def test_numTopologyHistories(self):
"""numTopologyHistories"""
tree = treelib.parseNewick("((a,b),(c,d));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 2)
self.assertEqual(numTopologyHistories(tree.root), 2)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("(((a,b),(c,d)),(e,f));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 8)
self.assertEqual(numTopologyHistories(tree.root), 8)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("((((a,b),(c,d)),(e,f)),g);")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 8)
self.assertEqual(numTopologyHistories(tree.root), 8)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("((((a,b),(c,d)),(e,f)),((g,h),i));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 7 * 6 / 2 * 8)
self.assertEqual(numTopologyHistories(tree.root), 7 * 6 / 2 * 8)
spidir.deleteTree(ctree)
def test_numTopologyHistories(self):
"""numTopologyHistories"""
tree = treelib.parseNewick("((a,b),(c,d));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 2)
self.assertEqual(numTopologyHistories(tree.root), 2)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("(((a,b),(c,d)),(e,f));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 8)
self.assertEqual(numTopologyHistories(tree.root), 8)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("((((a,b),(c,d)),(e,f)),g);")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 8)
self.assertEqual(numTopologyHistories(tree.root), 8)
spidir.deleteTree(ctree)
tree = treelib.parseNewick("((((a,b),(c,d)),(e,f)),((g,h),i));")
ctree = spidir.tree2ctree(tree)
self.assertEqual(spidir.numTopologyHistories(ctree), 7*6/2*8)
self.assertEqual(numTopologyHistories(tree.root), 7*6/2*8)
spidir.deleteTree(ctree)
def assert_doom_table(self, tree, l, u, maxdoom):
ctree = spidir.tree2ctree(tree)
ptree, nodes, nodelookup = spidir.make_ptree(tree)
treelib.draw_tree(tree, scale=10)
doomtable = [0] * len(tree.nodes)
doomtable = spidir.c_list(ctypes.c_double, doomtable)
spidir.calcDoomTable(ctree, l, u, maxdoom, doomtable)
spidir.deleteTree(ctree)
doomtable2 = calc_doom_table(tree, l, u, maxdoom)
print list(doomtable)
print doomtable2
for i, j in zip(doomtable, doomtable2):
fequal(i, j)
def assert_doom_table(self, tree, l, u, maxdoom):
ctree = spidir.tree2ctree(tree)
ptree, nodes, nodelookup = spidir.make_ptree(tree)
treelib.draw_tree(tree, scale=10)
doomtable = [0] * len(tree.nodes)
doomtable = spidir.c_list(ctypes.c_double, doomtable)
spidir.calcDoomTable(ctree, l, u, maxdoom, doomtable)
spidir.deleteTree(ctree)
doomtable2 = calc_doom_table(tree, l, u, maxdoom)
print list(doomtable)
print doomtable2
for i, j in zip(doomtable, doomtable2):
fequal(i, j)
def test_make_trees(self):
"""makeTree"""
tree = treelib.parse_newick("((a,b),(c,d));")
ctree = spidir.tree2ctree(tree)
spidir.deleteTree(ctree)
ctree = spidir.ptree2ctree([3,3,4,4,-1])
spidir.deleteTree(ctree)
ctree = spidir.makeTree(5, spidir.c_list(spidir.c_int, [3,3,4,4,-1]))
spidir.deleteTree(ctree)
def test_make_trees(self):
"""makeTree"""
tree = treelib.parse_newick("((a,b),(c,d));")
ctree = spidir.tree2ctree(tree)
spidir.deleteTree(ctree)
ctree = spidir.ptree2ctree([3, 3, 4, 4, -1])
spidir.deleteTree(ctree)
ctree = spidir.makeTree(5, spidir.c_list(spidir.c_int,
[3, 3, 4, 4, -1]))
spidir.deleteTree(ctree)