\HeaderA{HmmParameter-class}{Class "HmmParameter"}{HmmParameter.Rdash.class}
\aliasA{emission,HmmParameter-method}{HmmParameter-class}{emission,HmmParameter.Rdash.method}
\aliasA{emission<-,HmmParameter,array-method}{HmmParameter-class}{emission<.Rdash.,HmmParameter,array.Rdash.method}
\aliasA{genomicDistance,HmmParameter-method}{HmmParameter-class}{genomicDistance,HmmParameter.Rdash.method}
\aliasA{genomicDistance<-,HmmParameter,numeric-method}{HmmParameter-class}{genomicDistance<.Rdash.,HmmParameter,numeric.Rdash.method}
\aliasA{initialize,HmmParameter-method}{HmmParameter-class}{initialize,HmmParameter.Rdash.method}
\aliasA{Pi,HmmParameter-method}{HmmParameter-class}{Pi,HmmParameter.Rdash.method}
\aliasA{show,HmmParameter-method}{HmmParameter-class}{show,HmmParameter.Rdash.method}
\aliasA{states,HmmParameter-method}{HmmParameter-class}{states,HmmParameter.Rdash.method}
\aliasA{states<-,HmmParameter,character-method}{HmmParameter-class}{states<.Rdash.,HmmParameter,character.Rdash.method}
\aliasA{tau,HmmParameter-method}{HmmParameter-class}{tau,HmmParameter.Rdash.method}
\aliasA{transitionScale,HmmParameter-method}{HmmParameter-class}{transitionScale,HmmParameter.Rdash.method}
\aliasA{transitionScale<-,HmmParameter,matrix-method}{HmmParameter-class}{transitionScale<.Rdash.,HmmParameter,matrix.Rdash.method}
\aliasA{[,HmmParameter-method}{HmmParameter-class}{[,HmmParameter.Rdash.method}
\keyword{classes}{HmmParameter-class}
\begin{Description}\relax
Parameters needed for the Viterbi algorithm, including
emission probabilities, the genomic distance, and the initial state probabilities
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("HmmParameter", states, initialStateProbability, emission, genomicDistance, transitionScale)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{states}:] Object of class \code{"character"} 
\item[\code{initialStateProbability}:] Object of class \code{"numeric"} 
\item[\code{emission}:] Object of class \code{"array"} 
\item[\code{genomicDistance}:] Object of class \code{"numeric"} 
\item[\code{transitionScale}:] Object of class \code{"matrix"} 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "HmmParameter")}:  
\item[emission] \code{signature(object = "HmmParameter")}:  
\item[emission<-] \code{signature(object = "HmmParameter", value = "array")}:  
\item[genomicDistance] \code{signature(object = "HmmParameter")}:  
\item[genomicDistance<-] \code{signature(object = "HmmParameter", value = "numeric")}:  
\item[hmm] \code{signature(object = "HmmOptions", params = "HmmParameter")}:  
\item[initialize] \code{signature(.Object = "HmmParameter")}:  
\item[pi] \code{signature(object = "HmmParameter")}:  
\item[show] \code{signature(object = "HmmParameter")}:  
\item[states] \code{signature(object = "HmmParameter")}:  
\item[states<-] \code{signature(object = "HmmParameter", value = "character")}:  
\item[tau] \code{signature(object = "HmmParameter")}:  
\item[transitionScale] \code{signature(object = "HmmParameter")}:  
\item[transitionScale<-] \code{signature(object = "HmmParameter", value = "matrix")}:  
}
\end{Section}
\begin{Note}\relax
See HmmParameter vignette
\end{Note}
\begin{Author}\relax
RS
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{HmmOptions-class}{HmmOptions.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("HmmParameter")
\end{ExampleCode}
\end{Examples}

