Ref.Rnw

<<knitr, echo=FALSE>>=
library("knitr")
opts_chunk$set(tidy.opts = 
               list(width.cutoff = 50, 
                    tidy = FALSE),
               fig.align = 'center',
               stop_on_error = 1L,
               comment = NA,
               prompt = TRUE)
options(width = 60)
@ 

\section{S4 Reference Classes}

\begin{frame}[fragile]{Reference classes}
  \begin{block}{Reference classes}
    \begin{itemize}
      \item This paradigm uses \textbf{pass-by-reference} semantics:
        invoking a method may modify the content of the fields.
      \item Methods in this paradigm are associated with the object (rather than to generics)
      \item Java-like logic.
      \item See \texttt{?ReferenceClasses} for all the details.
    \end{itemize}
  \end{block}
  \begin{example}
\begin{verbatim}
## here, you would have
> a$seq() ## equivalent of seq(a)
[1] "AGCATG"
> a$comp()
> a$seq()
[1] "TCGTAC"
\end{verbatim}
  \end{example}
\end{frame}


\begin{frame}[fragile]{Reference classes - objects and fields}
\begin{block}{Defining a reference class}
Slots $\rightarrow$ a list of \textbf{fields}
\end{block}
\bigskip
<<RefClass-1,tidy=FALSE>>=
Seq <- setRefClass("Seq",
                   fields = list(
                     id = "character",
                     alphabet = "character",
                     sequence = "character"))
@

\begin{block}{Generator objects}
The return value of \code{setRefClass} is a \textbf{generator object} that is used
to construct new object of given class. 
\end{block}
\end{frame}



\begin{frame}[fragile]{Reference classes - methods}
  \begin{block}{Defining a reference class}
    Methods $\rightarrow$ a list of \textbf{functions}
  \end{block}
\begin{scriptsize}
<<RefClass-2, tidy = FALSE>>=
Seq <- setRefClass("Seq",
                   fields = list(
                     id = "character",
                     alphabet = "character",
                     sequence = "character"),
                   methods = list(
                     comp = function() {
                       "Complements the (DNA) sequence" ## inline docs
                       sequence <<- chartr("ACGT","TGCA",.self$sequence)
                       id <<- paste(.self$id, "-- complemented")                     
                     }
                     ## there can be more, of course
                     ))

@
\end{scriptsize}

\begin{block}{}
  Methods can be added either directly in class definition or later by calling
  \code{Seq\$methods(functionName = function() \{ ...code... \})}. 
\end{block}
\end{frame}


\begin{frame}[fragile]{Using the reference classes}
  \begin{block}{You also need to know that...}
    \begin{itemize}
    \item accessing fields and calling methods is done with the \code{\$} operator.
    \item the current object can be referred to in a method by the reserved name \code{.self}.
    \item Changing fields of an object within methods needs to be done with the \code{{<}{<}-} operator.
    \end{itemize}
  \end{block}
\end{frame}


\begin{frame}[fragile]
\begin{scriptsize}
<<RefClass-example,echo=TRUE, tidy=FALSE>>=
s <- Seq$new(id="foo", sequence="GATCATCA")
s
s$sequence
s$comp()
s$sequence
@
%$
\end{scriptsize}
\end{frame}

\begin{frame}[fragile]{Reference classes}
  \begin{block}{Suitable for...}
    Reference classes are suitable for objects that are \textit{dynamically tracked} by all the code: 
    GUI components, read-only access to files (streams, data bases), internet resources, 
    editing facilities, ...
  \end{block}
\end{frame}

%% Final Reference class exercises

\begin{frame}[fragile,t]{S4 introspection and methods exercises}
\begin{block}{\exercise (code: \code{05_seqRefClass.R})}
We implemented some more methods using Reference Classes. Read through the methods
and make sure you understand how they work. Then try out the test code in
\code{05_seqRefClass.R}. What happens when we assign one Reference Class object
to another? 
\end{block}

%% \begin{block}{\exercise}
%% What is the result of \code{isS4(Seq)}? Can you find out more about the implementation of
%% Reference Classes? \\
%% {\small Tip: try \code{ls(envir=....)}}
%% \end{block}

\end{frame}