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+\name{GmapGenomeDirectory-class}

+\Rdversion{1.1}

+\docType{class}

+\alias{GmapGenomeDirectory-class}

+\alias{path,GmapGenomeDirectory-method}

+\alias{path,NULL-method}

+\alias{genome,GmapGenomeDirectory-method}

+

+\alias{GmapGenomeDirectory}

+

+\title{Class \code{"GmapGenomeDirectory"}}

+\description{

+  The GmapGenomeDirectory class stores a path to a directory containing

+  a one or more genome-specific subdirectories, each represented by a

+  \code{\linkS4class{GmapGenome}}. Inside those directories are the

+  files that the GMAP suite of tools uses for alignment, tallying, and

+  other operations. This class is typically used to create a

+  \code{GmapGenome} object. The default directory is

+  \code{~/.local/share/gmap}, following the freedesktop.org XDG

+  standard.

+}

+\section{Constructor}{

+  \describe{

+    \item{}{\code{GmapGenomeDirectory(path = getDefaultGmapGenomePath(),

+        create = FALSE)}:

+      Creates an object pointing to the directory at \code{path},

+      creating it if it does not yet exist and \code{create} is \code{TRUE}.

+    }

+  }

+}

+\section{Methods}{

+  \describe{

+    \item{}{\code{path(object)}: gets the path to the genome directory.}

+    \item{}{\code{genome(x)}: gets the names of the genomes in the

+      directory.}

+  }

+}

+\author{

+  Michael Lawrence

+}

+

+%% ~Make other sections like Warning with \section{Warning }{....} ~

+

+\seealso{

+  \code{\link{GmapGenome-class}}

+}

+

+\examples{

+gmapGenomePath <- file.path(getwd(), "newGmapGenomeDirectory")

+gmapGenomeDirectory <- GmapGenomeDirectory(gmapGenomePath, create = TRUE)

+}

+

+\keyword{classes}