def _do_test_longest(self, t, level="1"):
if t.n_leaves < 3:
return
before_br_len = [
e.length for e in t._tree.preorder_edge_iter() if e.length
]
_LOG.debug("code=%s\n before = %s" % (level, t.compose_newick()))
_LOG.debug(" after len(before_br_len) = %d" % (len(before_br_len)))
num_real_edges_before = len(before_br_len)
if len(t._tree.seed_node.child_nodes()) < 3:
num_real_edges_before -= 1
t1, t2 = bisect_tree(t, 'longest')
after_1_br_len = [
e.length for e in t1._tree.preorder_edge_iter() if e.length
]
after_2_br_len = [
e.length for e in t2._tree.preorder_edge_iter() if e.length
]
num_branches_1 = len(after_1_br_len)
num_branches_2 = len(after_2_br_len)
if num_branches_2 == 0:
num_branches_2 = 1
if num_branches_1 == 0:
num_branches_1 = 1
expected_diff = 3
if num_branches_2 == 1:
expected_diff -= 2
if num_branches_1 == 1:
expected_diff -= 2
# cherries are rooted, so they make 1 edge look like 2
if len(t1._tree.seed_node.child_nodes()) == 2:
num_branches_1 -= 1
if len(t2._tree.seed_node.child_nodes()) == 2:
num_branches_2 -= 1
_LOG.debug(" after 1 = %s" % (t1.compose_newick()))
_LOG.debug(" after num_branches_1 = %d" % (num_branches_1))
_LOG.debug(" after 2 = %s" % (t2.compose_newick()))
_LOG.debug(" after num_branches_2 = %d" % (num_branches_2))
#self.assertEqual(len(before_br_len), expected_diff + num_branches_1 + num_branches_2)
before_br_len.sort(reverse=True)
before_br_len.pop(0)
before_sum = sum(before_br_len)
after_sum = sum(after_1_br_len) + sum(after_2_br_len)
diff = before_sum - after_sum
self.assertTrue(abs(diff) < TOL)
if t1.n_leaves > 2:
nl = level + ".1"
self._do_test_longest(t1, level=nl)
if t2.n_leaves > 2:
nl = level + ".2"
self._do_test_longest(t2, level=nl)
def _do_test_longest(self, t, level="1"):
if t.n_leaves < 3:
return
before_br_len = [e.length for e in t._tree.preorder_edge_iter() if e.length]
_LOG.debug("code=%s\n before = %s" % (level, t.compose_newick()))
_LOG.debug(" after len(before_br_len) = %d" % (len(before_br_len)))
num_real_edges_before = len(before_br_len)
if len(t._tree.seed_node.child_nodes()) < 3:
num_real_edges_before -= 1
t1, t2 = bisect_tree(t, 'longest')
after_1_br_len = [e.length for e in t1._tree.preorder_edge_iter() if e.length]
after_2_br_len = [e.length for e in t2._tree.preorder_edge_iter() if e.length]
num_branches_1 = len(after_1_br_len)
num_branches_2 = len(after_2_br_len)
if num_branches_2 == 0:
num_branches_2 = 1
if num_branches_1 == 0:
num_branches_1 = 1
expected_diff = 3
if num_branches_2 == 1:
expected_diff -= 2
if num_branches_1 == 1:
expected_diff -= 2
# cherries are rooted, so they make 1 edge look like 2
if len(t1._tree.seed_node.child_nodes()) == 2:
num_branches_1 -= 1
if len(t2._tree.seed_node.child_nodes()) == 2:
num_branches_2 -= 1
_LOG.debug(" after 1 = %s" % (t1.compose_newick()))
_LOG.debug(" after num_branches_1 = %d" % (num_branches_1))
_LOG.debug(" after 2 = %s" % (t2.compose_newick()))
_LOG.debug(" after num_branches_2 = %d" % (num_branches_2))
#self.assertEqual(len(before_br_len), expected_diff + num_branches_1 + num_branches_2)
before_br_len.sort(reverse=True)
before_br_len.pop(0)
before_sum = sum(before_br_len)
after_sum = sum(after_1_br_len) + sum(after_2_br_len)
diff = before_sum - after_sum
self.assertTrue(abs(diff) < TOL)
if t1.n_leaves > 2:
nl = level+ ".1"
self._do_test_longest(t1, level=nl)
if t2.n_leaves > 2:
nl = level+ ".2"
self._do_test_longest(t2, level=nl)
def _do_test_centroid(self, t, level="1"):
if t.n_leaves < 5:
return
t.calc_splits()
t1, t2 = bisect_tree(t, 'centroid')
assert t1.n_leaves + t2.n_leaves == t.n_leaves
# indent = level.count(".")
# print("==============\nInput tree has %s leaf nodes." % t.n_leaves)
# print("Subtree 1 tree has %s leaf nodes." % t1.n_leaves)
# print("Subtree 2 tree has %s leaf nodes." % t2.n_leaves)
# print("==============\n")
if t1.n_leaves > 2:
nl = level + ".1"
self._do_test_centroid(t1, level=nl)
if t2.n_leaves > 2:
nl = level + ".2"
self._do_test_centroid(t2, level=nl)
def _do_test_centroid(self, t, level="1"):
if t.n_leaves < 5:
return
t.calc_splits()
t1, t2 = bisect_tree(t, 'centroid')
assert t1.n_leaves + t2.n_leaves == t.n_leaves
# indent = level.count(".")
# print("==============\nInput tree has %s leaf nodes." % t.n_leaves)
# print("Subtree 1 tree has %s leaf nodes." % t1.n_leaves)
# print("Subtree 2 tree has %s leaf nodes." % t2.n_leaves)
# print("==============\n")
if t1.n_leaves > 2:
nl = level+ ".1"
self._do_test_centroid(t1, level=nl)
if t2.n_leaves > 2:
nl = level+ ".2"
self._do_test_centroid(t2, level=nl)