Uses of Class
statalign.base.hmm.Hmm

Packages that use Hmm

statalign.base.hmm
statalign.model.ext
statalign.model.ext.plugins

Uses of Hmm in statalign.base.hmm

Subclasses of Hmm in statalign.base.hmm

class	Hmm2 This is an abstract class for HMMs that are pair-HMMs and do not emit characters into unobservable sequences.
class	HmmNonParam An implementation of the abstract pair-HMM that emits characters into non-observable sequences Used when a new alignment is proposed that aligns together two substrings via an ancestral sequence.
class	HmmSilent This is the abstract class of pair-HMMs that emit characters into one unobservable sequence, namely that aligns two observable sequences via an unobservable ancestral sequence.
class	HmmTkf92 This class implements a simplified version of the TKF92 pair-HMM.

Uses of Hmm in statalign.model.ext

Methods in statalign.model.ext with parameters of type Hmm

void	ModelExtManager.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted)
void	ModelExtension.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted) Called after a proposed indel parameter change (accepted or rejected).
void	ModelExtManager.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
void	ModelExtension.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) Called before an indel parameter change is proposed, but after the affected parameter is selected.
double	ModelExtManager.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.
double	ModelExtension.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)

Uses of Hmm in statalign.model.ext.plugins

Methods in statalign.model.ext.plugins with parameters of type Hmm

double

StructAlign.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)