def _send_message(node, **kwargs):
"""
Calc the desired LH distribution of the parent
"""
if node.msg_to_parent.is_delta:
res = Distribution.shifted_x(node.branch_length_interpolator, node.msg_to_parent.peak_pos)
else: # convolve two distributions
res = NodeInterpolator.convolve(node.msg_to_parent,
node.branch_length_interpolator, n_integral=self.n_integral,
rel_tol=self.rel_tol_refine)
self.logger("ClockTree._ml_t_leaves_root._send_message: "
"computed convolution with %d points at node %s"%(len(res.x),node.name),4)
return res
def _set_final_dates(self):
"""
Given the location of the node in branch length units, convert it to the
date-time information.
Args:
- node(Phylo.Clade): tree node. NOTE the node should have the abs_t attribute
to have a valid value. This is automatically taken care of in the
procedure to get the node location probability distribution.
"""
self.logger("ClockTree: Setting dates and node distributions...", 2)
def collapse_func(dist):
if dist.is_delta:
return dist.peak_pos
else:
return dist.peak_pos
for node in self.tree.find_clades(order='preorder'): # ancestors first, msg to children
# set marginal distribution
## This is the root node
if node.up is None:
node.marginal_lh = node.msg_to_parent
elif node.msg_to_parent is None:
node.marginal_lh = node.msg_from_parent
elif node.msg_to_parent.is_delta:
node.marginal_lh = node.msg_to_parent
else:
node.marginal_lh = NodeInterpolator.multiply((node.msg_from_parent, node.msg_to_parent))
if node.up is None:
node.joint_lh = node.msg_to_parent
node.time_before_present = collapse_func(node.joint_lh)
node.branch_length = self.one_mutation
else:
# shift position of parent node (time_before_present) by the branch length
# towards the present. To do so, add branch length to negative time_before_present
# and rescale the resulting distribution by -1.0
res = Distribution.shifted_x(node.branch_length_interpolator, -node.up.time_before_present)
res.x_rescale(-1.0)
# multiply distribution from parent with those from children and determine peak
if node.msg_to_parent is not None:
node.joint_lh = NodeInterpolator.multiply((node.msg_to_parent, res))
else:
node.joint_lh = res
node.time_before_present = collapse_func(node.joint_lh)
node.branch_length = node.up.time_before_present - node.time_before_present
node.clock_length = node.branch_length
