def get_pre_Q(cls,
         log_counts, codon_distn,
         ts, tv, syn, nonsyn, compo, asym_compo,
         natural_theta,
         ):
     cls.check_theta(natural_theta)
     kappa = natural_theta[0]
     omega = natural_theta[1]
     nt_distn = markovutil.ratios_to_distn(natural_theta[2:5])
     pre_Q = codon1994.get_MG_pre_Q(
             ts, tv, syn, nonsyn, asym_compo,
             nt_distn, kappa, omega)
     return pre_Q
 def get_pre_Q(cls,
         log_counts, codon_distn,
         ts, tv, syn, nonsyn, compo, asym_compo,
         theta,
         ):
     cls.check_theta(theta)
     kappa = algopy.exp(theta[0])
     omega = algopy.exp(theta[1])
     nt_distn = markovutil.log_ratios_to_distn(theta[2:5])
     pre_Q = codon1994.get_MG_pre_Q(
             ts, tv, syn, nonsyn, asym_compo,
             nt_distn, kappa, omega)
     return pre_Q