def runTest(self):
# rooted tree: so clade bitmasks
tree_list = dendropy.TreeList.get_from_stream(
StringIO("""[&R]((t5:0.161175,t6:0.161175):0.392293,((t4:0.104381,(t2:0.075411,t1:0.075411):1):0.065840,t3:0.170221):0.383247);"""),
"newick")
for i in tree_list:
_LOG.debug(i._get_indented_form())
i.encode_bipartitions()
_LOG.debug(i._get_indented_form(splits=True))
i._debug_check_tree(splits=True, logger_obj=_LOG)
root1 = tree_list[0].seed_node
root1e = root1.edge
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask), list(range(6)))
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, one_based=True), list(range(1,7)))
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, fill_bitmask=21, one_based=True), [1, 3, 5])
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, fill_bitmask=21), [0, 2, 4])
self.assertEqual(bitprocessing.num_set_bits(root1e.split_bitmask), 6)
fc1 = root1.child_nodes()[0]
fc1e = fc1.edge
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask), [0, 1])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, one_based=True), [1, 2])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, fill_bitmask=0x15, one_based=True), [1])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, fill_bitmask=0x15), [0])
self.assertEqual(bitprocessing.num_set_bits(fc1e.split_bitmask), 2)
def runTest(self):
# rooted tree: so clade bitmasks
tree_list = dendropy.TreeList.get_from_stream(
StringIO("""[&R]((t5:0.161175,t6:0.161175):0.392293,((t4:0.104381,(t2:0.075411,t1:0.075411):1):0.065840,t3:0.170221):0.383247);"""),
"newick")
for i in tree_list:
_LOG.debug(i._get_indented_form())
i.encode_bipartitions()
_LOG.debug(i._get_indented_form(splits=True))
i._debug_check_tree(splits=True, logger_obj=_LOG)
root1 = tree_list[0].seed_node
root1e = root1.edge
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask), list(range(6)))
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, one_based=True), list(range(1,7)))
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, fill_bitmask=21, one_based=True), [1, 3, 5])
self.assertEqual(bitprocessing.indexes_of_set_bits(root1e.split_bitmask, fill_bitmask=21), [0, 2, 4])
self.assertEqual(bitprocessing.num_set_bits(root1e.split_bitmask), 6)
fc1 = root1.child_nodes()[0]
fc1e = fc1.edge
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask), [0, 1])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, one_based=True), [1, 2])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, fill_bitmask=0x15, one_based=True), [1])
self.assertEqual(bitprocessing.indexes_of_set_bits(fc1e.split_bitmask, fill_bitmask=0x15), [0])
self.assertEqual(bitprocessing.num_set_bits(fc1e.split_bitmask), 2)
def split_to_list(s, mask=-1, one_based=False, ordination_in_mask=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.split_to_list()'.",
old_construct="from dendropy import treesplit\nd = treesplit.split_to_list(...)",
new_construct="from dendropy.utility import bitprocessing\nd = bitprocessing.indexes_of_set_bits(...)")
return bitprocessing.indexes_of_set_bits(
s=s,
fill_bitmask=mask,
one_based=one_based,
ordination_in_mask=ordination_in_mask)
def split_to_list(s, mask=-1, one_based=False, ordination_in_mask=False):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.split_to_list()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.split_to_list(...)",
new_construct=
"from dendropy.utility import bitprocessing\nd = bitprocessing.indexes_of_set_bits(...)"
)
return bitprocessing.indexes_of_set_bits(
s=s,
fill_bitmask=mask,
one_based=one_based,
ordination_in_mask=ordination_in_mask)
