treeflow.tree.taxon_set module

class treeflow.tree.taxon_set.TaxonSet(taxa: Iterable[str])

Bases: Protocol

Interface representing a taxon set.

A TaxonSet is an ordered set of taxon names, usually associated with the ordered leaves of a phylogenetic tree.

class treeflow.tree.taxon_set.DictTaxonSet(taxa: Iterable[str])

Bases: Dict[str, None]

Taxon set implementation based on the built-in dictionary type.

An TaxonSet is an ordered set of taxon names, usually associated with the ordered leaves of a phylogenetic tree. The dictionary is used as an ordered set - the keys are the taxon names.

clear() → None. Remove all items from D.

copy() → a shallow copy of D

fromkeys(value=None, /): Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /): Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

pop(k[, d]) → v, remove specified key and return the corresponding value.: If the key is not found, return the default if given; otherwise, raise a KeyError.

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None. Update D from mapping/iterable E and F.: If E is present and has a .keys() method, then does: for k in E.keys(): D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D's values

class treeflow.tree.taxon_set.TupleTaxonSet(iterable=(), /)

Bases: Tuple[str, …]

Taxon set implementation based on the built-in tuple type.

An TaxonSet is an ordered set of taxon names, usually associated with the ordered leaves of a phylogenetic tree. This implementation is required for some TensorFlow functionality.

count(value, /): Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.