def __TreeFromBipartition(self, bp):
"""Generate an initial non-binary tree from a bipartition"""
e = Edge(tree=self.__tree)
left = Inner(edges=[e], tree=self.__tree)
right = Inner(edges=[e], tree=self.__tree)
[
Edge(nodes=[Leaf(label=str(leaf), tree=self.__tree), left],
tree=self.__tree) for leaf in bp.left
]
[
Edge(nodes=[Leaf(label=str(leaf), tree=self.__tree), right],
tree=self.__tree) for leaf in bp.right
]
def __AddNewEdge(self, smallerLeafIds, commonAncestorNodes):
"""Add a new edge to one of the common ancestor nodes"""
# For each common ancestor find the subtrees containing
# members of the smaller set.
edgesToMove = []
for ancestorNode in commonAncestorNodes:
for downEdge in ancestorNode.edges:
childNode = downEdge.Other(ancestorNode)
if childNode not in commonAncestorNodes:
childLeafIds = set(
str(l) for l in childNode.Leaves(downEdge))
if len(childLeafIds.intersection(smallerLeafIds)):
edgesToMove.append((downEdge, ancestorNode))
# Disconnect the subtrees from their common ancestors
[edgeTuple[1].RemoveEdge(edgeTuple[0]) for edgeTuple in edgesToMove]
# Find the new position for the edges looking for a node with the smallest number
# of edges
oldInner = min(commonAncestorNodes, key=lambda e: len(e.edges))
newInner = Inner(edges=[e[0] for e in edgesToMove], tree=self.__tree)
Edge(nodes=[newInner, oldInner], tree=self.__tree)
# If any of the ancestor nodes now only have two edges, condense them out
[
self.__CondenseNode(n) for n in commonAncestorNodes
if len(n.edges) == 2
]
def MakeBinary(self):
"""Convert vertices of degree >3 to degree 3 by breaking off pairs of edges"""
# Loop through the non-binary vertices
for nbv in (v for v in self.__tree.vertices if len(v.edges) > 3):
# Split off pair of edges until the vertex is properly binary
while len(nbv.edges) > 3:
depths = sorted(((e.Depth(nbv), e) for e in nbv.edges),
key=itemgetter(0))
e1 = depths[0][1]
e2 = depths[1][1]
e1.RemoveNode(nbv)
e2.RemoveNode(nbv)
Edge(nodes=[nbv, Inner(edges=[e1, e2], tree=self.__tree)],
tree=self.__tree)
def __SplitEdge(self, edge, id):
"""
Add a new taxa by splitting an existing edge
"""
# Disconnect the edge
nright = edge.nodes[0]
nleft = edge.nodes[1]
nright.RemoveEdge(edge)
nleft.RemoveEdge(edge)
# Connect it all up
Leaf(label=id, edge=edge, tree=self.__tree)
Inner(edges=[
Edge(nodes=[nleft], tree=self.__tree),
Edge(nodes=[nright], tree=self.__tree), edge
],
tree=self.__tree)