def makeFundamentalParamControllerDefns(self, bin_names):
"""Everything one step short of the psubs, because cogent.align code
needs to handle Q*t itself."""
defns = self.makeParamControllerDefns(bin_names, endAtQd=True)
assert not 'length' in defns
defns['length'] = LengthDefn()
return defns
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