initial commit

R/default.R

@@ -0,0 +1,52 @@
+#' @include taxonomy.R
+NULL
+
+
+#
+#
+# Manage le loading of the default taxonomy
+#
+#
+
+.__default__taxonomy__ = NULL
+
+#' Returns the default taxonomy
+#' 
+#' Returns a \code{\linkS4class{obitools.taxonomy}} instance corresponding
+#' to a NCBI taxonomy included by default in the \pkg{\link{ROBITaxonomy}} package.
+#' 
+#' @return a \code{\linkS4class{obitools.taxonomy}} instance.
+#' 
+#' @examples
+#' 
+#' # Load the default taxonomy
+#' taxo = default.taxonomy()
+#' 
+#' # and use it for requesting a scientific name
+#' scientificname(taxo,7742)
+#' 
+#' @seealso \code{\linkS4class{obitools.taxonomy}}
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @export
+#' 
+default.taxonomy = function() {
+  if (is.null(get(".__default__taxonomy__",envir = environment())))
+    assign(".__default__taxonomy__", 
+           read.taxonomy(paste(system.file("extdata", 
+                                           package="ROBITaxonomy"),
+                                           'ncbitaxo',
+                                        sep='/')), 
+           envir=globalenv())
+  
+  return(get(".__default__taxonomy__",envir = globalenv()))
+}
+
+
+#' @export
+#' 
+is.obitools.taxonomy = function(taxonomy) {
+  class(t)[1] == "obitools.taxonomy"
+}
+