def test_unique(self):
self.assertEqual(
sorted(
util.unique([
1, 2, 2, 4, 2, 2, 3, 4, 3, 2, 1, 2, 4, 1, 3, 2, 1, 4, 1, 2,
4, 1, 2, 1, 1, 1
])), [1, 2, 3, 4])
self.assertEqual(
util.unique([
1, 2, 2, 4, 2, 2, 3, 4, 3, 2, 1, 2, 4, 1, 3, 2, 1, 4, 1, 2, 4,
1, 2, 1, 1, 1
],
sort=True), [1, 2, 3, 4])
self.assertEqual(
sorted(util.unique([[], [1, 2, 3], [], [1, 2], [1, 2, 3]])),
sorted([[], [1, 2], [1, 2, 3]]))
self.assertEqual(util.unique([]), [])
self.assertEqual(util.unique([], sort=True), [])
def cherry_picking(tree, k):
if tree.is_leaf():
return [tree]
elif tree == Shape.CHERRY:
return [Shape.LEAF]
else:
def go(t, i, d): # for binary eyes only
if d != k and not (t.is_leaf() or t.is_cherry()):
chs = [go(ch, i, d + 1) for ch in t.children]
if any(ch is None for ch in chs):
return None
else:
return PhyloTree(None, sorted(chs))
elif d != k and (t == PhyloTree(
None, [PhyloTree(i), PhyloTree(i + 1)]) or t == PhyloTree(
None,
[PhyloTree(i - 1), PhyloTree(i)])):
return None
elif d == k and (t == PhyloTree(
None, [PhyloTree(i), PhyloTree(i + 1)]) or t == PhyloTree(
None,
[PhyloTree(i - 1), PhyloTree(i)])):
return PhyloTree(i)
elif t == PhyloTree(i):
return None
else:
return t
n = count_leaves(tree)
phyl = shape_to_phylotree(tree, gen=int)
ts = []
for i in range(n):
t = go(phyl, i, 1)
if t:
ts.append(phylotree_to_shape(t))
return unique(sorted(ts))
def min_sackin(n):
"""
Returns all the `Shape` instances that attain the minimum Sackin index with `int` n leaves.
:param n: `int` instance.
:return: `list` instance.
"""
k = log2(n)
nk = 2**k
if n == nk:
return [binary_max_balanced(nk)]
else:
ts = []
for t in min_sackin(n + 1):
ts = ts + cherry_picking(t, k)
return unique(sorted(ts))
def min_colless(n):
"""
Returns all the `Shape` instances that attain the minimum Colless index with `int` n leaves.
:param n: `int` instance.
:return: `list` instance.
"""
if n == 0:
return []
elif n == 1:
return [Shape.LEAF]
elif n == 2:
return [Shape.CHERRY]
else:
tss = []
for n1, n2 in min_colless_root(n):
ts = unique([
Shape(sorted([t1, t2])) for t1 in min_colless(n1)
for t2 in min_colless(n2)
])
tss.extend(ts)
return tss