tree< TValue >