skbio.tree.TreeNode.cache_attr

TreeNode.cache_attr(func, cache_attrname, cache_type=<class 'list'>)[source]

Cache attributes on internal nodes of the tree

State: Experimental as of 0.4.0.

Parameters
  • func (function) – func will be provided the node currently being evaluated and must return a list of item (or items) to cache from that node or an empty list.

  • cache_attrname (str) – Name of the attribute to decorate on containing the cached values

  • cache_type ({set, frozenset, list}) – The type of the cache

Notes

This method is particularly useful if you need to frequently look up attributes that would normally require a traversal of the tree.

WARNING: any cache created by this method will be invalidated if the topology of the tree changes (e.g., if TreeNode.invalidate_caches is called).

Raises

TypeError – If an cache_type that is not a set or a list is specified.

Examples

Cache the tip names of the tree on its internal nodes

>>> from skbio import TreeNode
>>> tree = TreeNode.read(["((a,b,(c,d)e)f,(g,h)i)root;"])
>>> f = lambda n: [n.name] if n.is_tip() else []
>>> tree.cache_attr(f, 'tip_names')
>>> for n in tree.traverse(include_self=True):
...     print("Node name: %s, cache: %r" % (n.name, n.tip_names))
Node name: root, cache: ['a', 'b', 'c', 'd', 'g', 'h']
Node name: f, cache: ['a', 'b', 'c', 'd']
Node name: a, cache: ['a']
Node name: b, cache: ['b']
Node name: e, cache: ['c', 'd']
Node name: c, cache: ['c']
Node name: d, cache: ['d']
Node name: i, cache: ['g', 'h']
Node name: g, cache: ['g']
Node name: h, cache: ['h']