Lines Matching refs:admix
29 Profile<Abc> Pseudocounts<Abc>::AddTo(const Sequence<Abc>& seq, Admix& admix) const { in AddTo() argument
33 AdmixToTargetNeff(seq, p, admix); in AddTo()
35 AdmixTo(seq, p, admix); in AddTo()
44 Profile<Abc> Pseudocounts<Abc>::AddTo(const CountProfile<Abc>& cp, Admix& admix) const { in AddTo() argument
48 AdmixToTargetNeff(cp, p, admix); in AddTo()
50 AdmixTo(cp, p, admix); in AddTo()
59 void Pseudocounts<Abc>::AdmixTo(const Sequence<Abc>& q, Profile<Abc>& p, const Admix& admix) const { in AdmixTo() argument
60 double tau = admix(1.0); in AdmixTo()
70 void Pseudocounts<Abc>::AdmixTo(const CountProfile<Abc>& q, Profile<Abc>& p, const Admix& admix) co… in AdmixTo() argument
72 double tau = admix(q.neff[i]); in AdmixTo()
82 double Pseudocounts<Abc>::AdmixToTargetNeff(const T& q, Profile<Abc>& p, Admix& admix) const { in AdmixToTargetNeff() argument
86 admix.SetTargetNeffParam(kTargetNeffParamInit); in AdmixToTargetNeff()
90 AdmixTo(q, pp, admix); in AdmixToTargetNeff()
95 if (ne < target_neff_) l = admix.GetTargetNeffParam(); in AdmixToTargetNeff()
96 else r = admix.GetTargetNeffParam(); in AdmixToTargetNeff()
98 admix.SetTargetNeffParam(0.5 * (l + r)); in AdmixToTargetNeff()
101 admix.SetTargetNeffParam(kTargetNeffParamMax); in AdmixToTargetNeff()
102 AdmixTo(q, p, admix); in AdmixToTargetNeff()
104 admix.SetTargetNeffParam(kTargetNeffParamMin); in AdmixToTargetNeff()
105 AdmixTo(q, p, admix); in AdmixToTargetNeff()
109 return admix.GetTargetNeffParam(); in AdmixToTargetNeff()