def extend(t, P, Q):
n = len(t)
s = canonical_newick_string(t.write(format=9))
# 1: add the leaf to an external arc
# P[m+1] = factor(((1-a)/(m-a))*P[m])
leaves = [node for node in t]
for node in leaves:
x = node.add_child(name=node.name)
y = node.add_child(name=n + 1)
z = t.copy()
# print "case 1", s, z.write(format=9)
Q[canonical_newick_string(z.write(format=9))] = factor(
((1 - a) / (n - a)) * P[s])
x.detach()
y.detach()
# 2: add the leaf to an internal arc
# P[m+1] = factor((g/(m-a))*P[m])
internal = [node for node in t.iter_descendants() if not node.is_leaf()]
for node in internal:
node.add_features(name="internal")
x = t.copy("deepcopy")
node.del_feature("name")
y = x.search_nodes(name="internal")[0]
parent = y.up
old = y.detach()
new = Tree()
new.add_child(old)
new.add_child(name=n + 1)
parent.add_child(new)
# print "case 2", s, x.write(format=9)
Q[canonical_newick_string(x.write(format=9))] = factor(
(g / (n - a)) * P[s])
# 3: add the leaf to a new root
# P[m+1] = factor(g/(m-a)*P[m])
x = t.copy()
y = Tree()
y.add_child(x)
y.add_child(name=n + 1)
# print "case 3", s, y.write(format=9)
Q[canonical_newick_string(y.write(format=9))] = factor(g / (n - a) * P[s])
# 4: add the leaf to the root
# P[m+1] = factor(((len(t.children)-1)*a-g)/(m-a)*P[m])
if not t.is_leaf():
x = t.copy()
x.add_child(name=n + 1)
# print "case 4r", s, x.write(format=9)
Q[canonical_newick_string(x.write(format=9))] = factor(
((len(t.children) - 1) * a - g) / (n - a) * P[s])
# 4: add the leaf to an internal node
# P[m+1] = factor(((len(node.children)-1)*a-g)/(m-a)*P[m])
for node in t.iter_descendants():
if not node.is_leaf():
y = node.add_child(name=n + 1)
# print "case 4i", s, t.write(format=9)
Q[canonical_newick_string(t.write(format=9))] = factor(
((len(node.children) - 2) * a - g) / (n - a) * P[s])
y.detach()
def generate(taxa):
if len(taxa) == 3:
return [Tree('(' + ','.join(taxa) + ');')]
else:
res = []
sister = Tree('(' + taxa[-1] + ');')
for tree in generate(taxa[:-1]):
for node in tree.traverse('preorder'):
if not node.is_root():
node.up.add_child(sister)
node.detach()
sister.add_child(node)
res.append(copy.deepcopy(tree))
node.detach()
sister.up.add_child(node)
sister.detach()
return res
