def make_fundamental_param_controller_defns(self, bin_names):
"""Everything one step short of the psubs, because cogent3.align code
needs to handle Q*t itself."""
defns = self.make_param_controller_defns(bin_names, endAtQd=True)
assert "length" not in defns
defns["length"] = LengthDefn()
return defns
def make_distance_defn(self, bprobs):
length = LengthDefn()
if self.with_rate and bprobs is not None:
b_rate = self._make_bin_param_defn("rate", "rate", bprobs)
distance = ProductDefn(length, b_rate, name="distance")
else:
distance = length
return distance