#### renaming gmapR2 to gmapR: it lives again

 1 1 new file mode 100644 ... ... @@ -0,0 +1,53 @@ 1 +\name{GmapGenomeDirectory-class} 2 +\Rdversion{1.1} 3 +\docType{class} 4 +\alias{GmapGenomeDirectory-class} 5 +\alias{path,GmapGenomeDirectory-method} 6 +\alias{path,NULL-method} 7 +\alias{genome,GmapGenomeDirectory-method} 8 + 9 +\alias{GmapGenomeDirectory} 10 + 11 +\title{Class \code{"GmapGenomeDirectory"}} 12 +\description{ 13 + The GmapGenomeDirectory class stores a path to a directory containing 14 + a one or more genome-specific subdirectories, each represented by a 15 + \code{\linkS4class{GmapGenome}}. Inside those directories are the 16 + files that the GMAP suite of tools uses for alignment, tallying, and 17 + other operations. This class is typically used to create a 18 + \code{GmapGenome} object. The default directory is 19 + \code{~/.local/share/gmap}, following the freedesktop.org XDG 20 + standard. 21 +} 22 +\section{Constructor}{ 23 + \describe{ 24 + \item{}{\code{GmapGenomeDirectory(path = getDefaultGmapGenomePath(), 25 + create = FALSE)}: 26 + Creates an object pointing to the directory at \code{path}, 27 + creating it if it does not yet exist and \code{create} is \code{TRUE}. 28 + } 29 + } 30 +} 31 +\section{Methods}{ 32 + \describe{ 33 + \item{}{\code{path(object)}: gets the path to the genome directory.} 34 + \item{}{\code{genome(x)}: gets the names of the genomes in the 35 + directory.} 36 + } 37 +} 38 +\author{ 39 + Michael Lawrence 40 +} 41 + 42 +%% ~Make other sections like Warning with \section{Warning }{....} ~ 43 + 44 +\seealso{ 45 + \code{\link{GmapGenome-class}} 46 +} 47 + 48 +\examples{ 49 +gmapGenomePath <- file.path(getwd(), "newGmapGenomeDirectory") 50 +gmapGenomeDirectory <- GmapGenomeDirectory(gmapGenomePath, create = TRUE) 51 +} 52 + 53 +\keyword{classes}