def testCanonicalizeByNumberOfTipsAheadOfName(self):
"""
In forming a canonical tree, child nodes must be sorted by number of
tips in preference to name.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(name='a',
children=[
TreeNode(),
TreeNode(),
TreeNode(),
]),
TreeNode(name='b',
children=[
TreeNode(),
]),
TreeNode(name='c',
children=[
TreeNode(),
TreeNode(),
]),
])
self.assertEqual(
['a', 'b', 'c'],
[child.name for child in njtree.tree.children])
self.assertEqual(
['b', 'c', 'a'],
[child.name for child in njtree.canonicalize().tree.children])
def testCanonicalizeByNameAheadOfNamesOfDescendants(self):
"""
In forming a canonical tree, child nodes must be sorted by name in
preference to the sorted names of all their descendants.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(name='b',
children=[
TreeNode(name='e'),
TreeNode(name='f'),
TreeNode(name='g'),
]),
TreeNode(name='c',
children=[
TreeNode(name='h'),
TreeNode(name='i'),
TreeNode(name='j'),
]),
TreeNode(name='a',
children=[
TreeNode(name='k'),
TreeNode(name='l'),
TreeNode(name='m'),
]),
])
self.assertEqual(
['b', 'c', 'a'],
[child.name for child in njtree.tree.children])
self.assertEqual(
['a', 'b', 'c'],
[child.name for child in njtree.canonicalize().tree.children])
def testCanonicalizeByTipSubset(self):
"""
In forming a canonical tree, child nodes must be sorted by the names of
the set of tips they lead to, if all else is equal.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(children=[
TreeNode(name='d'),
TreeNode(name='e'),
TreeNode(name='f'),
]),
TreeNode(children=[
TreeNode(name='g'),
TreeNode(name='h'),
TreeNode(name='i'),
]),
TreeNode(children=[
TreeNode(name='a'),
TreeNode(name='b'),
TreeNode(name='c'),
]),
])
self.assertEqual(
['d', 'e', 'f', 'g', 'h', 'i', 'a', 'b', 'c'],
[grandchild.name for child in njtree.tree.children
for grandchild in child.children])
self.assertEqual(
['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i'],
[grandchild.name for child in njtree.canonicalize().tree.children
for grandchild in child.children])
def testCanonicalizeByNumberOfTips(self):
"""
In forming a canonical tree, child nodes must be sorted by number
of tips (assuming child lengths are all equal).
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(children=[
TreeNode(),
TreeNode(),
TreeNode(),
]),
TreeNode(children=[
TreeNode(),
TreeNode(),
TreeNode(),
TreeNode(),
TreeNode(),
]),
TreeNode(children=[
TreeNode(),
TreeNode(),
]),
])
self.assertEqual(
[3, 5, 2],
[len(child.children) for child in njtree.tree.children])
self.assertEqual(
[2, 3, 5],
[len(child.children)
for child in njtree.canonicalize().tree.children])
def testCanonicalizeByNodeLength(self):
"""
In forming a canonical tree, child nodes must be sorted by length.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(length=13),
TreeNode(length=11),
TreeNode(length=18),
TreeNode(length=14)])
self.assertEqual(
[13, 11, 18, 14],
[child.length for child in njtree.tree.children])
self.assertEqual(
[11, 13, 14, 18],
[child.length for child in njtree.canonicalize().tree.children])
def testCanonicalizeByNodeName(self):
"""
In forming a canonical tree, child nodes must be sorted by name if node
lengths and number of tips are equal.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(name='c'),
TreeNode(name='d'),
TreeNode(name='b'),
TreeNode(name='a')])
self.assertEqual(
['c', 'd', 'b', 'a'],
[child.name for child in njtree.tree.children])
self.assertEqual(
['a', 'b', 'c', 'd'],
[child.name for child in njtree.canonicalize().tree.children])
def testCanonicalizeByLengthAheadOfNumberOfTips(self):
"""
In forming a canonical tree, child nodes must be sorted by length
in preference to number of tips.
"""
njtree = NJTree()
njtree.tree = TreeNode(children=[
TreeNode(
length=13,
children=[
TreeNode(),
TreeNode(),
TreeNode(),
],
),
TreeNode(
length=11,
children=[
TreeNode(),
TreeNode(),
TreeNode(),
TreeNode(),
],
),
TreeNode(
length=12,
children=[
TreeNode(),
TreeNode(),
],
),
])
self.assertEqual(
[13, 11, 12],
[child.length for child in njtree.tree.children])
self.assertEqual(
[11, 12, 13],
[child.length for child in njtree.canonicalize().tree.children])
