def __init__(self, *args, **kwargs):
"""
__init__ takes a new `DataSet` object from another DataSet object or by
parsing an input stream.
Can be invoked with:
- a single unnamed argument that is an instance of a DataSet (which will result in a deep copy of all taxa, trees and characters),
- 1 or more unnamed TaxonSet, TreeList or CharacterMatrix (which is like calling DataSet.add with each argument)
- keyword arguments that supply a file-like object (`stream`) to be parsed and a string (`schema`) specifying the schema of the data in the file-like object.
"""
AnnotatedDataObject.__init__(self,
label=kwargs.get('label'),
oid=kwargs.get('oid'))
iosys.Writeable.__init__(self)
iosys.Readable.__init__(self)
self.taxon_sets = containers.OrderedSet()
self.tree_lists = containers.OrderedSet()
self.char_matrices = containers.OrderedSet()
self.attached_taxon_set = None
taxon_set, attach_taxon_set = self.process_taxon_set_directives(
**kwargs)
stream = kwargs.get("stream")
if len(args) > 0:
if (stream is not None) or (kwargs.get("schema") is not None):
raise error.MultipleInitializationSourceError(
self.__class__.__name__, args[0])
if len(args) == 1 and isinstance(args[0], DataSet):
if attach_taxon_set or (taxon_set is not None):
raise error.MultipleInitializationSourceError(
"Cannot initialize DataSet from another DataSet object when taxon_set or attach_taxon_set are specified"
)
self.clone_from(args[0])
else:
for arg in args:
if isinstance(arg, DataSet):
raise error.MultipleInitializationSourceError(
"Cannot initialize DataSet from another DataSet object when multiple other initialization objects are given"
)
else:
self.add(arg)
elif stream is not None:
# if self.attached_taxon_set is not None:
# kwargs["taxon_set"] = self.attached_taxon_set
self.process_source_kwargs(**kwargs)
def __init__(self, *args, **kwargs):
"""
__init__ takes a new `DataSet` object from another DataSet object or by
parsing an input stream.
Can be invoked with:
- a single unnamed argument that is an instance of a DataSet (which will result in a deep copy of all taxa, trees and characters),
- 1 or more unnamed TaxonSet, TreeList or CharacterMatrix (which is like calling DataSet.add with each argument)
- keyword arguments that supply a file-like object (`stream`) to be parsed and a string (`schema`) specifying the schema of the data in the file-like object.
"""
AnnotatedDataObject.__init__(self, label=kwargs.get('label'), oid=kwargs.get('oid'))
iosys.Writeable.__init__(self)
iosys.Readable.__init__(self)
self.taxon_sets = containers.OrderedSet()
self.tree_lists = containers.OrderedSet()
self.char_matrices = containers.OrderedSet()
self.attached_taxon_set = None
taxon_set, attach_taxon_set = self.process_taxon_set_directives(**kwargs)
stream = kwargs.get("stream")
if len(args) > 0:
if (stream is not None) or (kwargs.get("schema") is not None):
raise error.MultipleInitializationSourceError(self.__class__.__name__, args[0])
if len(args) == 1 and isinstance(args[0], DataSet):
if attach_taxon_set or (taxon_set is not None):
raise error.MultipleInitializationSourceError("Cannot initialize DataSet from another DataSet object when taxon_set or attach_taxon_set are specified")
self.clone_from(args[0])
else:
for arg in args:
if isinstance(arg, DataSet):
raise error.MultipleInitializationSourceError("Cannot initialize DataSet from another DataSet object when multiple other initialization objects are given")
else:
self.add(arg)
elif stream is not None:
# if self.attached_taxon_set is not None:
# kwargs["taxon_set"] = self.attached_taxon_set
self.process_source_kwargs(**kwargs)
def __deepcopy__(self, memo):
taxon_sets = []
for ts0 in self.taxon_sets:
ts1 = TaxonSet(label=ts0.label)
memo[id(ts0)] = ts1
taxon_sets.append(ts1)
for t in ts0:
taxon = ts1.new_taxon(label=t.label)
memo[id(t)] = taxon
memo[id(self.taxon_sets)] = taxon_sets
o = AnnotatedDataObject.__deepcopy__(self, memo)
memo[id(self)] = o
o.taxon_sets = taxon_sets
assert o.annotations.target is o
return o
def __deepcopy__(self, memo):
taxon_sets = []
for ts0 in self.taxon_sets:
ts1 = TaxonSet(label=ts0.label)
memo[id(ts0)] = ts1
taxon_sets.append(ts1)
for t in ts0:
taxon = ts1.new_taxon(label=t.label)
memo[id(t)] = taxon
memo[id(self.taxon_sets)] = taxon_sets
o = AnnotatedDataObject.__deepcopy__(self, memo)
memo[id(self)] = o
o.taxon_sets = taxon_sets
assert o.annotations.target is o
return o
