1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
#
# To extract a subsequence from a sequence
#
getFrag <- function(object, begin, end, ...) UseMethod("getFrag")
getFrag.default <- function(object, begin, end, ...)
stop(paste("no getFrag method for objects of class:", class(object)))
getFrag.list <- function(object, begin, end, ...)
lapply(seq_len(length(object)), function(i) getFrag(object[[i]], begin = begin, end = end, ...))
getFrag.character <- function(object, begin, end, ...){
if(length(object) == 1) object <- s2c(object)
if(begin > length(object) || end > length(object) || begin > end) stop("borns are not correct")
return(object[begin:end])
}
getFrag.SeqFastadna <- function(object, begin, end, ..., name = getName(object)){
if(end > getLength(object)) stop("invalid end")
as.SeqFrag(getSequence(object, as.string = FALSE)[begin:end], begin = begin, end = end,
name = name)
}
getFrag.SeqFastaAA <- getFrag.SeqFastadna
getFrag.SeqFrag <- function(object, begin, end, ..., name = getName(object)){
if((end<begin) || (end>getLength(object))) stop("invalid end")
newBegin <- attr(object, "begin") + begin - 1
newEnd <- attr(object, "begin") + end - 1
newSeq <- object[begin:end]
as.SeqFrag(object = newSeq, begin = newBegin, end = newEnd, name = name)
}
getFrag.SeqAcnucWeb <- function(object, begin, end, ..., socket = autosocket(), name = getName(object)){
lobj <- getLength(object)
if(end > lobj) stop("end parameter is too large")
if(begin > lobj) stop("begin parameter is too large")
length <- end - begin + 1
# newSeq <- getSequenceSocket(socket, object, start = begin, length = length)
newSeq <- gfrag(what = name, start = begin, length = length, idby = "name", socket = socket)
as.SeqFrag(newSeq, begin = begin, end = end, name = name)
}
getFrag.qaw <- function(object, begin, end, ...) getFrag(object$req, begin, end, ...)
getFrag.logical <- function (object, begin, end, ...)
object # so that NA is returned for virtual lists
|
