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All Samples(6)  |  Call(4)  |  Derive(0)  |  Import(2)

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,
        expm = NonParamDefn('expm')
        exp = ExpDefn(expm)
        Qd = CallDefn(exp, Q, name='Qd')
        return Qd
 
    def makeContinuousPsubDefn(self, word_probs, mprobs_matrix, distance, rate_params):
        Qd = self.makeQdDefn(word_probs, mprobs_matrix, rate_params)
        P = CallDefn(Qd, distance, name='psubs')
        return P
 

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,
        expm = NonParamDefn('expm')
        exp = ExpDefn(expm)
        Qd = CallDefn(exp, Q, name='Qd')
        return Qd
 
    def makeContinuousPsubDefn(self, word_probs, mprobs_matrix, distance, rate_params):
        Qd = self.makeQdDefn(word_probs, mprobs_matrix, rate_params)
        P = CallDefn(Qd, distance, name='psubs')
        return P