def _write(self,
stream,
taxon_namespaces=None,
tree_lists=None,
char_matrices=None,
global_annotations_target=None):
# reset book-keeping
self._taxon_namespaces_to_write = []
self._taxon_namespace_id_map = {}
self._taxon_id_map = {}
self._node_id_map = {}
self._state_alphabet_id_map = {}
self._state_id_map = {}
# Destination:
# Writing to buffer instead of directly to output
# stream so that all namespaces referenced in metadata
# can be written
body = StringIO()
# comments and metadata
self._write_annotations_and_comments(global_annotations_target, body, 1)
# Taxon namespace discovery
candidate_taxon_namespaces = collections.OrderedDict()
if self.attached_taxon_namespace is not None:
candidate_taxon_namespaces[self.attached_taxon_namespace] = True
elif taxon_namespaces is not None:
if self.suppress_unreferenced_taxon_namespaces:
# preload to preserve order
for tns in taxon_namespaces:
candidate_taxon_namespaces[tns] = False
else:
for tns in taxon_namespaces:
candidate_taxon_namespaces[tns] = True
for data_collection in (tree_lists, char_matrices):
if data_collection is not None:
for i in data_collection:
if self.attached_taxon_namespace is None or i.taxon_namespace is self.attached_taxon_namespace:
candidate_taxon_namespaces[i.taxon_namespace] = True
self._taxon_namespaces_to_write = [tns for tns in candidate_taxon_namespaces if candidate_taxon_namespaces[tns]]
for tns in self._taxon_namespaces_to_write:
self._write_taxon_namespace(tns, body)
if char_matrices:
for char_matrix in char_matrices:
self._write_char_matrix(char_matrix=char_matrix, dest=body)
if tree_lists:
for tree_list in tree_lists:
self._write_tree_list(tree_list=tree_list, dest=body)
self._write_to_nexml_open(stream, indent_level=0)
stream.write(body.getvalue())
self._write_to_nexml_close(stream, indent_level=0)
def write_out_validate_equal_and_return(self, writeable, schema, kwargs):
self.maxDiff = None
sio = StringIO()
writeable.write(file=sio, schema=schema, **kwargs)
s0 = sio.getvalue()
s1 = writeable.as_string(schema=schema, **kwargs)
self.assertEqual(s0, s1)
with pathmap.SandboxedFile() as tempf:
writeable.write(path=tempf.name, schema=schema, **kwargs)
tempf.flush()
tempf.close()
with open(tempf.name, "r") as src:
s2 = src.read()
self.assertEqual(s0, s2)
return s0
def write_out_validate_equal_and_return(self, writeable, schema, kwargs):
self.maxDiff = None
sio = StringIO()
writeable.write(file=sio, schema=schema, **kwargs)
s0 = sio.getvalue()
s1 = writeable.as_string(schema=schema, **kwargs)
self.assertEqual(s0, s1)
with pathmap.SandboxedFile() as tempf:
writeable.write(path=tempf.name, schema=schema, **kwargs)
tempf.flush()
tempf.close()
with open(tempf.name, "r") as src:
s2 = src.read()
self.assertEqual(s0, s2)
return s0
def description_text():
from dendropy.utility.textprocessing import StringIO
s = StringIO()
description(s)
return s.getvalue()
def _write(self,
stream,
taxon_namespaces=None,
tree_lists=None,
char_matrices=None,
global_annotations_target=None):
# reset book-keeping
self._taxon_namespaces_to_write = []
self._taxon_namespace_id_map = {}
self._taxon_id_map = {}
self._node_id_map = {}
self._state_alphabet_id_map = {}
self._state_id_map = {}
# Destination:
# Writing to buffer instead of directly to output
# stream so that all namespaces referenced in metadata
# can be written
body = StringIO()
# comments and metadata
self._write_annotations_and_comments(global_annotations_target, body,
1)
# Taxon namespace discovery
candidate_taxon_namespaces = collections.OrderedDict()
if self.attached_taxon_namespace is not None:
candidate_taxon_namespaces[self.attached_taxon_namespace] = True
elif taxon_namespaces is not None:
if self.suppress_unreferenced_taxon_namespaces:
# preload to preserve order
for tns in taxon_namespaces:
candidate_taxon_namespaces[tns] = False
else:
for tns in taxon_namespaces:
candidate_taxon_namespaces[tns] = True
for data_collection in (tree_lists, char_matrices):
if data_collection is not None:
for i in data_collection:
if self.attached_taxon_namespace is None or i.taxon_namespace is self.attached_taxon_namespace:
candidate_taxon_namespaces[i.taxon_namespace] = True
self._taxon_namespaces_to_write = [
tns for tns in candidate_taxon_namespaces
if candidate_taxon_namespaces[tns]
]
for tns in self._taxon_namespaces_to_write:
self._write_taxon_namespace(tns, body)
if char_matrices:
for char_matrix in char_matrices:
self._write_char_matrix(char_matrix=char_matrix, dest=body)
if tree_lists:
for tree_list in tree_lists:
self._write_tree_list(tree_list=tree_list, dest=body)
self._write_to_nexml_open(stream, indent_level=0)
stream.write(body.getvalue())
self._write_to_nexml_close(stream, indent_level=0)
def description_text():
from dendropy.utility.textprocessing import StringIO
s = StringIO()
description(s)
return s.getvalue()