def AddLeafToTree(self, id, diameter):
"""
Add a single leaf to the tree. The position is guided
by the diameter parameter which indicates the precentage
of the maximum possible tree diameter to use.
"""
# Handle the cases where the tree is empty (or a single node)
if len(self.__tree.vertices) == 0:
Leaf(label=id, tree=self.__tree)
elif len(self.__tree.vertices) == 1:
Edge(nodes=[
self.__tree.vertices[0],
Leaf(label=id, tree=self.__tree)
],
tree=self.__tree)
else:
# Find the edges which will (and will not) increase the diameter
(will, willnot) = self.__PartitionEdges()
# if no unmarked edges exist or we want to increase diameter
# randomly select an edge to split
if not len(willnot) or random.random() > (1.0 - diameter):
esplit = random.choice(will)
else:
esplit = random.choice(willnot)
# Add new taxa splitting the edge
self.__SplitEdge(esplit, id)
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 __FindAncestors(self, leaves):
"""
Finds all inner nodes in the path between the leaves.
Leaves not found will be added.
"""
leafIdSet = set(str(l) for l in leaves)
# Find any new leafs
newLeafIds = leafIdSet.difference(self.__tree.leafSet)
assert len(newLeafIds) != len(leafIdSet)
oldLeafIds = leafIdSet - newLeafIds
oldLeafObjs = [l for l in self.__tree.leaves if str(l) in oldLeafIds]
# Only one id, add any nodes to it's parent
if len(oldLeafObjs) == 1:
parent = oldLeafObjs[0].edges[0].Other(oldLeafObjs[0])
newLeafObjs = []
for l in newLeafIds:
leaf = Leaf(edge=Edge(nodes=[parent], tree=self.__tree),
label=l,
tree=self.__tree)
newLeafObjs.append(leaf)
inodes = self.__FindInnerNodes(oldLeafObjs + newLeafObjs)
# Multiple old id's, find the overall path and add to the common node
else:
# Get the paths for the existing (old) leafs
inodes = self.__FindInnerNodes(oldLeafObjs)
assert not len(newLeafIds) or len(inodes) == 1
# Add new nodes to the tree at the inode point
[
Leaf(edge=Edge(nodes=[inodes[0]], tree=self.__tree),
label=l,
tree=self.__tree) for l in newLeafIds
]
return inodes
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)