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#
# To get sequence data
#
getSequence <- function(object, as.string = FALSE, ...) UseMethod("getSequence")
getSequence.default <- function(object, as.string = FALSE, ...)
stop(paste("no getSequence method for objects of class:", class(object)))
getSequence.list <- function(object, as.string = FALSE, ...)
lapply(seq_len(length(object)), function(i) getSequence(object[[i]], as.string = as.string, ...))
getSequence.character <- function(object, as.string = FALSE, ...){
is.single.string <- function(x) length(x) == 1 && nchar(x) > 1
if(is.single.string(object)){
if(as.string) return(as.list(object)) else return(s2c(object))
} else {
if(as.string) return(as.list(c2s(object))) else return(object)
}
}
getSequence.SeqFastadna <- function(object, as.string = FALSE, ...){
attributes(object) <- NULL # not needed here
getSequence.character(object, as.string, ...)
}
getSequence.SeqFrag <- getSequence.SeqFastaAA <- getSequence.SeqFastadna
getSequence.SeqAcnucWeb <- function(object, as.string = FALSE, ..., socket = autosocket()){
#
# Should call gfrag directly... need to implement as.string for this
#
getSequenceSocket <- function(socket, name, start, length, as.string = FALSE){
request <- paste("gfrag&name=", name, "&start=", formatC(start, format = "d"),
"&length=", formatC(length, format = "d"), sep = "")
writeLines(request, socket, sep = "\n")
answerFromServer <- readLines(socket, n = 1)
#
# Check that there is an answer from server:
#
if(length(answerFromServer) == 0){
warning(paste("Empty answer from server with sequence name:", name))
return(NA)
} else {
#
# Check that no error code is returned by server:
#
if(substr(x = answerFromServer, start = 1, stop = 5) == "code="){
warning(paste("Server returned error code:", answerFromServer, "with sequence name:", name))
return(NA)
}
#
# Extract sequence from server answer:
#
sequence <- unlist(strsplit(answerFromServer, split = "&"))[2]
#
# Returns the sequence either as a string or as a vector of single chars:
#
if( as.string ){
return(sequence)
} else {
return(s2c(sequence))
}
}
}
getSequenceSocket(socket, object, start = 1, length = attr(object, "length"), as.string = as.string)
}
getSequence.qaw <- function(object, as.string = FALSE, ...) getSequence(object$req, ...)
getSequence.logical <- function (object, as.string = FALSE, ...)
object # so that NA is returned for virtual lists
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