\HeaderA{XStringQuality-class}{PhredQuality and SolexaQuality objects}{XStringQuality.Rdash.class}
\aliasA{as.integer,PhredQuality-method}{XStringQuality-class}{as.integer,PhredQuality.Rdash.method}
\aliasA{as.integer,SolexaQuality-method}{XStringQuality-class}{as.integer,SolexaQuality.Rdash.method}
\aliasA{as.numeric,PhredQuality-method}{XStringQuality-class}{as.numeric,PhredQuality.Rdash.method}
\aliasA{as.numeric,SolexaQuality-method}{XStringQuality-class}{as.numeric,SolexaQuality.Rdash.method}
\aliasA{class:PhredQuality}{XStringQuality-class}{class:PhredQuality}
\aliasA{class:SolexaQuality}{XStringQuality-class}{class:SolexaQuality}
\aliasA{class:XStringQuality}{XStringQuality-class}{class:XStringQuality}
\aliasA{coerce,BString,PhredQuality-method}{XStringQuality-class}{coerce,BString,PhredQuality.Rdash.method}
\aliasA{coerce,BString,SolexaQuality-method}{XStringQuality-class}{coerce,BString,SolexaQuality.Rdash.method}
\aliasA{coerce,BStringSet,PhredQuality-method}{XStringQuality-class}{coerce,BStringSet,PhredQuality.Rdash.method}
\aliasA{coerce,BStringSet,SolexaQuality-method}{XStringQuality-class}{coerce,BStringSet,SolexaQuality.Rdash.method}
\aliasA{coerce,character,PhredQuality-method}{XStringQuality-class}{coerce,character,PhredQuality.Rdash.method}
\aliasA{coerce,character,SolexaQuality-method}{XStringQuality-class}{coerce,character,SolexaQuality.Rdash.method}
\aliasA{coerce,integer,PhredQuality-method}{XStringQuality-class}{coerce,integer,PhredQuality.Rdash.method}
\aliasA{coerce,integer,SolexaQuality-method}{XStringQuality-class}{coerce,integer,SolexaQuality.Rdash.method}
\aliasA{coerce,numeric,PhredQuality-method}{XStringQuality-class}{coerce,numeric,PhredQuality.Rdash.method}
\aliasA{coerce,numeric,SolexaQuality-method}{XStringQuality-class}{coerce,numeric,SolexaQuality.Rdash.method}
\aliasA{coerce,PhredQuality,integer-method}{XStringQuality-class}{coerce,PhredQuality,integer.Rdash.method}
\aliasA{coerce,PhredQuality,numeric-method}{XStringQuality-class}{coerce,PhredQuality,numeric.Rdash.method}
\aliasA{coerce,SolexaQuality,integer-method}{XStringQuality-class}{coerce,SolexaQuality,integer.Rdash.method}
\aliasA{coerce,SolexaQuality,numeric-method}{XStringQuality-class}{coerce,SolexaQuality,numeric.Rdash.method}
\aliasA{PhredQuality}{XStringQuality-class}{PhredQuality}
\aliasA{PhredQuality-class}{XStringQuality-class}{PhredQuality.Rdash.class}
\aliasA{SolexaQuality}{XStringQuality-class}{SolexaQuality}
\aliasA{SolexaQuality-class}{XStringQuality-class}{SolexaQuality.Rdash.class}
\aliasA{XStringQuality}{XStringQuality-class}{XStringQuality}
\keyword{methods}{XStringQuality-class}
\keyword{classes}{XStringQuality-class}
\begin{Description}\relax
Objects for storing string quality measures.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## Constructors:
  PhredQuality(x)
  SolexaQuality(x)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Either a character vector, \LinkA{BString}{BString}, \LinkA{BStringSet}{BStringSet}, integer vector,
or number vector of error probabilities.

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{PhredQuality} objects store characters that are interpreted as [0 - 99] quality
measures by subtracting 33 from their ASCII decimal representation
(e.g. ! = 0, " = 1, \# = 2, ...).

\code{SolexaQuality} objects store characters are interpreted as [-5 - 99] quality
measures by subtracting 64 from their ASCII decimal representation
(e.g. ; = -5, < = -4, = = -3, ...).
\end{Details}
\begin{Author}\relax
P. Aboyoun
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{pairwiseAlignment}{pairwiseAlignment}},
\LinkA{PairwiseAlignedXStringSet-class}{PairwiseAlignedXStringSet.Rdash.class},
\LinkA{DNAString-class}{DNAString.Rdash.class},
\LinkA{BStringSet-class}{BStringSet.Rdash.class}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  PhredQuality(0:40)
  SolexaQuality(0:40)

  PhredQuality(seq(1e-4,0.5,length=10))
  SolexaQuality(seq(1e-4,0.5,length=10))
\end{ExampleCode}
\end{Examples}

