def makeDistanceDefn(self, bprobs):
length = LengthDefn()
if self.with_rate and bprobs is not None:
b_rate = self._makeBinParamDefn('rate', 'rate', bprobs)
distance = ProductDefn(length, b_rate, name="distance")
else:
distance = length
return distance
def makeRateParams(self, bprobs):
params = []
for param_name in self.parameter_order:
if bprobs is None or param_name not in self.partitioned_params:
defn = ParamDefn(param_name)
else:
e_defn = ParamDefn(param_name, dimensions=['edge', 'locus'])
# should be weighted by bprobs*rates not bprobs
b_defn = self._makeBinParamDefn(param_name,
param_name + '_factor', bprobs)
defn = ProductDefn(b_defn, e_defn, name=param_name + '_BE')
params.append(defn)
return params