biotite.sequence.phylo.TreeNode

class biotite.sequence.phylo.TreeNode(child1=None, child2=None, child1_distance=None, child2_distance=None, index=None)

Bases: object

TreeNode objects are part of a rooted tree (e.g. alignment guide tree). There are two TreeNode subtypes:

  • Leaf node - Cannot have child nodes but has an index referring to an array-like reference object.

  • Intermediate node - Has child nodes but no reference index

This type is determined by the time of the object’s creation.

Every TreeNode has a reference to its parent node. A root node is node without a parent node, that is finalized using as_root(). The call of this function prevents that a the node can be used as child.

TreeNode objects are semi-immutable: The child nodes or the reference index are fixed at the time of creation. Only the parent can be set once, when the parent node is created. TreeNode objects that are finalized using as_root() are completely immutable.

All object properties are read-only.

Parameters
children: array-like object of TreeNode, length=n, optional

The children of this node. As this causes the creation of an intermediate node, this parameter cannot be used in combination with index.

distances: array-like object of float, length=n, optional

The distances of the child nodes to this node. Must be set if children is set.

index: int, optional

Index to a reference array-like object (e.g. list of sequences or labels). Must be a positive integer. As this causes the creation of a leaf node, this parameter cannot be used in combination with the other parameters.

Examples

>>> leaf1 = TreeNode(index=0)
>>> leaf2 = TreeNode(index=1)
>>> leaf3 = TreeNode(index=2)
>>> inter = TreeNode([leaf1, leaf2], [5.0, 7.0])
>>> root  = TreeNode([inter, leaf3], [3.0, 10.0])
>>> print(root)
((0:5.0,1:7.0):3.0,2:10.0):0.0
Attributes
parentTreeNode

The parent node. None if node has no parent.

childrentuple of TreeNode

The child nodes. None if node is a leaf node.

indexint

The index to a reference array-like object. None if node is not a leaf node.

distancefloat

Distance to parent node. None if parent is Ǹone.

as_root()

Convert the node into a root node.

When a root node is used as child parameter in the construction of a potential parent node, a TreeError is raised.

copy()

Create a deep copy of this TreeNode.

The copy includes this node, its reference index and deep copies of its child nodes. The parent node and the distance to it is not included.

distance_to(node, topological=False)

Get the distance of this node to another node.

The distance is the sum of all distances from this and the other node to the lowest common ancestor.

Parameters
nodeTreeNode

The second node for distance calculation.

Returns
distancefloat

The distance of this node to node.

Raises
TreeError

If the nodes have no common ancestor.

Examples

>>> leaf1 = TreeNode(index=0)
>>> leaf2 = TreeNode(index=1)
>>> leaf3 = TreeNode(index=2)
>>> inter = TreeNode([leaf1, leaf2], [5.0, 7.0])
>>> root  = TreeNode([inter, leaf3], [3.0, 10.0])
>>> print(leaf1.distance_to(leaf2))
12.0
>>> print(leaf1.distance_to(leaf3))
18.0
static from_newick(newick, labels=None)

Create a node and all its child nodes from a Newick notation.

Parameters
newickstr

The Newick notation to create the node from.

labelslist of str, optional

If the Newick notation contains labels, that are not parseable into reference indices, i.e. they are not integers, this parameter can be provided to convert these labels into reference indices. The corresponding index is the position of the label in the provided list.

Returns
nodeTreeNode

The tree node parsed from the Newick notation.

distancefloat

Distance of the node to its parent. If the newick notation does not provide a distance, it is set to 0 by default.

Notes

The provided Newick notation must not have a terminal semicolon. If you have a Newick notation that covers an entire tree, you may use the same method in the Tree class instead. Keep in mind that the TreeNode class does support any labels on intermediate nodes. If the string contains such labels, they are discarded.

get_indices()

Get an array of reference indices that leaf nodes of this node contain.

This method identifies all leaf nodes, which have this node as ancestor and puts the contained indices into an array. If this node is a leaf node itself, the array contains the reference index of this node as single element.

Returns
indicesndarray, dtype=int32

The reference indices of direct and indirect child leaf nodes of this node.

Examples

>>> leaf0 = TreeNode(index=0)
>>> leaf1 = TreeNode(index=1)
>>> leaf2 = TreeNode(index=2)
>>> leaf3 = TreeNode(index=3)
>>> intr0 = TreeNode([leaf0, leaf2], [0, 0])
>>> intr1 = TreeNode([leaf1, leaf3], [0, 0])
>>> root  = TreeNode([intr0, intr1], [0, 0])
>>> print(leaf0.get_indices())
[0]
>>> print(intr0.get_indices())
[0 2]
>>> print(intr1.get_indices())
[1 3]
>>> print(root.get_indices())
[0 2 1 3]
get_leaf_count()

” get_leaf_count()

Get the number of direct or indirect leaves of this ńode.

This method identifies all leaf nodes, which have this node as ancestor. If this node is a leaf node itself, 1 is returned.

get_leaves()

Get a list of leaf nodes that are direct or indirect child nodes of this node.

This method identifies all leaf nodes, which have this node as ancestor. If this node is a leaf node itself, the list contains this node as single element.

Returns
leaf_nodeslist

The leaf nodes, that are direct or indirect child nodes of this node.

is_leaf()

Check if the node is a leaf node.

Returns
is_leafbool

True if the node is a leaf node, false otherwise.

is_root()

Check if the node is a root node.

Returns
is_rootbool

True if the node is a root node, false otherwise.

lowest_common_ancestor(node)

Get the lowest common ancestor of this node and another node.

Parameters
nodeTreeNode

The node to get the lowest common ancestor with.

Returns
ancestorTreeNode or None

The lowest common ancestor. None if the nodes have no common ancestor, i.e. they are not in the same tree

to_newick(labels=None, include_distance=True)

Obtain the node represented in Newick notation.

The terminal semicolon is not included.

Parameters
labelsiterable object of str

The labels the indices in the leaf nodes refer to

include_distancebool

If true, the distances are displayed in the newick notation, otherwise they are omitted.

Returns
newickstr

The Newick notation of the node.

Examples

>>> leaf1 = TreeNode(index=0)
>>> leaf2 = TreeNode(index=1)
>>> leaf3 = TreeNode(index=2)
>>> inter = TreeNode([leaf1, leaf2], [5.0, 7.0])
>>> root  = TreeNode([inter, leaf3], [3.0, 10.0])
>>> print(root.to_newick())
((0:5.0,1:7.0):3.0,2:10.0):0.0
>>> print(root.to_newick(include_distance=False))
((0,1),2)
>>> labels = ["foo", "bar", "foobar"]
>>> print(root.to_newick(labels=labels, include_distance=False))
((foo,bar),foobar)