def _do_test(self, content, expected):
e = [
deepcopy(i) for i in NewickEventFactory(tokenizer=NewickTokenizer(
stream=StringIO(content)))
]
# print(e)
self.assertEqual(e, expected)
def testOddQuotes(self):
content = "((h_ ,'p)h p,g()[],:_)hpg;"
tok = NewickTokenizer(StringIO(content))
content = "((h_ ,'p')h p,'g()[]',:_')hpg;"
tok = NewickTokenizer(StringIO(content))
self.assertRaises(Exception, tok.tokens)
def _do_test(self, content, expected):
self.assertEqual([i for i in NewickTokenizer(StringIO(content))],
expected)
def pretty_dict_str(d, indent=2):
"""shows JSON indented representation of d"""
b = StringIO()
write_pretty_dict_str(b, d, indent=indent)
return b.getvalue()
def _do_full_check_of_tree_invariants(tree, testCase, id2par=None, leaf_ids=None):
post_order = [nd for nd in tree.postorder_node_iter()]
post_order_ids = []
psio = set()
for node in post_order:
i = node._id
testCase.assertNotIn(i, psio)
testCase.assertIn(i, tree._id2node)
psio.add(i)
post_order_ids.append(i)
pre_order = [nd for nd in tree.preorder_node_iter()]
pre_order_ids = []
prsio = set()
for node in pre_order:
i = node._id
prsio.add(i)
pre_order_ids.append(i)
testCase.assertEqual(psio, prsio)
for i in tree._id2node.keys():
testCase.assertIn(i, psio)
if leaf_ids is None:
leaf_ids = [i for i in tree.leaf_id_iter()]
for i in leaf_ids:
testCase.assertIn(i, tree._leaves)
if not id2par:
for l in leaf_ids:
testCase.assertTrue(l in psio)
for node in post_order:
if node.is_leaf:
testCase.assertIn(node._id, leaf_ids)
else:
#_LOG.debug(node._children)
testCase.assertNotIn(node._id, leaf_ids)
else:
anc_ref_count = {}
anc_set = set()
checked_node = set()
#_LOG.debug('post_order_ids = {}'.format(post_order_ids))
for t in leaf_ids:
anc_id = id2par[t]
#_LOG.debug('anc_id = {}'.format(anc_id))
anc_ref_count[anc_id] = 1 + anc_ref_count.get(anc_id, 0)
if anc_ref_count[anc_id] > 1:
anc_set.add(anc_id)
testCase.assertTrue(tree.find_node(t).is_leaf)
testCase.assertIn(t, post_order_ids)
if (anc_id in tree._id2node) and (anc_id == tree.find_node(anc_id)._id):
testCase.assertIn(anc_id, post_order_ids)
testCase.assertLess(post_order_ids.index(t), post_order_ids.index(anc_id))
testCase.assertGreater(pre_order_ids.index(t), pre_order_ids.index(anc_id))
else:
testCase.assertNotIn(anc_id, psio)
checked_node.add(t)
while len(anc_set - checked_node) > 0:
ns = set()
for t in anc_set:
if t in checked_node:
continue
testCase.assertNotIn(t, leaf_ids)
testCase.assertFalse(tree.find_node(t).is_leaf)
anc_id = id2par[t]
#_LOG.debug('anc_id = {}'.format(anc_id))
anc_ref_count[anc_id] = 1 + anc_ref_count.get(anc_id, 0)
if anc_ref_count[anc_id] > 1:
ns.add(anc_id)
testCase.assertIn(t, psio)
checked_node.add(t)
if anc_id is not None:
if (anc_id in tree._id2node) and (anc_id == tree.find_node(anc_id)._id):
testCase.assertIn(anc_id, psio)
testCase.assertLess(post_order_ids.index(t), post_order_ids.index(anc_id))
testCase.assertGreater(pre_order_ids.index(t), pre_order_ids.index(anc_id))
else:
testCase.assertNotIn(anc_id, psio)
anc_set.update(ns)
#_LOG.debug('anc_set = {}'.format(anc_set))
#_LOG.debug('checked_node = {}'.format(checked_node))
if len(tree._id2node) > 1:
from peyotl.utility.str_util import StringIO
o = StringIO()
tree.write_newick(o)
from peyotl.utility.tokenizer import NewickEventFactory
nef = NewickEventFactory(newick=o.getvalue())
ptree = TreeWithPathsInEdges(newick_events=nef)
def _do_full_check_of_tree_invariants(tree, testCase, id2par=None, leaf_ids=None):
post_order = [nd for nd in tree.postorder_node_iter()]
post_order_ids = []
psio = set()
for node in post_order:
i = node._id
testCase.assertNotIn(i, psio)
testCase.assertIn(i, tree._id2node)
psio.add(i)
post_order_ids.append(i)
pre_order = [nd for nd in tree.preorder_node_iter()]
pre_order_ids = []
prsio = set()
for node in pre_order:
i = node._id
prsio.add(i)
pre_order_ids.append(i)
testCase.assertEqual(psio, prsio)
for i in tree._id2node.keys():
testCase.assertIn(i, psio)
if leaf_ids is None:
leaf_ids = [i for i in tree.leaf_id_iter()]
for i in leaf_ids:
testCase.assertIn(i, tree._leaves)
if not id2par:
for l in leaf_ids:
testCase.assertTrue(l in psio)
for node in post_order:
if node.is_leaf:
testCase.assertIn(node._id, leaf_ids)
else:
# _LOG.debug(node._children)
testCase.assertNotIn(node._id, leaf_ids)
else:
anc_ref_count = {}
anc_set = set()
checked_node = set()
# _LOG.debug('post_order_ids = {}'.format(post_order_ids))
for t in leaf_ids:
anc_id = id2par[t]
# _LOG.debug('anc_id = {}'.format(anc_id))
anc_ref_count[anc_id] = 1 + anc_ref_count.get(anc_id, 0)
if anc_ref_count[anc_id] > 1:
anc_set.add(anc_id)
testCase.assertTrue(tree.find_node(t).is_leaf)
testCase.assertIn(t, post_order_ids)
if (anc_id in tree._id2node) and (anc_id == tree.find_node(anc_id)._id):
testCase.assertIn(anc_id, post_order_ids)
testCase.assertLess(post_order_ids.index(t), post_order_ids.index(anc_id))
testCase.assertGreater(pre_order_ids.index(t), pre_order_ids.index(anc_id))
else:
testCase.assertNotIn(anc_id, psio)
checked_node.add(t)
while len(anc_set - checked_node) > 0:
ns = set()
for t in anc_set:
if t in checked_node:
continue
testCase.assertNotIn(t, leaf_ids)
testCase.assertFalse(tree.find_node(t).is_leaf)
anc_id = id2par[t]
# _LOG.debug('anc_id = {}'.format(anc_id))
anc_ref_count[anc_id] = 1 + anc_ref_count.get(anc_id, 0)
if anc_ref_count[anc_id] > 1:
ns.add(anc_id)
testCase.assertIn(t, psio)
checked_node.add(t)
if anc_id is not None:
if (anc_id in tree._id2node) and (anc_id == tree.find_node(anc_id)._id):
testCase.assertIn(anc_id, psio)
testCase.assertLess(post_order_ids.index(t), post_order_ids.index(anc_id))
testCase.assertGreater(pre_order_ids.index(t), pre_order_ids.index(anc_id))
else:
testCase.assertNotIn(anc_id, psio)
anc_set.update(ns)
# _LOG.debug('anc_set = {}'.format(anc_set))
# _LOG.debug('checked_node = {}'.format(checked_node))
if len(tree._id2node) > 1:
from peyotl.utility.str_util import StringIO
o = StringIO()
tree.write_newick(o)
from peyotl.utility.tokenizer import NewickEventFactory
nef = NewickEventFactory(newick=o.getvalue())
TreeWithPathsInEdges(newick_events=nef)
def __str__(self):
out = StringIO()
for name, sep in self.separators.items():
out.write('top-level name={}\n'.format(name))
sep.write_str(out)
return out.getvalue()
def __str__(self):
out = StringIO()
self.write_str(out)
return out.getvalue()
