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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 Node child management.
"""
import unittest
import dendropy
import copy
from dendropy.test.support import compare_and_validate
class TestNodeConstruction(unittest.TestCase):
def test_basic_construction(self):
taxon = dendropy.Taxon("z")
nd = dendropy.Node(taxon=taxon, label="x", edge_length=1)
self.assertIs(nd.taxon, taxon)
self.assertEqual(nd.label, "x")
edge = nd.edge
self.assertEqual(edge.length, 1)
self.assertIs(edge.head_node, nd)
self.assertIs(edge.tail_node, None)
class NodeIdentity(unittest.TestCase):
def setUp(self):
taxon = dendropy.Taxon("a")
self.n1 = dendropy.Node(label="a", taxon=taxon)
self.n2 = dendropy.Node(label="a", taxon=taxon)
def test_equal(self):
# two distinct |Node| objects are never equal, even if all
# member values are the same.
self.assertNotEqual(self.n1, self.n2)
self.assertIs(self.n1.taxon, self.n2.taxon)
def test_hash_dict_membership(self):
k = {}
k[self.n1] = 1
k[self.n2] = 2
self.assertEqual(len(k), 2)
self.assertEqual(k[self.n1], 1)
self.assertEqual(k[self.n2], 2)
self.assertIn(self.n1, k)
self.assertIn(self.n2, k)
del k[self.n1]
self.assertNotIn(self.n1, k)
self.assertIn(self.n2, k)
self.assertEqual(len(k), 1)
k1 = {self.n1: 1}
k2 = {self.n2: 1}
self.assertIn(self.n1, k1)
self.assertIn(self.n2, k2)
self.assertNotIn(self.n2, k1)
self.assertNotIn(self.n1, k2)
def test_hash_set_membership(self):
k = set()
k.add(self.n1)
k.add(self.n2)
self.assertEqual(len(k), 2)
self.assertIn(self.n1, k)
self.assertIn(self.n2, k)
k.discard(self.n1)
self.assertNotIn(self.n1, k)
self.assertIn(self.n2, k)
self.assertEqual(len(k), 1)
k1 = {self.n1: 1}
k2 = {self.n2: 1}
self.assertIn(self.n1, k1)
self.assertIn(self.n2, k2)
self.assertNotIn(self.n2, k1)
self.assertNotIn(self.n1, k2)
class NodeCloning(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")
def test_unsupported_copy(self):
with self.assertRaises(TypeError):
self.n0.clone(0)
with self.assertRaises(TypeError):
copy.copy(self.n0)
with self.assertRaises(TypeError):
self.n0.clone(1)
with self.assertRaises(TypeError):
self.n0.taxon_namespace_scoped_copy()
def test_deepcopy(self):
for clone in (
self.n0.clone(2),
copy.deepcopy(self.n0),
):
self.compare_distinct_nodes(
clone, self.n0,
taxon_namespace_scoped=False,
compare_tree_annotations=True)
class TestNodeSetChildNodes(unittest.TestCase):
def test_set_child_nodes(self):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in ["c1", "c2", "c3"]]
for nd in assigned_ch:
x = [dendropy.Node(label=c) for c in ["s1", "s2"]]
nd.set_child_nodes(x)
nd._expected_children = x
parent.set_child_nodes(assigned_ch)
for ch in parent._child_nodes:
self.assertIn(ch, assigned_ch)
self.assertIs(ch._parent_node, parent)
self.assertIs(ch.edge.tail_node, parent)
self.assertIs(ch.edge.head_node, ch)
self.assertEqual(len(ch._child_nodes), len(ch._expected_children))
for sch in ch._child_nodes:
self.assertIn(sch, ch._expected_children)
self.assertIs(sch._parent_node, ch)
self.assertIs(sch.edge.tail_node, ch)
self.assertIs(sch.edge.head_node, sch)
for ch in assigned_ch:
self.assertTrue(ch in parent._child_nodes)
def test_add_child(self):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in ["c1", "c2", "c3"]]
for nd in assigned_ch:
x = [dendropy.Node(label=c) for c in ["s1", "s2"]]
for y in x:
nd.add_child(y)
nd._expected_children = x
for ch in assigned_ch:
k = parent.add_child(ch)
self.assertIs(k, ch)
for ch in parent._child_nodes:
self.assertIn(ch, assigned_ch)
self.assertIs(ch._parent_node, parent)
self.assertIs(ch.edge.tail_node, parent)
self.assertIs(ch.edge.head_node, ch)
self.assertEqual(len(ch._child_nodes), len(ch._expected_children))
for sch in ch._child_nodes:
self.assertIn(sch, ch._expected_children)
self.assertIs(sch._parent_node, ch)
self.assertIs(sch.edge.tail_node, ch)
self.assertIs(sch.edge.head_node, sch)
for ch in assigned_ch:
self.assertTrue(ch in parent._child_nodes)
def test_insert_child_at_pos(self):
new_child_labels = ["c1", "c2", "c3"]
insert_ch_label = "x1"
for pos in range(len(new_child_labels)+1):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in new_child_labels]
parent.set_child_nodes(assigned_ch)
insert_ch = dendropy.Node(label=insert_ch_label)
parent.insert_child(pos, insert_ch)
x = 0
for idx, ch in enumerate(parent._child_nodes):
if idx == pos:
self.assertEqual(ch.label, insert_ch_label)
else:
self.assertEqual(ch.label, new_child_labels[x])
x += 1
def test_redundant_set(self):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in ["c1", "c2", "c3"]]
parent.set_child_nodes(assigned_ch)
parent.set_child_nodes(assigned_ch)
ch2 = assigned_ch + assigned_ch
parent.set_child_nodes(ch2)
self.assertEqual(parent._child_nodes, assigned_ch)
for nd in parent.child_node_iter():
self.assertIs(nd.parent_node, parent)
def test_redundant_insert_child_at_pos(self):
new_child_labels = ["c1", "c2", "c3"]
for child_to_insert_idx in range(len(new_child_labels)):
for insertion_idx in range(len(new_child_labels)):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in new_child_labels]
parent.set_child_nodes(assigned_ch)
self.assertEqual(parent._child_nodes, assigned_ch)
insert_ch = assigned_ch[child_to_insert_idx]
parent.insert_child(insertion_idx, insert_ch)
self.assertEqual(len(parent._child_nodes), len(assigned_ch))
self.assertEqual(len(set(parent._child_nodes)), len(parent._child_nodes))
x = 0
for idx, ch in enumerate(parent._child_nodes):
if idx == insertion_idx:
self.assertIs(ch, insert_ch)
self.assertIn(ch, assigned_ch)
for ch in assigned_ch:
self.assertIn(ch, parent._child_nodes)
self.assertEqual(parent._child_nodes.count(ch), 1)
def test_redundant_add(self):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in ["c1", "c2", "c3"]]
parent.set_child_nodes(assigned_ch)
for ch in assigned_ch:
parent.add_child(ch)
self.assertEqual(parent._child_nodes, assigned_ch)
for nd in parent.child_node_iter():
self.assertIs(nd.parent_node, parent)
def test_parent_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.parent_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_new_child(self):
parent = dendropy.Node(label="parent")
new_child_labels = ["c1", "c2", "c3"]
sub_child_labels = ["s1", "s2"]
for label in new_child_labels:
nd = parent.new_child(label=label)
for y in sub_child_labels:
x = nd.new_child(label=y)
self.assertTrue(isinstance(x, dendropy.Node))
self.assertEqual(x.label, y)
self.assertIs(x.parent_node, nd)
self.assertIs(x.edge.head_node, x)
self.assertIs(x.edge.tail_node, nd)
self.assertEqual(len(parent._child_nodes), len(new_child_labels))
for ch in parent._child_nodes:
self.assertIn(ch.label, new_child_labels)
self.assertIs(ch._parent_node, parent)
self.assertIs(ch.edge.tail_node, parent)
self.assertIs(ch.edge.head_node, ch)
for sch in ch._child_nodes:
self.assertIn(sch.label, sub_child_labels)
self.assertIs(sch._parent_node, ch)
self.assertIs(sch.edge.tail_node, ch)
self.assertIs(sch.edge.head_node, sch)
def test_new_child_at_pos(self):
new_child_labels = ["c1", "c2", "c3"]
insert_ch_label = "x1"
for pos in range(len(new_child_labels)+1):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in new_child_labels]
parent.set_child_nodes(assigned_ch)
parent.insert_new_child(pos, label=insert_ch_label)
x = 0
for idx, ch in enumerate(parent._child_nodes):
if idx == pos:
self.assertEqual(ch.label, insert_ch_label)
else:
self.assertEqual(ch.label, new_child_labels[x])
x += 1
def test_remove_child(self):
assigned_child_labels = ["c1", "c2", "c3"]
for remove_idx in range(len(assigned_child_labels)):
parent = dendropy.Node(label="parent")
assigned_ch = [dendropy.Node(label=c) for c in assigned_child_labels]
parent.set_child_nodes(assigned_ch)
ch_nodes = list(parent._child_nodes)
to_remove = ch_nodes[remove_idx]
x = parent.remove_child(to_remove)
self.assertIs(to_remove, x)
ch_nodes.remove(to_remove)
ch_nodes2 = list(parent._child_nodes)
self.assertEqual(ch_nodes, ch_nodes2)
def test_edge_head_node_setting(self):
node = dendropy.Node(label="x")
edge1 = node.edge
edge2 = dendropy.Edge()
node.edge = edge2
self.assertIs(node.edge, edge2)
self.assertIs(node.edge.head_node, node)
if __name__ == "__main__":
unittest.main()
|
