def test_singlular(self):
"""Clade, Phylogeny: Singular properties for plural attributes."""
conf = PX.Confidence(0.9, "bootstrap")
taxo = PX.Taxonomy(rank="genus")
# Clade.taxonomy, Clade.confidence
clade = PX.Clade(confidences=[conf], taxonomies=[taxo])
self.assertEqual(clade.confidence.type, "bootstrap")
self.assertEqual(clade.taxonomy.rank, "genus")
# raise if len > 1
clade.confidences.append(conf)
self.assertRaises(AttributeError, getattr, clade, "confidence")
clade.taxonomies.append(taxo)
self.assertRaises(AttributeError, getattr, clade, "taxonomy")
# None if []
clade.confidences = []
self.assertEqual(clade.confidence, None)
clade.taxonomies = []
self.assertEqual(clade.taxonomy, None)
# Phylogeny.confidence
tree = PX.Phylogeny(True, confidences=[conf])
self.assertEqual(tree.confidence.type, "bootstrap")
tree.confidences.append(conf)
self.assertRaises(AttributeError, getattr, tree, "confidence")
tree.confidences = []
self.assertEqual(tree.confidence, None)
def _parse_clade(self, parent):
"""Parse a Clade node and its children, recursively (PRIVATE)."""
clade = PX.Clade(**parent.attrib)
if clade.branch_length is not None:
clade.branch_length = float(clade.branch_length)
# NB: Only evaluate nodes at the current level
tag_stack = []
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == "start":
if tag == "clade":
clade.clades.append(self._parse_clade(elem))
continue
if tag == "taxonomy":
clade.taxonomies.append(self._parse_taxonomy(elem))
continue
if tag == "sequence":
clade.sequences.append(self._parse_sequence(elem))
continue
if tag in self._clade_tracked_tags:
tag_stack.append(tag)
if event == "end":
if tag == "clade":
elem.clear()
break
if tag != tag_stack[-1]:
continue
tag_stack.pop()
# Handle the other non-recursive children
if tag in self._clade_list_types:
getattr(clade, self._clade_list_types[tag]).append(
getattr(self, tag)(elem)
)
elif tag in self._clade_complex_types:
setattr(clade, tag, getattr(self, tag)(elem))
elif tag == "branch_length":
# NB: possible collision with the attribute
if clade.branch_length is not None:
raise PhyloXMLError(
"Attribute branch_length was already set for this Clade."
)
clade.branch_length = _float(elem.text)
elif tag == "width":
clade.width = _float(elem.text)
elif tag == "name":
clade.name = _collapse_wspace(elem.text)
elif tag == "node_id":
clade.node_id = PX.Id(
elem.text.strip(), elem.attrib.get("provider")
)
elif namespace != NAMESPACES["phy"]:
clade.other.append(self.other(elem, namespace, tag))
elem.clear()
else:
raise PhyloXMLError("Misidentified tag: " + tag)
return clade
