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()
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_to_from_tsk_tree(self):
for n in range(5):
for tree in RankTree.all_labelled_trees(n):
self.assertTrue(tree.is_canonical())
tsk_tree = tree.to_tsk_tree()
reconstructed = RankTree.from_tsk_tree(tsk_tree)
self.assertTrue(tree.is_canonical())
self.assertEqual(tree, reconstructed)
def test_to_from_tsk_tree(self):
for n in range(5):
for tree in RankTree.all_labelled_trees(n):
assert tree.is_canonical()
tsk_tree = tree.to_tsk_tree()
reconstructed = RankTree.from_tsk_tree(tsk_tree)
assert tree.is_canonical()
assert tree == reconstructed
def test_generate_treeseq_roundtrip(self):
n = 5
span = 9
all_rank_trees = RankTree.all_labelled_trees(n)
all_tsk_trees = tskit.all_trees(n, span=span)
for rank_tree, tsk_tree in zip(all_rank_trees, all_tsk_trees):
ts1 = tsk_tree.tree_sequence
ts2 = rank_tree.to_tsk_tree(span=span).tree_sequence
assert ts1.tables.equals(ts2.tables, ignore_provenance=True)
def test_all_labelled_trees_4(self):
expected = [
# 1 + 1 + 1 + 1 (partition of num leaves)
"(0,1,2,3)",
# 1 + 1 + 2
"(0,1,(2,3))",
"(0,2,(1,3))",
"(0,3,(1,2))",
"(1,2,(0,3))",
"(1,3,(0,2))",
"(2,3,(0,1))",
# 1 + 3
# partition of 3 = 1 + 1 + 1
"(0,(1,2,3))",
"(1,(0,2,3))",
"(2,(0,1,3))",
"(3,(0,1,2))",
# partition of 3 = 1 + 2
"(0,(1,(2,3)))",
"(0,(2,(1,3)))",
"(0,(3,(1,2)))",
"(1,(0,(2,3)))",
"(1,(2,(0,3)))",
"(1,(3,(0,2)))",
"(2,(0,(1,3)))",
"(2,(1,(0,3)))",
"(2,(3,(0,1)))",
"(3,(0,(1,2)))",
"(3,(1,(0,2)))",
"(3,(2,(0,1)))",
# 2 + 2
"((0,1),(2,3))",
"((0,2),(1,3))",
"((0,3),(1,2))",
]
actual = [t.newick() for t in RankTree.all_labelled_trees(4)]
self.assertEqual(expected, actual)
def test_generate_trees_roundtrip(self):
n = 5
all_rank_trees = RankTree.all_labelled_trees(n)
all_tsk_trees = tskit.all_trees(n)
for rank_tree, tsk_tree in zip(all_rank_trees, all_tsk_trees):
self.assertEqual(rank_tree, RankTree.from_tsk_tree(tsk_tree))
def test_all_labelled_trees_3(self):
expected = ["(0,1,2)", "(0,(1,2))", "(1,(0,2))", "(2,(0,1))"]
actual = [t.newick() for t in RankTree.all_labelled_trees(3)]
self.assertEqual(expected, actual)
def test_num_labelled_trees(self):
# Number of leaf-labelled trees with n leaves on OEIS
n_trees = [0, 1, 1, 4, 26, 236, 2752, 39208]
for i, expected in zip(range(len(n_trees)), n_trees):
actual = sum(1 for _ in RankTree.all_labelled_trees(i))
self.assertEqual(actual, expected)
