def test_is_symmetrical(self):
unlabelled_leaf = RankTree(children=[])
assert unlabelled_leaf.is_symmetrical()
three_leaf_asym = RankTree(children=[
unlabelled_leaf,
RankTree(children=[unlabelled_leaf, unlabelled_leaf]),
])
assert not three_leaf_asym.is_symmetrical()
six_leaf_sym = RankTree(children=[three_leaf_asym, three_leaf_asym])
assert six_leaf_sym.is_symmetrical()
def test_is_symmetrical(self):
unlabelled_leaf = RankTree(children=[])
self.assertTrue(unlabelled_leaf.is_symmetrical())
three_leaf_asym = RankTree(children=[
unlabelled_leaf,
RankTree(children=[unlabelled_leaf, unlabelled_leaf]),
])
self.assertFalse(three_leaf_asym.is_symmetrical())
six_leaf_sym = RankTree(children=[three_leaf_asym, three_leaf_asym])
self.assertTrue(six_leaf_sym.is_symmetrical())
def test_add_sibling_topologies_simple(self):
a = RankTree(children=[], label="A")
b = RankTree(children=[], label="B")
ab = RankTree(children=[a, b])
a_counter = comb.TopologyCounter()
a_counter["A"][a.rank()] = 1
self.assertEqual(a_counter, comb.TopologyCounter.from_sample("A"))
b_counter = comb.TopologyCounter()
b_counter["B"][b.rank()] = 1
self.assertEqual(b_counter, comb.TopologyCounter.from_sample("B"))
partial_counter = comb.PartialTopologyCounter()
partial_counter.add_sibling_topologies(a_counter)
partial_counter.add_sibling_topologies(b_counter)
expected = comb.TopologyCounter()
expected["A"][a.rank()] = 1
expected["B"][b.rank()] = 1
expected["A", "B"][ab.rank()] = 1
joined_counter = partial_counter.join_all_combinations()
self.assertEqual(joined_counter, expected)
def test_join_topologies(self):
a = RankTree(children=[], label="A")
b = RankTree(children=[], label="B")
c = RankTree(children=[], label="C")
a_tuple = (("A"), a.rank())
b_tuple = (("B"), b.rank())
c_tuple = (("C"), c.rank())
ab_tuple = (("A", "B"), RankTree(children=[a, b]).rank())
ac_tuple = (("A", "C"), RankTree(children=[a, c]).rank())
bc_tuple = (("B", "C"), RankTree(children=[b, c]).rank())
self.verify_join_topologies((a_tuple, b_tuple), (0, 0))
self.verify_join_topologies((b_tuple, a_tuple), (0, 0))
self.verify_join_topologies((b_tuple, c_tuple), (0, 0))
self.verify_join_topologies((a_tuple, b_tuple, c_tuple), (0, 0))
self.verify_join_topologies((a_tuple, bc_tuple), (1, 0))
self.verify_join_topologies((b_tuple, ac_tuple), (1, 1))
self.verify_join_topologies((c_tuple, ab_tuple), (1, 2))
def test_equal(self):
unlabelled_leaf = RankTree(children=[])
self.assertEqual(unlabelled_leaf, unlabelled_leaf)
self.assertTrue(unlabelled_leaf.shape_equal(unlabelled_leaf))
leaf_zero = RankTree(children=[], label=0)
leaf_one = RankTree(children=[], label=1)
leaf_two = RankTree(children=[], label=2)
self.assertEqual(leaf_zero, leaf_zero)
self.assertNotEqual(leaf_zero, leaf_one)
self.assertTrue(leaf_zero.shape_equal(leaf_one))
tree1 = RankTree(children=[leaf_zero, leaf_one])
self.assertEqual(tree1, tree1)
self.assertNotEqual(tree1, unlabelled_leaf)
self.assertFalse(tree1.shape_equal(unlabelled_leaf))
tree2 = RankTree(children=[leaf_two, leaf_one])
self.assertNotEqual(tree1, tree2)
self.assertTrue(tree1.shape_equal(tree2))
def test_equal(self):
unlabelled_leaf = RankTree(children=[])
assert unlabelled_leaf == unlabelled_leaf
assert unlabelled_leaf.shape_equal(unlabelled_leaf)
leaf_zero = RankTree(children=[], label=0)
leaf_one = RankTree(children=[], label=1)
leaf_two = RankTree(children=[], label=2)
assert leaf_zero == leaf_zero
assert leaf_zero != leaf_one
assert leaf_zero.shape_equal(leaf_one)
tree1 = RankTree(children=[leaf_zero, leaf_one])
assert tree1 == tree1
assert tree1 != unlabelled_leaf
assert not tree1.shape_equal(unlabelled_leaf)
tree2 = RankTree(children=[leaf_two, leaf_one])
assert tree1 != tree2
assert tree1.shape_equal(tree2)
def test_add_sibling_topologies_polytomy(self):
"""
Goes through the topology-merging step at the root
of this tree:
|
|
+----+-----+----+
| | | |
| | | |
| | | +---+
| | | | |
| | | | |
A A B A C
"""
partial_counter = comb.PartialTopologyCounter()
a = RankTree(children=[], label="A")
c = RankTree(children=[], label="C")
ac = RankTree(children=[a, c])
expected = collections.defaultdict(collections.Counter)
a_counter = comb.TopologyCounter.from_sample("A")
b_counter = comb.TopologyCounter.from_sample("B")
ac_counter = comb.TopologyCounter()
ac_counter["A"][a.rank()] = 1
ac_counter["C"][c.rank()] = 1
ac_counter["A", "C"][ac.rank()] = 1
partial_counter.add_sibling_topologies(a_counter)
expected[("A",)] = collections.Counter({((("A",), (0, 0)),): 1})
self.assertEqual(partial_counter.partials, expected)
partial_counter.add_sibling_topologies(a_counter)
expected[("A",)][((("A",), (0, 0)),)] += 1
self.assertEqual(partial_counter.partials, expected)
partial_counter.add_sibling_topologies(b_counter)
expected[("B",)][((("B",), (0, 0)),)] = 1
expected[("A", "B")][((("A",), (0, 0)), (("B",), (0, 0)))] = 2
self.assertEqual(partial_counter.partials, expected)
partial_counter.add_sibling_topologies(ac_counter)
expected[("A",)][((("A",), (0, 0)),)] += 1
expected[("C",)][((("C",), (0, 0)),)] = 1
expected[("A", "B")][((("A",), (0, 0)), (("B",), (0, 0)))] += 1
expected[("A", "C")][((("A",), (0, 0)), (("C",), (0, 0)))] = 2
expected[("A", "C")][((("A", "C"), (0, 0)),)] = 1
expected[("B", "C")][((("B",), (0, 0)), (("C",), (0, 0)))] = 1
expected[("A", "B", "C")][
((("A",), (0, 0)), (("B",), (0, 0)), (("C",), (0, 0)))
] = 2
expected[("A", "B", "C")][((("A", "C"), (0, 0)), (("B",), (0, 0)))] = 1
self.assertEqual(partial_counter.partials, expected)
expected_topologies = comb.TopologyCounter()
expected_topologies["A"][(0, 0)] = 3
expected_topologies["B"][(0, 0)] = 1
expected_topologies["C"][(0, 0)] = 1
expected_topologies["A", "B"][(0, 0)] = 3
expected_topologies["A", "C"][(0, 0)] = 3
expected_topologies["B", "C"][(0, 0)] = 1
expected_topologies["A", "B", "C"][(0, 0)] = 2
expected_topologies["A", "B", "C"][(1, 1)] = 1
joined_topologies = partial_counter.join_all_combinations()
self.assertEqual(joined_topologies, expected_topologies)
def test_is_canonical(self):
for n in range(7):
for tree in RankTree.all_labelled_trees(n):
self.assertTrue(tree.is_canonical())
shape_not_canonical = RankTree(
children=[
RankTree(children=[], label=0),
RankTree(
children=[
RankTree(
children=[
RankTree(children=[], label=1),
RankTree(children=[], label=2),
]
),
RankTree(children=[], label=3),
]
),
]
)
self.assertFalse(shape_not_canonical.is_canonical())
labels_not_canonical = RankTree(
children=[
RankTree(children=[], label=0),
RankTree(
children=[
RankTree(
children=[
RankTree(children=[], label=2),
RankTree(children=[], label=3),
]
),
RankTree(
children=[
RankTree(children=[], label=1),
RankTree(children=[], label=4),
]
),
]
),
]
)
self.assertFalse(labels_not_canonical.is_canonical())
def test_is_canonical(self):
for n in range(7):
for tree in RankTree.all_labelled_trees(n):
assert tree.is_canonical()
shape_not_canonical = RankTree(children=[
RankTree(children=[], label=0),
RankTree(children=[
RankTree(children=[
RankTree(children=[], label=1),
RankTree(children=[], label=2),
]),
RankTree(children=[], label=3),
]),
])
assert not shape_not_canonical.is_canonical()
labels_not_canonical = RankTree(children=[
RankTree(children=[], label=0),
RankTree(children=[
RankTree(children=[
RankTree(children=[], label=2),
RankTree(children=[], label=3),
]),
RankTree(children=[
RankTree(children=[], label=1),
RankTree(children=[], label=4),
]),
]),
])
assert not labels_not_canonical.is_canonical()