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# Copyright (C) 2013 by Ben Morris ([email protected])
# based on code by Eric Talevich ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes corresponding to CDAO trees.
See classes in ``Bio.Nexus``: Trees.Tree, Trees.NodeData, and Nodes.Chain.
"""
from Bio.Phylo import BaseTree
class Tree(BaseTree.Tree):
"""CDAO Tree object."""
def __init__(self, root=None, rooted=False, id=None, name=None, weight=1.0):
"""Initialize value of for the CDAO tree object."""
BaseTree.Tree.__init__(
self, root=root or Clade(), rooted=rooted, id=id, name=name
)
self.weight = weight
# a list of (predicate, object) pairs, containing additional triples
# using this tree as subject
self.attributes = []
class Clade(BaseTree.Clade):
"""CDAO Clade (sub-tree) object."""
def __init__(
self, branch_length=1.0, name=None, clades=None, confidence=None, comment=None
):
"""Initialize values for the CDAO Clade object."""
BaseTree.Clade.__init__(
self,
branch_length=branch_length,
name=name,
clades=clades,
confidence=confidence,
)
self.comment = comment
# a list of (predicate, object) pairs, containing additional triples
# using this clade as subject
self.attributes = []
self.tu_attributes = []
self.edge_attributes = []
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