\HeaderA{BCRANKsearch-class}{Class "BCRANKsearch"}{BCRANKsearch.Rdash.class}
\aliasA{BCRANKsearch}{BCRANKsearch-class}{BCRANKsearch}
\aliasA{plot,BCRANKsearch,missing-method}{BCRANKsearch-class}{plot,BCRANKsearch,missing.Rdash.method}
\aliasA{pwm}{BCRANKsearch-class}{pwm}
\aliasA{searchPath}{BCRANKsearch-class}{searchPath}
\keyword{classes}{BCRANKsearch-class}
\begin{Description}\relax
Holds the whole search path from a single
\code{\LinkA{bcrank}{bcrank}} run. Each individual search step
is stored in a
\code{\LinkA{BCRANKmatch-class}{BCRANKmatch.Rdash.class}}
object.  Several objects of this class are collected in a
\code{\LinkA{BCRANKresult-class}{BCRANKresult.Rdash.class}} object
\end{Description}
\begin{Section}{Objects from the Class}
Objects are not intended to be created directly but as a result from
running \code{\LinkA{bcrank}{bcrank}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{searchPath}:] a collection of \code{BCRANKmatch-class}
objects, ontaining all bcrank search steps from a start guess to a
locally optimal solution.
\item[\code{finalPWM}:] position weight matrix containing all DNA
sites for the highest scoring consensus in this bcrank run.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[searchPath] \code{signature(object = "BCRANKsearch", i=NULL)}:
If \code{i} is NULL, returns a data frame containing consensus and score
for the whole search path. Otherwise, the i'th
\code{BCRANKmatch-class} object in the search path is returned.
\item[pwm] \code{signature(object = "BCRANKsearch", normalize=TRUE)}: Returns
the position weight matrix (pwm) for the highest scoring consensus in
this bcrank run. Matrix positions are between between 0 and 1 when \code{normalize}
is TRUE. When FALSE, the number of matching sequences is reported.  
\item[plot] \code{signature(x = "BCRANKsearch", y = "missing")}:
A plot method for the searchPath.
}
\end{Section}
\begin{Author}\relax
Adam Ameur, \email{adam.ameur@lcb.uu.se}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{bcrank}{bcrank}},
\code{\LinkA{BCRANKmatch-class}{BCRANKmatch.Rdash.class}},
\code{\LinkA{BCRANKresult-class}{BCRANKresult.Rdash.class}}
\end{SeeAlso}

