R/getDasSequence.R

In gthar/DASiR: Distributed Annotation System in R

.getSequence <- function(sequence)
{
    seq <- xmlValue(sequence)
    pattern <- "\n"
    seq <- gsub(pattern, "", seq)
    return(seq)
}

getDasSequence <- function(source, ranges,
                           class=c("character", "DNAStringSet", "RNAStringSet",
                                   "AAStringSet"))
{
    class <- match.arg(class)
    str_ran <- .makeSegments(ranges)
    url <- paste(getDasServer(), "/", source, "/sequence?", str_ran, sep="")

    message("Quering url: ",
            paste(getDasServer(), "/", source, "/sequence", sep=""))

    isLong <- nchar(url) > 2000

    doc <- tryCatch(
        xmlTreeParse(url, useInternalNodes = TRUE, error=NULL),
        XMLError=function(e) {
          message("Error: ", e$message)
            if (e$code == 1549 & isLong) {
                message("Maybe URL is too long. Try querying less ranges")
            }
        },
        error=function(e) {
            message("Error: ",
                    substr(e$message, 1, 500),
                    ifelse(nchar(e$message>500), "...", ""))
        },
        finally=function() {
            return(NULL)
        }
    )

    if (is.null(doc)) {
        return(NULL)
    }

    top <- xmlRoot(doc)

    res <- list()
    for (iseg in seq_along(names(top))) {  # Each Segment
        seg <- top[[iseg]]
        res[[iseg]] <- unlist(xmlApply(seg, .getSequence), use.names=FALSE)
    }

    all <- as(unlist(res), class)
    return(all)
}