Nothing
#' @include eutil.R
NULL
#' @export
.egquery <- setRefClass(
Class = "egquery",
contains = "eutil",
methods = list(
initialize = function(method, ...) {
callSuper()
perform_query(method = method, ...)
if (errors$all_empty()) {
errors$check_errors(.self)
}
},
show = function() {
cat("Object of class", sQuote(eutil()), "\n")
if (no_errors()) {
methods::show(get_content("xml"))
tail <- sprintf("EGQuery query for the search term %s.",
sQuote(xmlValue("/Result/Term")))
cat(tail, sep = "\n")
} else {
methods::show(get_error())
}
}
)
)
#' \code{egquery} retrieves the number of records in all Entrez databases for
#' a single text query.
#'
#' @details
#' See the official online documentation for NCBIs
#' \href{https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EGQuery}{EUtilities}
#' for additional information.
#'
#' @title egquery - performing a global Entrez search
#' @param term A valid Entrez text query.
#' @return An \code{\linkS4class{egquery}} object.
#' @export
#' @examples
#' ## Determine the number of records for mouse in Entrez.
#' e <- egquery("mouse[orgn]")
#' e
egquery <- function(term) {
if (missing(term)) {
stop("No search term provided")
}
if (length(term) > 1L) {
term <- paste(term, collapse=" OR ")
}
.egquery('GET', term = term, retmode = 'xml')
}
#' @describeIn content Access the data content from an \code{egquery} request.
setMethod("content", "egquery", function(x, as = NULL) {
callNextMethod(x = x, as = as)
})
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