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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 = [] | |