def testNormalized1(self):
for i in xrange(0xFF):
s = treesplit.split_as_string(i, 8, ".", "*")[::-1]
r = paup.paup_group_to_mask(s, normalized=True)
normalized = containers.NormalizedBitmaskDict.normalize(i, 0xFF)
self.assertEqual(r, normalized, "%s => %s => %s" \
% (treesplit.split_as_string(i, 8), s, treesplit.split_as_string(normalized, 8)))
def count_splits(self, is_rooted=False):
if self.tree_filepath is None:
_LOG.warning("Null Test Case")
return
p = paup.PaupRunner()
p.stage_execute_file(self.taxa_filepath, clear_trees=True)
p.stage_list_taxa()
p.stage_load_trees(tree_filepaths=[self.tree_filepath], is_rooted=is_rooted)
p.stage_count_splits()
p.run()
taxon_set = p.parse_taxon_set()
tree_count, bipartition_counts = p.parse_group_freqs()
self.assertEqual(self.expected_num_trees, tree_count)
self.assertEqual(len(self.expected_split_freqs), len(bipartition_counts))
for g in self.expected_split_freqs:
self.assertIn(g, bipartition_counts)
self.assertEqual(self.expected_split_freqs[g], bipartition_counts[g])
sd = paup.build_split_distribution(bipartition_counts,
tree_count,
taxon_set,
is_rooted=is_rooted)
sf = sd.split_frequencies
for g in bipartition_counts:
s = paup.paup_group_to_mask(g, normalized=not is_rooted)
self.assertIn(s, sd.splits)
self.assertIn(s, sd.split_counts)
self.assertEqual(sd.split_counts[s], bipartition_counts[g])
self.assertEqual(sd.total_trees_counted, self.expected_num_trees)
self.assertAlmostEqual(sf[s], float(bipartition_counts[g]) / self.expected_num_trees)
def testUnnormalized(self):
for i in xrange(0xFF):
s = treesplit.split_as_string(i, 8, ".", "*")[::-1]
r = paup.paup_group_to_mask(s, normalized=False)
self.assertEqual(r, i, "%s => %s => %s" \
% (treesplit.split_as_string(i, 8), s, treesplit.split_as_string(r, 8)))
def testUnnormalized(self):
for i in xrange(0xFF):
s = treesplit.split_as_string(i, 8, ".", "*")[::-1]
r = paup.paup_group_to_mask(s, normalized=False)
self.assertEqual(r, i, "%s => %s => %s" \
% (treesplit.split_as_string(i, 8), s, treesplit.split_as_string(r, 8)))
