def __init__(self, *args, **kwargs):
"""__init__ calls TaxonSetLinked.__init__ for handling of `oid`, `label` and `taxon_set` keyword arguments.
Can be initialized with:
- source keyword arguments (see Readable.process_source_kwargs), or
- a single unnamed CharacterMatrix instance (which will be deep-copied).
"""
TaxonSetLinked.__init__(
self, taxon_set=kwargs.get("taxon_set", None), label=kwargs.get("label", None), oid=kwargs.get("oid", None)
)
self.taxon_seq_map = CharacterDataMap()
self.character_types = []
self.character_subsets = containers.OrderedCaselessDict()
self.markup_as_sequences = True
if len(args) > 1:
raise error.TooManyArgumentsError(func_name=self.__class__.__name__, max_args=1, args=args)
if len(args) == 1:
if ("stream" in kwargs and kwargs["stream"] is not None) or (
"schema" in kwargs and kwargs["schema"] is not None
):
raise error.MultipleInitializationSourceError(class_name=self.__class__.__name__, arg=args[0])
if isinstance(args[0], self.__class__):
self.clone_from(args[0])
else:
raise error.InvalidArgumentValueError(func_name=self.__class__.__name__, arg=args[0])
else:
self.process_source_kwargs(**kwargs)
if "oid" in kwargs:
self.oid = kwargs["oid"]
if "label" in kwargs:
self.label = kwargs["label"]
def __deepcopy__(self, memo):
o = TaxonSetLinked.__deepcopy__(self, memo)
o.state_alphabets = self.state_alphabets
memo[id(self.state_alphabets)] = o.state_alphabets
o.default_state_alphabet = self.default_state_alphabet
memo[id(self.default_state_alphabet)] = o.default_state_alphabet
o._default_symbol_state_map = self._default_symbol_state_map
memo[id(self._default_symbol_state_map)] = o._default_symbol_state_map
o.character_types = copy.deepcopy(self.character_types, memo)
for taxon, cdv in self.taxon_seq_map.items():
otaxon = memo[id(taxon)]
ocdv = CharacterDataVector(oid=cdv.oid, label=cdv.label, taxon=otaxon)
for cell in cdv:
if cell.character_type is not None:
character_type = memo[id(cell.character_type)]
else:
character_type = None
ocdv.append(CharacterDataCell(value=cell.value, character_type=character_type))
o.taxon_seq_map[otaxon] = ocdv
memo[id(self.taxon_seq_map[taxon])] = o.taxon_seq_map[otaxon]
for k, v in self.__dict__.iteritems():
if k not in [
"taxon_set",
"_oid",
"state_alphabets",
"default_state_alphabet",
"_default_symbol_state_map",
"taxon_seq_map",
"character_types",
]:
o.__dict__[k] = copy.deepcopy(v, memo)
return o
def __deepcopy__(self, memo):
o = TaxonSetLinked.__deepcopy__(self, memo)
for k, v in self.__dict__.iteritems():
if k not in ["taxon_set", "_oid", "taxon_seq_map"]:
o.__dict__[k] = copy.deepcopy(v, memo)
for taxon, cdv in self.taxon_seq_map.items():
otaxon = memo[id(taxon)]
ocdv = CharacterDataVector(oid=cdv.oid, label=cdv.label, taxon=otaxon)
for cell in cdv:
if cell.character_type is not None:
character_type = memo[id(cell.character_type)]
else:
character_type = None
ocdv.append(CharacterDataCell(value=cell.value, character_type=character_type))
o.taxon_seq_map[otaxon] = ocdv
memo[id(self.taxon_seq_map[taxon])] = o.taxon_seq_map[otaxon]
return o