def test_missing_tip_name(self):
"""DndParser should produce the correct tree when missing a name"""
obs = DndParser(missing_tip_name)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.children[0].append(PhyloNode(name="a"))
exp.children[0].append(PhyloNode(name="b"))
exp.children[1].append(PhyloNode(name="c"))
exp.children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_nonames(self):
"""DndParser should produce the correct tree when there are no names"""
obs = DndParser(no_names)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.children[0].append(PhyloNode())
exp.children[0].append(PhyloNode())
exp.children[1].append(PhyloNode())
exp.children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_gops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
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 = PhyloNode()
p.append(q)
self.assertEqual(str(p), "()abc:3;")
r = PhyloNode()
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_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = DndParser(minimal)
exp = PhyloNode()
exp.append(PhyloNode())
self.assertEqual(str(obs), str(exp))