def test_adopt(self):
"""Adopt a node!"""
n1 = TreeNode(name='n1')
n2 = TreeNode(name='n2')
n3 = TreeNode(name='n3')
self.simple_t._adopt(n1)
self.simple_t.children[-1]._adopt(n2)
n2._adopt(n3)
# adopt doesn't update .children
self.assertEqual(len(self.simple_t.children), 2)
self.assertIs(n1.parent, self.simple_t)
self.assertIs(n2.parent, self.simple_t.children[-1])
self.assertIs(n3.parent, n2)
def test_gops(self):
"""Basic TreeNode operations should work as expected"""
p = TreeNode()
self.assertEqual(str(p), ';')
p.name = 'abc'
self.assertEqual(str(p), 'abc;')
p.length = 3
self.assertEqual(str(p), 'abc:3;') # don't suppress branch from root
q = TreeNode()
p.append(q)
self.assertEqual(str(p), '()abc:3;')
r = TreeNode()
q.append(r)
self.assertEqual(str(p), '(())abc:3;')
r.name = 'xyz'
self.assertEqual(str(p), '((xyz))abc:3;')
q.length = 2
self.assertEqual(str(p), '((xyz):2)abc:3;')
def test_siblings(self):
"""Get the siblings"""
exp = []
obs = self.simple_t.siblings()
self.assertEqual(obs, exp)
exp = ['i2']
obs = self.simple_t.children[0].siblings()
self.assertEqual([o.name for o in obs], exp)
exp = ['c']
obs = self.simple_t.children[1].children[1].siblings()
self.assertEqual([o.name for o in obs], exp)
self.simple_t.append(TreeNode(name="foo"))
self.simple_t.append(TreeNode(name="bar"))
exp = ['i1', 'foo', 'bar']
obs = self.simple_t.children[1].siblings()
self.assertEqual([o.name for o in obs], exp)
def test_missing_tip_name(self):
"""DndParser should produce the correct tree when missing a name"""
obs = TreeNode.from_newick(missing_tip_name)
exp = TreeNode()
exp.append(TreeNode())
exp.append(TreeNode())
exp.children[0].append(TreeNode(name='a'))
exp.children[0].append(TreeNode(name='b'))
exp.children[1].append(TreeNode(name='c'))
exp.children[1].append(TreeNode())
self.assertEqual(str(obs), str(exp))
def test_nonames(self):
"""DndParser should produce the correct tree when there are no names"""
obs = TreeNode.from_newick(no_names)
exp = TreeNode()
exp.append(TreeNode())
exp.append(TreeNode())
exp.children[0].append(TreeNode())
exp.children[0].append(TreeNode())
exp.children[1].append(TreeNode())
exp.children[1].append(TreeNode())
self.assertEqual(str(obs), str(exp))
def setUp(self):
"""Prep the self"""
self.simple_t = TreeNode.from_newick("((a,b)i1,(c,d)i2)root;")
nodes = dict([(x, TreeNode(x)) for x in 'abcdefgh'])
nodes['a'].append(nodes['b'])
nodes['b'].append(nodes['c'])
nodes['c'].append(nodes['d'])
nodes['c'].append(nodes['e'])
nodes['c'].append(nodes['f'])
nodes['f'].append(nodes['g'])
nodes['a'].append(nodes['h'])
self.TreeNode = nodes
self.TreeRoot = nodes['a']
def test_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = TreeNode.from_newick(minimal)
exp = TreeNode()
exp.append(TreeNode())
self.assertEqual(str(obs), str(exp))
def test_remove(self):
"""Remove nodes"""
self.assertTrue(self.simple_t.remove(self.simple_t.children[0]))
self.assertEqual(len(self.simple_t.children), 1)
n = TreeNode()
self.assertFalse(self.simple_t.remove(n))