\Header{pubRepo-class}{Class "pubRepo" a generic class for downloading/parsing data
provided by various public data repositories}
\alias{baseFile}{pubRepo-class}
\alias{baseFile<\Rdash}{pubRepo-class}
\alias{downloadData}{pubRepo-class}
\alias{parseData}{pubRepo-class}
\alias{parser}{pubRepo-class}
\alias{parser<\Rdash}{pubRepo-class}
\alias{pubRepo}{pubRepo-class}
\alias{readData}{pubRepo-class}
\alias{srcUrl}{pubRepo-class}
\alias{srcUrl<\Rdash}{pubRepo-class}
\keyword{classes}{pubRepo-class}
\begin{Description}\relax
This class provides the basic functions to download/parser
data from different public data repositories. More specific functions
can be provided by extending this class to include source specific
features\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("pubRepo", ...)}.
A constructor (\code{\Link{pubRepo}} is provided and should be used
to create objects of this class.\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{srcUrl}:] Object of class \code{"character"} a character
string for the url of a data source from a public repository
\item[\code{parser}:] Object of class \code{"character"} a character
string for the name of a file that will be used as part of perl
script to parse the source data. Parser is a segment of perl code
containing instructions on how the source data will be processed
and the content and format of the output
\item[\code{baseFile}:] Object of class \code{"character"} a
character string for the name of a file 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}{Methods}
\describe{
\item[baseFile<-] \code{signature(object = "pubRepo")}: Sets the
value for baseFile
\item[baseFile] \code{signature(object = "pubRepo")}: Gets the value
for baseFile
\item[downloadData] \code{signature(object = "pubRepo")}: Downloads
data from a data source defined by srcUrl
\item[parseData] \code{signature(object = "pubRepo")}:
DownLoads/parses data from a data source defined by srcUrl
\item[parser<-] \code{signature(object = "pubRepo")}: Sets the value
for parser
\item[parser] \code{signature(object = "pubRepo")}: Gets the value
for parser
\item[readData] \code{signature(object = "pubRepo")}: Reads data
using \code{\Link{readLines}} from a data source defined by srcUrl
\item[srcUrl<-] \code{signature(object = "pubRepo")}: Sets the value
for srcUrl
\item[srcUrl] \code{signature(object = "pubRepo")}: Gets the value
for srcUrl
}\end{Section}
\begin{Note}\relax
This class is part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{SeeAlso}\relax
\code{\Link{GO-class}}, \code{\Link{KEGG-class}},
\code{\Link{LL-class}}, \code{\Link{UG-class}}, \code{\Link{GEO-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Read a short test file from Bioconductor
test <- pubRepo(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/TGene.txt")
data <- readData(test)
\end{ExampleCode}
\end{Examples}

