def getAlignable(self, aligned_positions, ratio=None):
assert ratio is None, "already 2-branched"
children = self.pair.children # alignables
leaves = [c.leaf for c in children]
aligned_positions = [posn for (bin, posn) in aligned_positions]
pog = self.pair.getPOG(aligned_positions)
edge = LikelihoodTreeEdge(leaves, 'parent', pog.getAlignedPositions())
(plhs, gapscores) = self.makePartialLikelihoods(use_cost_function=False)
plh = self.pair.edge2plh(edge, plhs)
assert len(plh) == 1, ('bins!', len(plh))
leaf = edge.asLeaf(plh[0]) # like profile
return AlignablePOG(leaf, pog, children)
def getAlignable(self, aligned_positions, ratio=None):
assert ratio is None, "already 2-branched"
children = self.pair.children # alignables
leaves = [c.leaf for c in children]
aligned_positions = [posn for (bin, posn) in aligned_positions]
pog = self.pair.getPOG(aligned_positions)
edge = LikelihoodTreeEdge(leaves, 'parent', pog.getAlignedPositions())
(plhs, gapscores) = self.makePartialLikelihoods(use_cost_function=False)
plh = self.pair.edge2plh(edge, plhs)
assert len(plh) == 1, ('bins!', len(plh))
leaf = edge.asLeaf(plh[0]) # like profile
return AlignablePOG(leaf, pog, children)
def recursive_lht_build(edge, leaves):
if edge.istip():
lhe = leaves[edge.Name]
else:
lht_children = []
for child in edge.Children:
lht = recursive_lht_build(child, leaves)
lht_children.append(lht)
lhe = LikelihoodTreeEdge(lht_children, edge_name=edge.Name)
return lhe