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# Copyright (C) 2013 Ben Morris (ben@bendmorris.com)
# based on code 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 NeXML trees.
See classes in `Bio.Nexus`: Trees.Tree, Trees.NodeData, and Nodes.Chain.
"""
from Bio.Phylo import BaseTree
class Tree(BaseTree.Tree):
"""NeXML Tree object."""
def __init__(self, root=None, rooted=False, id=None, name=None, weight=1.0):
"""Instantiate a NeXML tree object with the given parameters."""
BaseTree.Tree.__init__(self, root=root or Clade(),
rooted=rooted, id=id, name=name)
self.weight = weight
class Clade(BaseTree.Clade):
"""NeXML Clade (sub-tree) object."""
def __init__(self, branch_length=1.0, name=None, clades=None,
confidence=None, comment=None, **kwargs):
"""Initialize parameters for NeXML Clade object."""
BaseTree.Clade.__init__(self, branch_length=branch_length,
name=name, clades=clades, confidence=confidence)
self.comment = comment
for key, value in kwargs.items():
setattr(self, key, value)
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