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