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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
All of these functions are now native methods of the Tree class. They are
maintained here only for background compatibility.
"""
from dendropy.utility import deprecate
def _deprecate_tree_manip(old, new):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: Tree structure manipulation and editing functionality are now native methods of the 'dendropy.Tree' class.",
old_construct=old,
new_construct=new,
stacklevel=4)
def collapse_edge(edge):
_deprecate_tree_manip("treemanip.collapse_edge(edge)", "edge.collapse()")
edge.collapse()
def collapse_clade(node):
_deprecate_tree_manip("treemanip.collapse_clade(node)", "node.collapse_clade()")
node.collapse_clade()
def prune_subtree(tree, node, suppress_unifurcations=True):
_deprecate_tree_manip("treemanip.prune_subtree(tree, node)", "tree.prune_subtree(node)")
tree.prune_subtree(node=node,
suppress_unifurcations=suppress_unifurcations)
return tree
def prune_leaves_without_taxa(tree, suppress_unifurcations=True):
_deprecate_tree_manip("treemanip.prune_leaves_without_taxa(tree)", "tree.prune_leaves_without_taxa()")
tree.prune_leaves_without_taxa(suppress_unifurcations=suppress_unifurcations)
return tree
def prune_taxa(tree, taxa, suppress_unifurcations=True):
_deprecate_tree_manip("treemanip.prune_taxa(tree, taxa)", "tree.prune_taxa(taxa)")
tree.prune_taxa(taxa=taxa,
suppress_unifurcations=suppress_unifurcations)
return tree
def retain_taxa(tree, taxa, suppress_unifurcations=True):
_deprecate_tree_manip("treemanip.retain_taxa(tree, taxa)", "tree.retain_taxa(taxa)")
tree.retain_taxa(taxa=taxa,
suppress_unifurcations=suppress_unifurcations)
def randomly_reorient_tree(tree, rng=None, splits=False):
_deprecate_tree_manip("randomly_reorient_tree(tree)", "tree.randomly_reorient()")
tree.randomly_reorient(rng=rng, update_splits=splits)
def randomly_rotate(tree, rng=None):
_deprecate_tree_manip("treemanip.randomly_rotate(tree)", "tree.randomly_rotate()")
tree.randomly_rotate(rng=rng)
def collapse_conflicting(subtree_root, split, split_bitmask):
_deprecate_tree_manip("treemanip.collapse_conflicting(node)", "node.collapse_conflicting()")
subtree_root.collapse_conflicting(split, split_bitmask)
def scale_edges(tree, edge_len_multiplier):
_deprecate_tree_manip("treemanip.scale_edges(tree)", "tree.scale_edges()")
tree.scale_edges(edge_len_multiplier=edge_len_multiplier)
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