\Header{GP-class}{Class "GP" a sub-class of pubRepo to get/process data from GoldenPath}
\alias{getStrand}{GP-class}
\alias{GP}{GP-class}
\keyword{classes}{GP-class}
\begin{Description}\relax
This class is a sub-class of pubRepo with source specific
functions to get/process data from GoldenPath
{\url{http://www.genome.ucsc.edu/goldenPath}} to obtain gene
location and orientation data\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("GP", ...)}.
A constructor (GP) is available and should be used to instantiate
objects of this class\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{organism}:] Object of class \code{"character", from
        class "UG"} s character string for the organism of concern
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "UG"} a character string for the url where the source data
are. As multiple data sources will be used, srcUlr in this case is
the location where the surce data are
(e.g. \url{http://www.genome.ucsc.edu/goldenPath/14nov2002/database/})  
\item[\code{parser}:] Object of class \code{"character", from class
        "UG"} not in use
\item[\code{baseFile}:] Object of class \code{"character", from
        class "UG"} not in use
}\end{Section}
\begin{Section}{Extends}
Class \code{"UG"}, directly.
Class \code{"pubRepo"}, by class "UG".\end{Section}
\begin{Section}{Methods}
\describe{
\item[getStrand] \code{signature(object = "GP")}: Processes the
refLink and refGene data files and returns a matrix with gene
location and orientation data
}\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{References}\relax
\url{http://www.genome.ucsc.edu}\end{References}
\begin{SeeAlso}\relax
\code{\Link{pubRepo-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# The example may take a few second to finish
if(interactive()){
  # The url (\url{http://www.genome.ucsc.edu/goldenPath/14nov2002/database/})
  # was correct at the time of coding. Replace with a correct one if it
  # is invalid 
  url <- getSrcUrl("GP", organism = "human")
  gp <- GP(srcUrl = url, organism = "human")
  strand <- getStrand(gp)
}
\end{ExampleCode}
\end{Examples}

