def _parse_and_add_from_stream(self,
stream,
schema,
exclude_trees=False,
exclude_chars=False,
**kwargs):
# exclude_trees = kwargs.pop("exclude_trees", False)
# exclude_chars = kwargs.pop("exclude_chars", False)
taxon_namespace = taxonmodel.process_kwargs_dict_for_taxon_namespace(kwargs, None)
if (self.attached_taxon_namespace is not None
and taxon_namespace is not None
and self.attached_taxon_namespace is not taxon_namespace):
raise ValueError("DataSet has attached TaxonNamespace that is not the same as ``taxon_namespace``")
if self.attached_taxon_namespace is not None and taxon_namespace is None:
taxon_namespace = self.attached_taxon_namespace
label = kwargs.pop("label", None)
reader = dataio.get_reader(schema, **kwargs)
n_tns = len(self.taxon_namespaces)
n_tree_lists = len(self.tree_lists)
n_char_matrices = len(self.char_matrices)
reader.read_dataset(
stream=stream,
dataset=self,
taxon_namespace=taxon_namespace,
exclude_trees=exclude_trees,
exclude_chars=exclude_chars,
state_alphabet_factory=charstatemodel.StateAlphabet,
)
n_tns2 = len(self.taxon_namespaces)
n_tree_lists2 = len(self.tree_lists)
n_char_matrices2 = len(self.char_matrices)
return (n_tns2-n_tns,
n_tree_lists2-n_tree_lists,
n_char_matrices2-n_char_matrices)
def _parse_and_create_from_stream(cls,
stream,
schema,
**kwargs):
"""
Constructs a new |DataSet| object and populates it with data
from file-like object ``stream``.
"""
exclude_trees = kwargs.pop("exclude_trees", False)
exclude_chars = kwargs.pop("exclude_chars", False)
taxon_namespace = taxonmodel.process_kwargs_dict_for_taxon_namespace(kwargs, None)
label = kwargs.pop("label", None)
dataset = DataSet(label=label)
if taxon_namespace is not None:
dataset.attached_taxon_namespace = taxon_namespace
reader = dataio.get_reader(schema, **kwargs)
reader.read_dataset(
stream=stream,
dataset=dataset,
taxon_namespace=taxon_namespace,
exclude_trees=exclude_trees,
exclude_chars=exclude_chars,
state_alphabet_factory=charstatemodel.StateAlphabet,
)
return dataset
