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src/c/o/cogent-1.5.3/cogent/evolve/substitution_model.py   cogent(Download)
from cogent.core import moltype
from cogent.evolve import parameter_controller, predicate, motif_prob_model
from cogent.evolve.substitution_calculation import (
    SubstitutionParameterDefn as ParamDefn, 
    RateDefn, LengthDefn, ProductDefn, CallDefn, CalcDefn,
        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")

src/p/y/pycogent-HEAD/cogent/evolve/substitution_model.py   pycogent(Download)
from cogent.core import moltype
from cogent.evolve import parameter_controller, predicate, motif_prob_model
from cogent.evolve.substitution_calculation import (
    SubstitutionParameterDefn as ParamDefn, 
    RateDefn, LengthDefn, ProductDefn, CallDefn, CalcDefn,
        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")