def constrained_consensus_tree_splits(self,
constrainTree=None,
min_freq=constants.GREATER_THAN_HALF,
is_rooted=None,
summarize_splits=True,
fill_bitmask=None,
is_bipartitions_constrain_updated=False,
**split_summarization_kwargs):
"""
Returns a consensus tree from splits in ``self``.
Parameters
----------
constrainTree : Tree to constrain the consensus method
min_freq : real
The minimum frequency of a split in this distribution for it to be
added to the tree.
is_rooted : bool
Should tree be rooted or not? If *all* trees counted for splits are
explicitly rooted or unrooted, then this will default to |True| or
|False|, respectively. Otherwise it defaults to |None|.
fill_bitmask : int
Leafset bitmask of the constraint Tree
\*\*split_summarization_kwargs : keyword arguments
These will be passed directly to the underlying
`SplitDistributionSummarizer` object. See
:meth:`SplitDistributionSummarizer.configure` for options.
Returns
-------
t : consensus tree
"""
assert constrainTree.taxon_namespace is self.taxon_namespace
if is_rooted is None:
if constrainTree.is_rooted & self.is_all_counted_trees_rooted():
is_rooted = True
elif constrainTree.is_unrooted & self.is_all_counted_trees_strictly_unrooted(
):
is_rooted = False
constraintSplits = SplitDistribution(
taxon_namespace=constrainTree.taxon_namespace)
constraintSplits.count_splits_on_tree(
tree=constrainTree,
is_bipartitions_updated=is_bipartitions_constrain_updated,
default_edge_length_value=None)
fill_bitmask = constrainTree.seed_node.edge.bipartition._leafset_bitmask
split_frequencies = self._get_split_frequencies()
to_try_to_add = []
_almost_one = lambda x: abs(x - 1.0) <= 0.0000001
for s in split_frequencies:
freq = split_frequencies[s]
if (min_freq is None) or (freq >= min_freq) or (_almost_one(min_freq)
and _almost_one(freq)):
to_try_to_add.append((freq, s))
to_try_to_add.sort(reverse=True)
##We initiate the list with the constraintSplits
splits_for_tree = [i for i in constraintSplits]
splits_for_tree.extend([i[1] for i in to_try_to_add])
con_tree = Tree.from_split_bitmasks(split_bitmasks=splits_for_tree,
taxon_namespace=self.taxon_namespace,
is_rooted=is_rooted)
if summarize_splits:
self.summarize_splits_on_tree(tree=con_tree,
is_bipartitions_updated=False,
**split_summarization_kwargs)
return con_tree
