/usr/share/pyshared/Bio/Phylo/Newick.py is in python-biopython 1.58-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | # Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Classes corresponding to Newick trees, also used for Nexus trees.
See classes in `Bio.Nexus`: Trees.Tree, Trees.NodeData, and Nodes.Chain.
"""
__docformat__ = "restructuredtext en"
import warnings
from Bio.Phylo import BaseTree
class Tree(BaseTree.Tree):
"""Newick Tree object."""
def __init__(self, root=None, rooted=False, id=None, name='', weight=1.0):
BaseTree.Tree.__init__(self, root=root or Clade(),
rooted=rooted, id=id, name=name)
self.weight = weight
class Clade(BaseTree.Clade):
"""Newick Clade (sub-tree) object."""
def __init__(self, branch_length=1.0, name=None, clades=None,
confidence=None, comment=None):
BaseTree.Clade.__init__(self, branch_length=branch_length,
name=name, clades=clades, confidence=confidence)
self.comment = comment
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