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## package: megaptera
## called by: stepA
## author: Christoph Heibl (at gmx.net)
## last update: 2014-10-25
term <- function(organism, locus) {
if ( !is.character(organism) )
stop("organism must be of mode 'character'")
if ( !inherits(locus, "locus") )
stop("locus must be of class 'locus'")
organism <- paste(organism, "[orgn]", sep = "")
## eventually move to higher level:
aliases <- paste("\"", locus@aliases, "\"", sep = "")
## create URL using 'sgene' object
## -------------------------------
URL <- vector(length = length(organism))
for ( i in seq_along(organism) ){
url <- paste(organism[i], "AND",
NCBI.wrap(aliases, field = locus@search.fields))
if ( !"not" %in% locus@not ){
not <- paste("\"", locus@not, "\"", sep = "")
url <- paste(url, "NOT",
NCBI.wrap(not, field = locus@search.fields))
}
if ( length(url) > 1 ){
url <- paste("(", url, ")", sep = "")
url <- paste(url, collapse = " OR ")
}
URL[i] <- url
} # end of FOR-loop over i
if ( length(URL) > 1 ){
URL <- paste("(", URL, ")", sep = "")
URL <- paste(URL, collapse = " OR ")
}
URL
}
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