def test_ops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), "()")
p.Data = "abc"
self.assertEqual(str(p), "()abc")
p.BranchLength = 3
self.assertEqual(str(p), "()abc") # suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), "(None)abc")
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), "((None))abc")
r.Data = "xyz"
self.assertEqual(str(p), "((xyz))abc")
q.BranchLength = 2
self.assertEqual(str(p), "((xyz):2)abc")
def setUp(self):
"""creates inputs"""
#create a list of PhyloNode objects
a = PhyloNode()
a.Data = 'a'
b = PhyloNode()
b.Data = 'b'
c = PhyloNode()
c.Data = 'c'
d = PhyloNode()
d.Data = 'd'
e = PhyloNode()
e.Data = 'e'
self.node_order = [a, b, c, d, e]
#create a Numeric matrix object to cluster
self.matrix = array(([9999999, 1, 4, 20, 22], \
[1, 9999999, 5, 21, 23], \
[4, 5, 9999999, 10, 12], \
[20, 21, 10, 9999999, 2], \
[22, 23, 12, 2, 9999999]), Float)
