def test_nj_dm1(self):
self.assertEqual(nj(self.dm1, result_constructor=str),
self.expected1_str)
# what is the correct way to compare TreeNode objects for equality?
actual_TreeNode = nj(self.dm1)
self.assertEqual(actual_TreeNode.compare_tip_distances(
self.expected1_TreeNode), 0.0)
def test_nj_dm1(self):
self.assertEqual(nj(self.dm1, result_constructor=str),
self.expected1_str)
# what is the correct way to compare TreeNode objects for equality?
actual_TreeNode = nj(self.dm1)
self.assertEqual(
actual_TreeNode.compare_tip_distances(self.expected1_TreeNode),
0.0)
def test_nj_zero_branch_length(self):
# no nodes have negative branch length when we disallow negative
# branch length. self is excluded as branch length is None
tree = nj(self.dm4)
for n in tree.postorder(include_self=False):
self.assertTrue(n.length >= 0)
# only tips associated with the large distance in the input
# have positive branch lengths when we allow negative branch
# length
tree = nj(self.dm4, False)
self.assertTrue(tree.find("a").length > 0)
self.assertTrue(tree.find("b").length < 0)
self.assertTrue(tree.find("c").length < 0)
self.assertTrue(tree.find("d").length < 0)
self.assertTrue(tree.find("e").length > 0)
def test_nj_trivial(self):
data = [[0, 3, 2],
[3, 0, 3],
[2, 3, 0]]
dm = DistanceMatrix(data, list('abc'))
expected_str = "(b:2.000000, a:1.000000, c:1.000000);"
self.assertEqual(nj(dm, result_constructor=str), expected_str)
def test_nj_dm3(self):
actual_TreeNode = nj(self.dm3)
self.assertAlmostEqual(actual_TreeNode.compare_tip_distances(self.expected3_TreeNode), 0.0)
def test_nj_trivial(self):
data = [[0, 3, 2], [3, 0, 3], [2, 3, 0]]
dm = DistanceMatrix(data, list('abc'))
expected_str = "(b:2.000000, a:1.000000, c:1.000000);"
self.assertEqual(nj(dm, result_constructor=str), expected_str)
def test_nj_dm3(self):
actual_TreeNode = nj(self.dm3)
self.assertAlmostEqual(
actual_TreeNode.compare_tip_distances(self.expected3_TreeNode),
0.0)