R/term.R

In heibl/megaptera: MEGAPhylogeny Techniques in R

## This code is part of the megaptera package
## © C. Heibl 2014 (last update 2019-09-11)

#' @importFrom methods is
#' @export

term <- function(organism, kingdom, locus) {
  
  if (!is.character(organism))
    stop("organism must be of mode 'character'")
  if (!is(locus, "locus"))
    stop("locus must be of class 'locus'")
  
  ## species names must not contain whitespace
  organism <- gsub(" ", "+", organism)
  
  ## kingdom added 2016-01-22
  organism <- paste0(organism, "[orgn]+AND+", kingdom, "[orgn]")
  ## eventually move to higher level:
  ##aliases <- paste("\"", locus@aliases, "\"", sep = "")
  aliases <- gsub(" ", "+", locus@aliases)
  
  ## add search fields *CURRENTLY DISABLED*
  if (FALSE){
    aliases <- NCBI.wrap(aliases, field = locus@search.fields)
    not <- NCBI.wrap(not, field = locus@search.fields)
  }
  
  ## create URL using 'sgene' object
  ## -------------------------------
  URL <- vector(length = length(organism))
  for (i in seq_along(organism)){
    url <- paste0(organism[i], "+AND+", aliases)
    if (!"not" %in% locus@not){
      not <- paste0("\"", locus@not, "\"")
      not <- paste(not, collapse = "+NOT+")
      url <- paste0(url, "+NOT+", not)
    }
    if (length(url) > 1){
      url <- paste0("(", url, ")")
      url <- paste(url, collapse = "+OR+")
    }
    URL[i] <- url
  } # end of FOR-loop over i
  if (length(URL) > 1){
    URL <- paste0("(", URL, ")")
    URL <- paste(URL, collapse = "+OR+")
  }
  URL
}