ivy.chars.cy_tree package

Submodules

ivy.chars.cy_tree.cy_tree module

class ivy.chars.cy_tree.cy_tree.Node

Bases: object

Node in a rooted, potentially multifurcating tree.

add_child()

bft()

breadth-first traversal of descendants

children

isleaf

isroot

iterchildren()

iternodes()

iterate (preorder) over nodes descendant from self - including self

label

leaves

left

leftchild

leftsib

length

nchildren

ni

parent

postiter()

iterate (postorder) over nodes descendant from self - including self

prune()

right

rightsib

treename

class ivy.chars.cy_tree.cy_tree.Tree

Bases: object

Convenience class for creating/storing node relationships and values as arrays.

index()

call on __cinit__, or when topology changes but no. nodes is the same

label

leftchild

length

nchildren

nleaves

nnodes

parent

postorder

rightsib

root

rootpathlen()

ivy.chars.cy_tree.cy_tree.cladesizes1()

ivy.chars.cy_tree.cy_tree.cladesizes2()

ivy.chars.cy_tree.cy_tree.cladesizes3()

ivy.chars.cy_tree.cy_tree.cladesizes4()

ivy.chars.cy_tree.cy_tree.tree_from_ivy()

Convert ivy Node to cython Tree

ivy.chars.cy_tree.newick module

Parse newick strings.

The function of interest is parse, which returns the root node of the parsed tree.

class ivy.chars.cy_tree.newick.Tokenizer(infile)

Bases: shlex.shlex

Provides tokens for parsing newick strings.

parse_embedded_comment()

ivy.chars.cy_tree.newick.add_label_chars(chars)

ivy.chars.cy_tree.newick.nexus_iter(infile)

ivy.chars.cy_tree.newick.parse(data, ttable=None, treename=None)

Parse a newick string.

data is any file-like object that can be coerced into shlex, or a string (converted to StringIO)

ttable is a dictionary mapping node labels in the newick string

to other values.

Returns: the root node.

ivy.chars.cy_tree.newick.parse_ampersand_comment(s)

ivy.chars.cy_tree.newick.test_parse_comment()

ivy.chars.cy_tree.nexus module

class ivy.chars.cy_tree.nexus.Newick(parse_results=None, ttable={})

Bases: object

convenience class for storing the results of a newick tree record from a nexus file, as parsed by newick.nexus_iter

parse(newick=<module 'ivy.chars.cy_tree.newick' from '/home/cziegler/mypy/local/lib/python2.7/site-packages/ivy/chars/cy_tree/newick.pyc'>)

populate(parse_results, ttable={})

ivy.chars.cy_tree.nexus.fetchaln(fname)

ivy.chars.cy_tree.nexus.parse_treesblock(infile)

ivy.chars.cy_tree.nexus.split_blocks(infile)

ivy.chars.cy_tree.setup module

ivy.chars.cy_tree.test module

Module contents