Classes
class	children_iterator

class	leaves_iterator

class	levelorder_iterator

class	postorder_iterator

class	preorder_iterator

Public Member Functions
	compact_tree (const char *const input, bool is_fn=true, bool store_labels=true, bool store_lengths=true, size_t reserve=0)

	compact_tree (const std::string &input, bool is_fn=true, bool store_labels=true, bool store_lengths=true, size_t reserve=0)

	compact_tree (const compact_tree &o)

CT_NODE_T	add_child (const CT_NODE_T parent_node, const std::string &new_label=EMPTY_STRING, CT_LENGTH_T new_length=ZERO_LENGTH)

void	print_newick (std::ostream &out, CT_NODE_T node=ROOT_NODE, bool include_semicolon=true)

std::string	get_newick (CT_NODE_T node=ROOT_NODE, bool include_semicolon=true)

size_t	get_num_nodes () const

size_t	get_num_leaves ()

size_t	get_num_internal ()

CT_NODE_T	get_root () const

bool	is_root (CT_NODE_T node) const

bool	is_leaf (CT_NODE_T node) const

CT_NODE_T	get_parent (CT_NODE_T node) const

const std::vector< CT_NODE_T > &	get_children (CT_NODE_T node) const

bool	has_edge_lengths () const

void	clear_edge_lengths (bool shrink=true)

CT_LENGTH_T	get_edge_length (CT_NODE_T node) const

const std::vector< CT_LENGTH_T > &	get_edge_lengths () const

void	set_edge_length (CT_NODE_T node, CT_LENGTH_T new_length)

bool	has_labels () const

void	clear_labels (bool shrink=true)

const std::string &	get_label (CT_NODE_T node) const

void	set_label (CT_NODE_T node, const std::string &new_label)

const std::vector< std::string > &	get_labels () const

void	replace_labels (const std::unordered_map< std::string, std::string > &label_map, bool include_internal=true)

std::tuple< const std::string , CT_LENGTH_T, CT_NODE_T, const std::vector< CT_NODE_T > >	operator[] (CT_NODE_T i) const

preorder_iterator	preorder_begin ()

preorder_iterator	preorder_end ()

postorder_iterator	postorder_begin ()

postorder_iterator	postorder_end ()

levelorder_iterator	levelorder_begin ()

levelorder_iterator	levelorder_end ()

leaves_iterator	leaves_begin ()

leaves_iterator	leaves_end ()

children_iterator	children_begin (CT_NODE_T node)

children_iterator	children_end (CT_NODE_T node)

CT_NODE_T	find_mrca (const std::unordered_set< CT_NODE_T > &nodes) const

compact_tree	extract_subtree (CT_NODE_T node)

double	calc_total_bl (bool include_internal=true, bool include_leaves=true) const

double	calc_avg_bl (bool include_internal=true, bool include_leaves=true) const

double	calc_dist (CT_NODE_T u, CT_NODE_T v) const

std::vector< std::pair< std::pair< CT_NODE_T, CT_NODE_T >, double > >	calc_distance_matrix ()

Constructor & Destructor Documentation

◆ compact_tree() [1/3]

compact_tree::compact_tree	(	const char *const	input,
		bool	is_fn = `true`,
		bool	store_labels = `true`,
		bool	store_lengths = `true`,
		size_t	reserve = `0`
	)

Load a tree from a Newick file or C string

Parameters

input	The filename or C string of the tree to load
is_fn	`true` if `input` is a filename (default), otherwise `false` if `input` is the Newick tree as a C string
store_labels	`true` to store node labels (default), otherwise `false` (saves memory)
store_lengths	`true` to store edge lengths (default), otherwise `false` (saves memory)
reserve	How many nodes to reserve memory for up-front to avoid `std::vector` resizes. It's fine if the true number of nodes in the tree exceeds this value (the `std::vector` will resize automatically), but get as close as possible for speed.

◆ compact_tree() [2/3]

compact_tree::compact_tree	(	const std::string &	input,
		bool	is_fn = `true`,
		bool	store_labels = `true`,
		bool	store_lengths = `true`,
		size_t	reserve = `0`
	)

inline

Load a tree from a Newick file or std::string

Parameters

input	The filename or `std::string` of the tree to load
is_fn	`true` if `input` is a filename (default), otherwise `false` if `input` is the Newick tree as an `std::string`
store_labels	`true` to store node labels (default), otherwise `false` (saves memory)
store_lengths	`true` to store edge lengths (default), otherwise `false` (saves memory)
reserve	How many nodes to reserve memory for up-front to avoid `std::vector` resizes. It's fine if the true number of nodes in the tree exceeds this value (the `std::vector` will resize automatically), but get as close as possible for speed.

◆ compact_tree() [3/3]

compact_tree::compact_tree ( const compact_tree & o )

inline

Copy constructor

Parameters

o	The other `compact_tree` to copy

Member Function Documentation

◆ add_child()

CT_NODE_T compact_tree::add_child	(	const CT_NODE_T	parent_node,
		const std::string &	new_label = `EMPTY_STRING`,
		CT_LENGTH_T	new_length = `ZERO_LENGTH`
	)

inline

Add a child to an existing node

Parameters

parent_node	The parent node
new_label	The label of the new child node
new_length	The length of edge incident to the new child node

Returns: The newly-created child node

◆ calc_avg_bl()

double compact_tree::calc_avg_bl	(	bool	include_internal = `true`,
		bool	include_leaves = `true`
	)		const

inline

Calculate the average branch length of this tree

Parameters

include_internal	`true` to include internal nodes, otherwise `false`
include_leaves	`true` to include leaves, otherwise `false`

Returns: The average branch length of this tree

◆ calc_dist()

double compact_tree::calc_dist	(	CT_NODE_T	u,
		CT_NODE_T	v
	)		const

inline

Calculate the (weighted) distance between two nodes

Parameters

u	The first node
v	The second node

Returns: The (weighted) distance between u and v

◆ calc_distance_matrix()

std::vector< std::pair< std::pair< CT_NODE_T, CT_NODE_T >, double > > compact_tree::calc_distance_matrix ( )

Calculate the (weighted) distance matrix between all pairs of leaves

Returns: A vector<pair<pair<node,node>,double>> containing all pairwise leaf distances as ((u,v), distance)

◆ calc_total_bl()

double compact_tree::calc_total_bl	(	bool	include_internal = `true`,
		bool	include_leaves = `true`
	)		const

inline

Calculate the total branch length of this tree

Parameters

include_internal	`true` to include internal nodes, otherwise `false`
include_leaves	`true` to include leaves, otherwise `false`

Returns: The total branch length of this tree

◆ children_begin()

children_iterator compact_tree::children_begin ( CT_NODE_T node )

inline

Return an iterator referring to the first child of a node

Parameters

node	The node to iterate over the children of

Returns: An iterator referring to the first child of node

◆ children_end()

children_iterator compact_tree::children_end ( CT_NODE_T node )

inline

Return an iterator referring to just past the last child of a node

Parameters

node	The node to iterate over the children of

Returns: An iterator referring to just past the last child of node

◆ clear_edge_lengths()

void compact_tree::clear_edge_lengths ( bool shrink = true )

inline

Clear all edge lengths in this tree

Parameters

shrink true to deallocate the memory that was allocated to store the edge lengths, otherwise false

◆ clear_labels()

void compact_tree::clear_labels ( bool shrink = true )

inline

Clear all labels in this tree

Parameters

shrink true to deallocate the memory that was allocated to store the labels, otherwise false

◆ extract_subtree()

compact_tree compact_tree::extract_subtree ( CT_NODE_T node )

Extract the subtree rooted at a given node

Parameters

node	The node that is the root of the desired subtree

Returns: The subtree rooted at node

◆ find_mrca()

CT_NODE_T compact_tree::find_mrca ( const std::unordered_set< CT_NODE_T > & nodes ) const

Find and return the Most Recent Common Ancestor (MRCA) of a collection of nodes

Parameters

nodes The nodes to find the MRCA of

Returns: The MRCA of the nodes in nodes

◆ get_children()

const std::vector< CT_NODE_T > & compact_tree::get_children ( CT_NODE_T node ) const

inline

Get the children of a node

Parameters

node	The node to get the children of

Returns: The children of node

◆ get_edge_length()

CT_LENGTH_T compact_tree::get_edge_length ( CT_NODE_T node ) const

inline

Get the incident edge length of a node

Parameters

node	The node to get the incident edge length of

Returns: The incident edge length of node

◆ get_edge_lengths()

const std::vector< CT_LENGTH_T > & compact_tree::get_edge_lengths ( ) const

inline

Get all edge lengths (return by reference)

◆ get_label()

const std::string & compact_tree::get_label ( CT_NODE_T node ) const

inline

Get the label of a node

Parameters

node	The node to get the label of

Returns: The label of node

◆ get_labels()

const std::vector< std::string > & compact_tree::get_labels ( ) const

inline

Get all labels (return by reference)

Returns: A vector<string> where the i-th value is the label of node i

◆ get_newick()

std::string compact_tree::get_newick	(	CT_NODE_T	node = `ROOT_NODE`,
		bool	include_semicolon = `true`
	)

inline

Return the Newick string of the subtree rooted at a specific node (defaults to the root = entire tree)

Parameters

node	The root of the subtree to print the Newick string of
include_semicolon	`true` to print a semicolon at the end of the Newick string (to end the tree), otherwise `false` (e.g. subtree)

◆ get_num_internal()

size_t compact_tree::get_num_internal ( )

inline

Get the total number of internal nodes in the tree. First time is O(n) scan; subsequent times are O(1) lookup

Returns: The number of internal nodes in the tree

◆ get_num_leaves()

size_t compact_tree::get_num_leaves ( )

inline

Get the total number of leaves in the tree. First time is O(n) scan; subsequent times are O(1) lookup

Returns: The number of leaves in the tree

◆ get_num_nodes()

size_t compact_tree::get_num_nodes ( ) const

inline

Get the total number of nodes in the tree using a O(1) lookup

Returns: The number of nodes in the tree

◆ get_parent()

CT_NODE_T compact_tree::get_parent ( CT_NODE_T node ) const

inline

Get the parent of a node

Parameters

node	The node to get the parent of

Returns: The parent of node

◆ get_root()

CT_NODE_T compact_tree::get_root ( ) const

inline

Get the root of this tree (should always be 0)

Returns: The root of this tree

◆ has_edge_lengths()

bool compact_tree::has_edge_lengths ( ) const

inline

Check if this tree is storing edge lengths

Returns: true if this tree is storing edge lengths, otherwise false

◆ has_labels()

bool compact_tree::has_labels ( ) const

inline

Check if this tree is storing labels

Returns: true if this tree is storing labels, otherwise false

◆ is_leaf()

bool compact_tree::is_leaf ( CT_NODE_T node ) const

inline

Check if a node is a leaf

Parameters

node	The node to check

Returns: true if node is a leaf, otherwise false

◆ is_root()

bool compact_tree::is_root ( CT_NODE_T node ) const

inline

Check if a node is the root

Parameters

node	The node to check

Returns: true if node is the root, otherwise false

◆ leaves_begin()

leaves_iterator compact_tree::leaves_begin ( )

inline

Return an iterator referring to the first node of a leaf iteration

Returns: An iterator referring to the first node of a leaf iteration

◆ leaves_end()

leaves_iterator compact_tree::leaves_end ( )

inline

Return an iterator referring to just past the last node of a leaf iteration

Returns: An iterator referring to just past the last node of a leaf iteration

◆ levelorder_begin()

levelorder_iterator compact_tree::levelorder_begin ( )

inline

Return an iterator referring to the first node of a level-order traversal

Returns: An iterator referring to the first node of a level-order traversal

◆ levelorder_end()

levelorder_iterator compact_tree::levelorder_end ( )

inline

Return an iterator referring just past the last node of a level-order traversal

Returns: An iterator referring just past the last node of a level-order traversal

◆ operator[]()

std::tuple< const std::string *, CT_LENGTH_T, CT_NODE_T, const std::vector< CT_NODE_T > * > compact_tree::operator[] ( CT_NODE_T i ) const

inline

Return the data associated with a given node

Parameters

i	The node whose data to return

Returns: A tuple<const string*, CT_LENGTH_T, CT_NODE_T, const vector<CT_NODE_T>*> containing (1) a pointer to the label, (2) the incident edge length, (3) the parent, and (4) a pointer to the collection of children of node i

◆ postorder_begin()

postorder_iterator compact_tree::postorder_begin ( )

inline

Return an iterator referring to the first node of a post-order traversal

Returns: An iterator referring to the first node of a post-order traversal

◆ postorder_end()

postorder_iterator compact_tree::postorder_end ( )

inline

Return an iterator referring just past the last node of a post-order traversal

Returns: An iterator referring just past the last node of a post-order traversal

◆ preorder_begin()

preorder_iterator compact_tree::preorder_begin ( )

inline

Return an iterator referring to the first node of a pre-order traversal

Returns: An iterator referring to the first node of a pre-order traversal

◆ preorder_end()

preorder_iterator compact_tree::preorder_end ( )

inline

Return an iterator referring just past the last node of a pre-order traversal

Returns: An iterator referring just past the last node of a pre-order traversal

◆ print_newick()

void compact_tree::print_newick	(	std::ostream &	out,
		CT_NODE_T	node = `ROOT_NODE`,
		bool	include_semicolon = `true`
	)

Print the Newick string of the subtree rooted at a specific node (defaults to the root = entire tree)

Parameters

out	The output stream to print the Newick string to
node	The root of the subtree to print the Newick string of
include_semicolon	`true` to print a semicolon at the end of the Newick string (to end the tree), otherwise `false` (e.g. subtree)

◆ replace_labels()

void compact_tree::replace_labels	(	const std::unordered_map< std::string, std::string > &	label_map,
		bool	include_internal = `true`
	)

inline

Replace all labels that match a user-provided mapping

Parameters

label_map	A mapping where keys are old labels and values are new labels (i.e., replace all occurrences of label `s` with `label_map[s]`)
include_internal	`true` to include internal nodes in the label replacement, otherwise `false` to only replace leaf labels

◆ set_edge_length()

void compact_tree::set_edge_length	(	CT_NODE_T	node,
		CT_LENGTH_T	new_length
	)

inline

Set the incident edge length of a node

Parameters

node	The node to set the incident edge length of
new_length	The new edge length to set

◆ set_label()

void compact_tree::set_label	(	CT_NODE_T	node,
		const std::string &	new_label
	)

inline

Set the label of a node

Parameters

node	The node to set the label of
new_label	The new label to set

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

CompactTree/compact_tree.h

Classes

Public Member Functions

Constructor & Destructor Documentation

◆ compact_tree() [1/3]

◆ compact_tree() [2/3]

◆ compact_tree() [3/3]

Member Function Documentation

◆ add_child()

◆ calc_avg_bl()

◆ calc_dist()

◆ calc_distance_matrix()

◆ calc_total_bl()

◆ children_begin()

◆ children_end()

◆ clear_edge_lengths()

◆ clear_labels()

◆ extract_subtree()

◆ find_mrca()

◆ get_children()

◆ get_edge_length()

◆ get_edge_lengths()

◆ get_label()

◆ get_labels()

◆ get_newick()

◆ get_num_internal()

◆ get_num_leaves()

◆ get_num_nodes()

◆ get_parent()

◆ get_root()

◆ has_edge_lengths()

◆ has_labels()

◆ is_leaf()

◆ is_root()

◆ leaves_begin()

◆ leaves_end()

◆ levelorder_begin()

◆ levelorder_end()

◆ operator[]()

◆ postorder_begin()

◆ postorder_end()

◆ preorder_begin()

◆ preorder_end()

◆ print_newick()

◆ replace_labels()

◆ set_edge_length()

◆ set_label()