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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 Tree copying etc.
"""
import unittest
import dendropy
import copy
from dendropy.test.support import curated_test_tree
from dendropy.test.support import compare_and_validate
class TestTreeIdentity(unittest.TestCase):
def setUp(self):
self.t1 = dendropy.Tree()
self.t2 = dendropy.Tree()
def test_equal(self):
self.assertNotEqual(self.t1, self.t2)
def test_hash_dict_membership(self):
k = {}
k[self.t1] = 1
k[self.t2] = 2
self.assertEqual(len(k), 2)
self.assertEqual(k[self.t1], 1)
self.assertEqual(k[self.t2], 2)
self.assertIn(self.t1, k)
self.assertIn(self.t2, k)
del k[self.t1]
self.assertNotIn(self.t1, k)
self.assertIn(self.t2, k)
self.assertEqual(len(k), 1)
k1 = {self.t1: 1}
k2 = {self.t2: 1}
self.assertIn(self.t1, k1)
self.assertIn(self.t2, k2)
self.assertNotIn(self.t2, k1)
self.assertNotIn(self.t1, k2)
def test_hash_set_membership(self):
k = set()
k.add(self.t1)
k.add(self.t2)
self.assertEqual(len(k), 2)
self.assertIn(self.t1, k)
self.assertIn(self.t2, k)
k.discard(self.t1)
self.assertNotIn(self.t1, k)
self.assertIn(self.t2, k)
self.assertEqual(len(k), 1)
k1 = {self.t1: 1}
k2 = {self.t2: 1}
self.assertIn(self.t1, k1)
self.assertIn(self.t2, k2)
self.assertNotIn(self.t2, k1)
self.assertNotIn(self.t1, k2)
class TestTreeCopying(
curated_test_tree.CuratedTestTree,
compare_and_validate.Comparator,
unittest.TestCase):
def add_annotations(self, tree):
for idx, nd in enumerate(tree):
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")
tree.annotations.add_new("a", 0)
tree.label = "hello"
b = tree.annotations.add_bound_attribute("label")
b.annotations.add_new("c", 3)
for idx, taxon in enumerate(tree.taxon_namespace):
a = taxon.annotations.add_new("!color", str(idx))
a.annotations.add_new("setbytest", "a")
def test_copy(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
self.add_annotations(tree1)
for tree2 in (
# tree1.clone(0),
# copy.copy(tree1),
# tree1.clone(1),
# tree1.taxon_namespace_scoped_copy(),
dendropy.Tree(tree1),
):
self.compare_distinct_trees(tree1, tree2,
taxon_namespace_scoped=True,
compare_tree_annotations=True,
compare_taxon_annotations=False)
# Redundant, given the above
# But for sanity's sake ...
nodes1 = [nd for nd in tree1]
nodes2 = [nd for nd in tree2]
self.assertEqual(len(nodes1), len(nodes2))
for nd1, nd2 in zip(nodes1, nodes2):
self.assertIsNot(nd1, nd2)
self.assertEqual(nd1.label, nd2.label)
self.assertIs(nd1.taxon, nd2.taxon)
def test_deepcopy_including_namespace(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
self.add_annotations(tree1)
for idx, tree2 in enumerate((
tree1.clone(2),
copy.deepcopy(tree1),
)):
self.compare_distinct_trees(tree1, tree2,
taxon_namespace_scoped=False,
compare_tree_annotations=True,
compare_taxon_annotations=False)
# Redundant, given the above
# But for sanity's sake ...
nodes1 = [nd for nd in tree1]
nodes2 = [nd for nd in tree2]
self.assertEqual(len(nodes1), len(nodes2))
for nd1, nd2 in zip(nodes1, nodes2):
self.assertIsNot(nd1, nd2)
self.assertEqual(nd1.label, nd2.label)
self.assertIsNot(nd1.taxon, nd2.taxon)
self.assertEqual(nd1.taxon.label, nd2.taxon.label)
def test_deepcopy_excluding_namespace(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
self.add_annotations(tree1)
tree2 = dendropy.Tree(tree1, taxon_namespace=dendropy.TaxonNamespace())
self.compare_distinct_trees(tree1, tree2,
taxon_namespace_scoped=False,
compare_tree_annotations=True,
compare_taxon_annotations=False)
class TestSpecialTreeConstruction(
curated_test_tree.CuratedTestTree,
unittest.TestCase):
def test_construction_from_another_tree_different_label(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
tree1.label = "tree1"
self.assertEqual(tree1.label, "tree1")
tree2 = dendropy.Tree(tree1, label="tree2")
self.assertEqual(tree2.label, "tree2")
self.assertNotEqual(tree1.label, "tree2")
self.assertNotEqual(tree1.label, tree2.label)
def test_construction_from_given_seed_node(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
tree2 = dendropy.Tree(seed_node=tree1.seed_node)
self.assertIs(tree2.seed_node, tree1.seed_node)
def test_construction_from_given_seed_node(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
tree2 = dendropy.Tree(seed_node=tree1.seed_node)
self.assertIs(tree2.seed_node, tree1.seed_node)
self.assertIsNot(tree1.taxon_namespace, tree2.taxon_namespace)
self.assertEqual(len(tree1.taxon_namespace), len(tree2.taxon_namespace))
for taxon1 in tree1.taxon_namespace:
self.assertIn(taxon1, tree2.taxon_namespace)
for taxon2 in tree2.taxon_namespace:
self.assertIn(taxon2, tree1.taxon_namespace)
for nd in tree2:
self.assertIn(nd.taxon, tree2.taxon_namespace)
def test_cloning_construction_with_taxon_namespace(self):
tree1, anodes1, lnodes1, inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
tns = dendropy.TaxonNamespace()
tree2 = dendropy.Tree(tree1, taxon_namespace=tns)
self.assertIs(tree2.taxon_namespace, tns)
self.assertIsNot(tree1.taxon_namespace, tree2.taxon_namespace)
self.assertEqual(len(tree1.taxon_namespace), len(tree2.taxon_namespace))
for nd in tree2:
self.assertIn(nd.taxon, tree2.taxon_namespace)
self.assertNotIn(nd.taxon, tree1.taxon_namespace)
for nd in tree1:
self.assertIn(nd.taxon, tree1.taxon_namespace)
self.assertNotIn(nd.taxon, tree2.taxon_namespace)
if __name__ == "__main__":
unittest.main()
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