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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.
##
##############################################################################
"""
Tests basic Edge operations.
"""
import copy
import unittest
from dendropy.test.support import compare_and_validate
import dendropy
class EdgeIdentity(unittest.TestCase):
def setUp(self):
self.e1 = dendropy.Edge(label="a")
self.e2 = dendropy.Edge(label="a")
def test_equal(self):
# two distinct |Edge| objects are never equal, even if all
# member values are the same.
self.assertNotEqual(self.e1, self.e2)
def test_hash_dict_membership(self):
k = {}
k[self.e1] = 1
k[self.e2] = 2
self.assertEqual(len(k), 2)
self.assertEqual(k[self.e1], 1)
self.assertEqual(k[self.e2], 2)
self.assertIn(self.e1, k)
self.assertIn(self.e2, k)
del k[self.e1]
self.assertNotIn(self.e1, k)
self.assertIn(self.e2, k)
self.assertEqual(len(k), 1)
k1 = {self.e1: 1}
k2 = {self.e2: 1}
self.assertIn(self.e1, k1)
self.assertIn(self.e2, k2)
self.assertNotIn(self.e2, k1)
self.assertNotIn(self.e1, k2)
def test_hash_set_membership(self):
k = set()
k.add(self.e1)
k.add(self.e2)
self.assertEqual(len(k), 2)
self.assertIn(self.e1, k)
self.assertIn(self.e2, k)
k.discard(self.e1)
self.assertNotIn(self.e1, k)
self.assertIn(self.e2, k)
self.assertEqual(len(k), 1)
k1 = {self.e1: 1}
k2 = {self.e2: 1}
self.assertIn(self.e1, k1)
self.assertIn(self.e2, k2)
self.assertNotIn(self.e2, k1)
self.assertNotIn(self.e1, k2)
class EdgeCloning(compare_and_validate.Comparator, unittest.TestCase):
def setUp(self):
self.taxa = [dendropy.Taxon(label=label) for label in ["a", "b", "c", "d"]]
self.n0 = dendropy.Node(label="0", taxon=self.taxa[0])
self.c1 = dendropy.Node(label="1", taxon=None)
self.c2 = dendropy.Node(label=None, taxon=self.taxa[1])
self.c3 = dendropy.Node(label=None, taxon=None)
self.c3 = dendropy.Node(label=None, taxon=self.taxa[2])
self.p1 = dendropy.Node(label="-1", taxon=self.taxa[3])
self.n0.parent_node = self.p1
self.n0.set_child_nodes([self.c1, self.c2])
self.c2.set_child_nodes([self.c3])
self.nodes = [self.n0, self.c1, self.c2, self.c3, self.p1]
for idx, nd in enumerate(self.nodes):
if idx % 2 == 0:
nd.edge.label = "E{}".format(idx)
nd.edge.length = idx
an1 = nd.annotations.add_new("a{}".format(idx),
"{}{}{}".format(nd.label, nd.taxon, idx))
an2 = nd.annotations.add_bound_attribute("label")
an3 = an1.annotations.add_bound_attribute("name")
ae1 = nd.edge.annotations.add_new("a{}".format(idx),
"{}{}".format(nd.edge.label, idx))
ae2 = nd.edge.annotations.add_bound_attribute("label")
ae3 = ae1.annotations.add_bound_attribute("name")
self.e0 = self.n0._edge
def test_unsupported_copy(self):
with self.assertRaises(TypeError):
self.e0.clone(0)
with self.assertRaises(TypeError):
copy.copy(self.e0)
with self.assertRaises(TypeError):
self.e0.clone(1)
with self.assertRaises(TypeError):
self.e0.taxon_namespace_scoped_copy()
def test_deepcopy(self):
for clone in (
self.e0.clone(2),
copy.deepcopy(self.e0),
):
self.compare_distinct_nodes(
clone._head_node, self.n0,
taxon_namespace_scoped=False,
compare_tree_annotations=True)
class EdgeNodeManagement(unittest.TestCase):
def test_edge_tail_node_setting(self):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in ["c1", "c2", "c3"]]
for ch in assigned_ch:
ch.edge.tail_node = parent
for ch in assigned_ch:
self.assertEqual(parent._child_nodes, assigned_ch)
for nd in parent.child_node_iter():
self.assertIs(nd.parent_node, parent)
self.assertIs(nd.edge.tail_node, parent)
self.assertIs(nd.edge.head_node, nd)
def test_edge_head_node_setting(self):
node1 = dendropy.Node()
parent_node1 = dendropy.Node()
node1.parent_node = parent_node1
self.assertIs(node1._parent_node, parent_node1)
edge1 = node1.edge
self.assertIs(edge1.head_node, node1)
self.assertIs(edge1.tail_node, parent_node1)
node2 = dendropy.Node()
parent_node2 = dendropy.Node()
node2.parent_node = parent_node2
edge2 = node2.edge
self.assertIs(edge2.head_node, node2)
self.assertIs(edge2.tail_node, parent_node2)
new_edge1 = dendropy.Edge()
new_edge1.head_node = node1
self.assertIs(node1.edge, new_edge1)
self.assertIs(new_edge1.head_node, node1)
self.assertIs(new_edge1.tail_node, parent_node1)
edge2.head_node = node1
self.assertIs(node1.edge, edge2)
self.assertIs(edge2.head_node, node1)
self.assertIs(edge2.tail_node, parent_node1)
if __name__ == "__main__":
unittest.main()
|
