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#
# To translate sequences:
#
getTrans <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
UseMethod("getTrans")
getTrans.default <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
stop(paste("no getTrans method for objects of class:", class(object)))
getTrans.list <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
lapply(seq_len(length(object)),
function(i) getTrans(object[[i]], sens = sens, NAstring = NAstring, ambiguous = ambiguous, ...))
getTrans.character <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
translate(seq = object, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
getTrans.SeqFastadna <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1){
dnaseq <- getSequence(object, as.string = FALSE)
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
}
getTrans.SeqFrag <- getTrans.SeqFastadna
getTrans.SeqAcnucWeb <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto"){
dnaseq <- getSequence(object, as.string = FALSE)
if(numcode == "auto") numcode <- attr(object, "ncbigc")
if(frame == "auto") frame <- attr(object, "frame")
translate(seq = dnaseq, frame = frame, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous)
}
getTrans.qaw <- function(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...) getTrans(object$req, ...)
getTrans.logical <- function (object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
object # so that NA is returned for virtual lists
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