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| # Copyright (C) 2009 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 Newick trees, also used for Nexus trees. | |
| See classes in ``Bio.Nexus``: Trees.Tree, Trees.NodeData, and Nodes.Chain. | |
| """ | |
| from Bio.Phylo import BaseTree | |
| class Tree(BaseTree.Tree): | |
| """Newick Tree object.""" | |
| def __init__(self, root=None, rooted=False, id=None, name=None, weight=1.0): | |
| """Initialize parameters for a Newick tree object.""" | |
| 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=None, name=None, clades=None, confidence=None, comment=None | |
| ): | |
| """Initialize parameters for a Newick Clade object.""" | |
| BaseTree.Clade.__init__( | |
| self, | |
| branch_length=branch_length, | |
| name=name, | |
| clades=clades, | |
| confidence=confidence, | |
| ) | |
| self.comment = comment | |