\Header{LL-class}{Class "LL" a sub-class of pubRepo to handle data from LocusLink}
\alias{LL}{LL-class}
\keyword{classes}{LL-class}
\begin{Description}\relax
This class is a sub-class of pubRepo that is implemented
specifically to parse data from LocusLink (ll\_teml.gz)\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("LL", ...)}.
A constructor (LL) is available and should be used to instatiate
objects of \code{\Link{LL}}\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "pubRepo"} a character string for the surce url where data
will be downloaded/processed
\item[\code{parser}:] Object of class \code{"character", from class
        "pubRepo"}  a character string for the name of the file
containing a segment of perl code with instructions on how the
source data will be processed and output be generated
\item[\code{baseFile}:] Object of class \code{"character", from
        class "pubRepo"} a character string for the name of the file
that contains data that will be used as the base to process the
source data.  Data from the source that are related to elements in
the base file will be extracted. baseFile is assumed to be a two
folumn file with the first column being some type of arbitrary ids
(e.g. Affymetrix probe ids) and the second cloumn being the
corresponding ids of a given public repository (e.g. GenBank
accession numbers or UniGene ids) 
}\end{Section}
\begin{Section}{Extends}
Class \code{"pubRepo"}, directly.\end{Section}
\begin{Section}{Methods}
No methods defined with class "LL" in the signature.\end{Section}
\begin{Note}\relax
This class is part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics funtionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{References}\relax
\url{www.ncbi.nlm.nih.gov/LocusLink}\end{References}
\begin{SeeAlso}\relax
\code{\Link{pubRepo-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if(interactive()){
# Parse a truncated version of LL\_tmpl.gz from Bioconductor
path <- file.path(.path.package("pubRepo"), "data")
temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
"X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
"M16652"), ncol = 2, byrow = TRUE)
write.table(temp, "tempfile", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)  
ll <- LL(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
parser = file.path(path, "basedLLParser"), baseFile = "tempfile")
data <- parseData(ll)
unlink("tempfile")
}
\end{ExampleCode}
\end{Examples}

