\HeaderA{QualityScaledXStringSet-class}{QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects}{QualityScaledXStringSet.Rdash.class}
\aliasA{append,QualityScaledXStringSet,QualityScaledXStringSet-method}{QualityScaledXStringSet-class}{append,QualityScaledXStringSet,QualityScaledXStringSet.Rdash.method}
\aliasA{class:QualityScaledAAStringSet}{QualityScaledXStringSet-class}{class:QualityScaledAAStringSet}
\aliasA{class:QualityScaledBStringSet}{QualityScaledXStringSet-class}{class:QualityScaledBStringSet}
\aliasA{class:QualityScaledDNAStringSet}{QualityScaledXStringSet-class}{class:QualityScaledDNAStringSet}
\aliasA{class:QualityScaledRNAStringSet}{QualityScaledXStringSet-class}{class:QualityScaledRNAStringSet}
\aliasA{class:QualityScaledXStringSet}{QualityScaledXStringSet-class}{class:QualityScaledXStringSet}
\aliasA{narrow,QualityScaledXStringSet-method}{QualityScaledXStringSet-class}{narrow,QualityScaledXStringSet.Rdash.method}
\aliasA{quality}{QualityScaledXStringSet-class}{quality}
\aliasA{quality,QualityScaledXStringSet-method}{QualityScaledXStringSet-class}{quality,QualityScaledXStringSet.Rdash.method}
\aliasA{QualityScaledAAStringSet}{QualityScaledXStringSet-class}{QualityScaledAAStringSet}
\aliasA{QualityScaledAAStringSet-class}{QualityScaledXStringSet-class}{QualityScaledAAStringSet.Rdash.class}
\aliasA{QualityScaledBStringSet}{QualityScaledXStringSet-class}{QualityScaledBStringSet}
\aliasA{QualityScaledBStringSet-class}{QualityScaledXStringSet-class}{QualityScaledBStringSet.Rdash.class}
\aliasA{QualityScaledDNAStringSet}{QualityScaledXStringSet-class}{QualityScaledDNAStringSet}
\aliasA{QualityScaledDNAStringSet-class}{QualityScaledXStringSet-class}{QualityScaledDNAStringSet.Rdash.class}
\aliasA{QualityScaledRNAStringSet}{QualityScaledXStringSet-class}{QualityScaledRNAStringSet}
\aliasA{QualityScaledRNAStringSet-class}{QualityScaledXStringSet-class}{QualityScaledRNAStringSet.Rdash.class}
\aliasA{QualityScaledXStringSet}{QualityScaledXStringSet-class}{QualityScaledXStringSet}
\aliasA{show,QualityScaledXStringSet-method}{QualityScaledXStringSet-class}{show,QualityScaledXStringSet.Rdash.method}
\aliasA{[,QualityScaledXStringSet-method}{QualityScaledXStringSet-class}{[,QualityScaledXStringSet.Rdash.method}
\keyword{methods}{QualityScaledXStringSet-class}
\keyword{classes}{QualityScaledXStringSet-class}
\begin{Description}\relax
The QualityScaledBStringSet class is a container for storing a
\code{\LinkA{BStringSet}{BStringSet}} object with an \code{\LinkA{XStringQuality}{XStringQuality}} object.

Similarly, the QualityScaledDNAStringSet (or QualityScaledRNAStringSet, or
QualityScaledAAStringSet) class is a container for storing a \code{\LinkA{DNAStringSet}{DNAStringSet}}
(or \code{\LinkA{RNAStringSet}{RNAStringSet}}, or \code{\LinkA{AAStringSet}{AAStringSet}}) objects with
an \code{\LinkA{XStringQuality}{XStringQuality}} object.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## Constructors:
  QualityScaledBStringSet(x, quality)
  QualityScaledDNAStringSet(x, quality)
  QualityScaledRNAStringSet(x, quality)
  QualityScaledAAStringSet(x, quality)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Either a character vector, or an \LinkA{XString}{XString}, \LinkA{XStringSet}{XStringSet}
or \LinkA{XStringViews}{XStringViews} object.

\item[\code{quality}] An \LinkA{XStringQuality}{XStringQuality} object.

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \code{QualityScaledBStringSet}, \code{QualityScaledDNAStringSet},
\code{QualityScaledRNAStringSet} and \code{QualityScaledAAStringSet}
functions are constructors that can be used to "naturally" turn
\code{x} into an QualityScaledXStringSet object of the desired base type.
\end{Details}
\begin{Section}{Accessor methods}
The QualityScaledXStringSet class derives from the \LinkA{XStringSet}{XStringSet}
class hence all the accessor methods defined for an \LinkA{XStringSet}{XStringSet}
object can also be used on an QualityScaledXStringSet object. Common
methods include (in the code snippets below, \code{x} is an
QualityScaledXStringSet object):

\describe{
\item[] \code{length(x)}:
The number of sequences in \code{x}.

\item[] \code{width(x)}:
A vector of non-negative integers containing the number
of letters for each element in \code{x}.

\item[] \code{nchar(x)}:
The same as \code{width(x)}.

\item[] \code{names(x)}:
\code{NULL} or a character vector of the same length as \code{x} containing
a short user-provided description or comment for each element in \code{x}.

\item[] \code{quality(x)}:
The quality of the strings.

}
\end{Section}
\begin{Section}{Subsetting and appending}
In the code snippets below,
\code{x} and \code{values} are XStringSet objects,
and \code{i} should be an index specifying the elements to extract.

\describe{
\item[] \code{x[i]}:
Return a new QualityScaledXStringSet object made of the selected elements.

}
\end{Section}
\begin{Author}\relax
P. Aboyoun
\end{Author}
\begin{SeeAlso}\relax
\LinkA{BStringSet-class}{BStringSet.Rdash.class},
\LinkA{DNAStringSet-class}{DNAStringSet.Rdash.class},
\LinkA{RNAStringSet-class}{RNAStringSet.Rdash.class},
\LinkA{AAStringSet-class}{AAStringSet.Rdash.class},
\LinkA{XStringQuality-class}{XStringQuality.Rdash.class}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  x1 <- DNAStringSet(c("TTGA", "CTCN"))
  q1 <- PhredQuality(c("*+,-", "6789"))
  qx1 <- QualityScaledDNAStringSet(x1, q1)
  qx1
\end{ExampleCode}
\end{Examples}

