\HeaderA{matchWCP}{A simple WCP matching function and related utilities}{matchWCP}
\aliasA{countWCP}{matchWCP}{countWCP}
\aliasA{countWCP,character-method}{matchWCP}{countWCP,character.Rdash.method}
\aliasA{countWCP,MaskedXString-method}{matchWCP}{countWCP,MaskedXString.Rdash.method}
\aliasA{countWCP,XString-method}{matchWCP}{countWCP,XString.Rdash.method}
\aliasA{countWCP,XStringViews-method}{matchWCP}{countWCP,XStringViews.Rdash.method}
\aliasA{matchWCP,character-method}{matchWCP}{matchWCP,character.Rdash.method}
\aliasA{matchWCP,MaskedXString-method}{matchWCP}{matchWCP,MaskedXString.Rdash.method}
\aliasA{matchWCP,XString-method}{matchWCP}{matchWCP,XString.Rdash.method}
\aliasA{matchWCP,XStringViews-method}{matchWCP}{matchWCP,XStringViews.Rdash.method}
\aliasA{WCPscoreStartingAt}{matchWCP}{WCPscoreStartingAt}
\keyword{methods}{matchWCP}
\keyword{manip}{matchWCP}
\keyword{utilities}{matchWCP}
\begin{Description}\relax
A function implementing a simple algorithm for matching a set of patterns
represented by Weighted Clustered Positions (WCP) to an XString sequence.
\end{Description}
\begin{Usage}
\begin{verbatim}
  matchWCP(wcp, subject, min.score="80%")
  countWCP(wcp, subject, min.score="80%")
  WCPscoreStartingAt(wcp, subject, starting.at=1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{wcp}] A \LinkA{WCP}{WCP} object.

\item[\code{subject}] An \LinkA{XString}{XString}, \LinkA{XStringViews}{XStringViews} or \LinkA{MaskedXString}{MaskedXString}
object for \code{matchWCP} and \code{countWCP}.

A \LinkA{XString}{XString} object for \code{WCPscoreStartingAt}.

\item[\code{min.score}] The minimum score for counting a match.
Can be given as a character string containing a percentage (e.g.
\code{"85\%"}) of the highest possible score or as a single number.

\item[\code{starting.at}] An integer vector specifying the starting positions of the
Weighted Clustered Positions relatively to the subject.

\end{ldescription}
\end{Arguments}
\begin{Value}
An \LinkA{XStringViews}{XStringViews} object for \code{matchWCP}.

A single integer for \code{countWCP}.

A numeric vector containing the Weighted Clustered Positions-based scores
for \code{WCPscoreStartingAt}.
\end{Value}
\begin{Author}\relax
P. Aboyoun
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{matchPWM}{matchPWM}},
\code{\LinkA{matchPattern}{matchPattern}},
\LinkA{WCP-class}{WCP.Rdash.class},
\LinkA{XString-class}{XString.Rdash.class},
\LinkA{XStringViews-class}{XStringViews.Rdash.class}
\end{SeeAlso}

