\name{SolexaSequenceQ-class}
\docType{class}
\alias{SolexaSequenceQ-class}
\alias{[,SolexaSequenceQ,ANY,missing-method}
\alias{length,SolexaSequenceQ-method}

\alias{scores}
\alias{sequences}

\alias{names,SolexaSequenceQ-method}
\alias{scores,SolexaSequenceQ-method}
\alias{sequences,SolexaSequenceQ-method}
\alias{show,SolexaSequenceQ-method}

\title{Class "SolexaSequenceQ" illustrates a class that coordinates
  Solexa sequence and base call quality scores.}

\description{This class represents Solexa reads, their names, and
  corresponding base call quality scores in a coordinate fashion. It is
  meant as an illustration, and is not a final implementation.
}
\section{Objects from the Class}{
  Objects from the class are usually created by reading Solexa
  \code{s_<lane>_sequence.txt} files. Objects can also be created using
  the function \code{SolexaSequenceQ}.
}
\section{Slots}{
  Use accessors (below) to retrieve information contained in these
  slots. Note that sequences, etc., should be treated as `read only'.
  \describe{
    \item{\code{sequences}:}{Object of class \code{"DNAStringSet"}
      containing called read sequences. Reads are all the same
      length. The Solexa missing base symbol \code{.} has been
      translated to the IUPAC standard \code{-}.}
    \item{\code{.names}:}{Object of class \code{"BStringSet"} containing
      the names of all sequence reads.}
    \item{\code{scores}:}{Object of class \code{"BStringSet"} containing
      the ASCII-encoded quality scores of each called base. Decode each
      nucleotide \code{nt} with \code{nt-64} to obtain a Solexa Q value
      (typically between -40 and 40).}
  }
}
\section{Methods}{
  \describe{
    \item{[}{\code{signature(x = "SolexaSequenceQ", i = "ANY", j =
        "missing")}: select a subset of reads indexed by \code{i},
      returned as a \code{DNAStringSet} object.}
    \item{length}{\code{signature(x = "SolexaSequenceQ")}: return the
      number of reads in the object.}
    \item{names}{\code{signature(x = "SolexaSequenceQ")}: return the
      names of the reads as a \code{BStringSet} object.}
    \item{scores}{\code{signature(x = "SolexaSequenceQ")}: return the
      scores of the reads as a \code{BStringSet} object.}
    \item{sequences}{\code{signature(x = "SolexaSequenceQ")}: return the
      sequences of the reads as a \code{DNAStringSet} object.}
    \item{show}{\code{signature(object = "SolexaSequenceQ")}: display the
      object in a compact fashion.}
	 }
}
\references{Refer to Solexa documentation for inforamtion on quality
  score interpretation.} 
\author{Martin Morgan <mtmorgan@fhcrc.org>}
\seealso{
  \code{link{readSolexaFastq}} for string input;
  \code{\linkS4class{DNAStringSet}}, \code{\linkS4class{BStringSet}}.
}
\examples{
egFile <- system.file('extdata', 's_1_sequence.txt',
                      package='BiostringsCinterfaceDemo')
obj <- readSolexaFastQ(egFile)
obj
length(obj)
sequences(obj)
scores(obj)
## coordinated subsetting
samp <- obj[sample(length(obj), 10)]
sequences(samp)
names(samp)
}
\keyword{classes}