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### =========================================================================
### XStringViews objects
### -------------------------------------------------------------------------
###
### The XStringViews class is the basic container for storing a set of views
### (start/end locations) on the same XString object, called the "subject"
### string.
###
setClass("XStringViews",
contains="Views",
representation(
subject="XString"
)
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Unsafe constructor (not exported). Use only when 'start' and 'width' are
### guaranteed to be valid.
###
unsafe.newXStringViews <- function(subject, start, width)
new2("XStringViews", subject=subject,
ranges=IRanges(start=start, width=width),
check=FALSE)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### User-friendly constructor.
###
setMethod("Views", "XString",
function(subject, start=NULL, end=NULL, width=NULL, names=NULL)
IRanges:::new_Views(subject, start=start,
end=end,
width=width,
names=names,
Class="XStringViews")
)
setMethod("Views", "character",
function(subject, start=NULL, end=NULL, width=NULL, names=NULL)
{
xsubject <- XString(NULL, subject)
Views(xsubject, start=start, end=end, width=width, names=names)
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Accessor-like methods.
###
setMethod("nchar", "XStringViews",
function(x, type="chars", allowNA=FALSE)
{
if (length(x) == 0)
return(integer(0))
start0 <- pmax.int(start(x), 1L)
end0 <- pmin.int(end(x), nchar(subject(x)))
ans <- end0 - start0 + 1L
ans[ans < 0L] <- 0L
ans
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "seqtype" and "seqtype<-" methods.
###
setMethod("seqtype", "XStringViews", function(x) seqtype(subject(x)))
### Does NOT downgrade 'x' to an XStringViews instance! (endomorphism)
setReplaceMethod("seqtype", "XStringViews",
function(x, value)
{
## could be done with 'seqtype(subject(x)) <- value'
## if `subject<-` was available
subject <- subject(x)
seqtype(subject) <- value
x@subject <- subject
x
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Coercion.
###
### From XStringViews to XStringSet.
fromXStringViewsToStringSet <- function(x,
out.of.limits=c("ok", "warning", "error"),
use.names=FALSE)
{
out.of.limits <- match.arg(out.of.limits)
ans_ranges <- restrict(as(x, "IRanges"), start=1L, end=nchar(subject(x)),
keep.all.ranges=TRUE,
use.names=use.names)
if (out.of.limits != "ok" && any(width(ans_ranges) < width(x))) {
if (out.of.limits == "warning")
warning("trimming \"out of limits\" views")
else
stop("'x' has \"out of limits\" views")
}
extractList(subject(x), ans_ranges)
}
### We need this so that B/DNA/RNA/AAStringSet() used below work on an
### XStringViews object.
setMethod("XStringSet", "XStringViews",
function(seqtype, x, start=NA, end=NA, width=NA, use.names=TRUE)
{
y <- fromXStringViewsToStringSet(x, out.of.limits="warning",
use.names=use.names)
XStringSet(seqtype, y,
start=start, end=end, width=width, use.names=TRUE)
}
)
setAs("XStringViews", "XStringSet",
function(from) fromXStringViewsToStringSet(from, out.of.limits="warning",
use.names=TRUE))
setAs("XStringViews", "BStringSet", function(from) BStringSet(from))
setAs("XStringViews", "DNAStringSet", function(from) DNAStringSet(from))
setAs("XStringViews", "RNAStringSet", function(from) RNAStringSet(from))
setAs("XStringViews", "AAStringSet", function(from) AAStringSet(from))
### From XStringSet to XStringViews.
.XStringSetAsViews <- function(from) successiveViews(unlist(from), width(from))
setAs("XStringSet", "Views", .XStringSetAsViews)
setAs("XStringSet", "XStringViews", .XStringSetAsViews)
setMethod("as.data.frame", "XStringViews",
function (x, row.names = NULL, optional = FALSE, ...)
{
as.data.frame(as(x, "XStringSet"), row.names, optional, ...)
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "show" method.
###
### The 2 helper functions below convert a given view on an XString object
### into a character-string.
### Both assume that 'start' <= 'end' (so they don't check it) and
### padd the result with spaces to produce the "margin effect"
### if 'start' or 'end' are out of limits.
### nchar(XStringViews.get_view(x, start, end)) is always end-start+1
XStringViews.get_view <- function(x, start, end)
{
lx <- length(x)
if (end < 1 || start > lx)
return(format("", width=end-start+1))
Lmargin <- ""
if (start < 1) {
Lmargin <- format("", width=1-start)
start <- 1
}
Rmargin <- ""
if (end > lx) {
Rmargin <- format("", width=end-lx)
end <- lx
}
paste(Lmargin, XString.read(x, start, end), Rmargin, sep="")
}
### nchar(XStringViews.get_snippet(x, start, end, snippetWidth)) is <= snippetWidth
XStringViews.get_snippet <- function(x, start, end, snippetWidth)
{
if (snippetWidth < 7)
snippetWidth <- 7
width <- end - start + 1
if (width <= snippetWidth) {
XStringViews.get_view(x, start, end)
} else {
w1 <- (snippetWidth - 2) %/% 2
w2 <- (snippetWidth - 3) %/% 2
paste(XStringViews.get_view(x, start, start+w1-1),
"...",
XStringViews.get_view(x, end-w2+1, end), sep="")
}
}
XStringViews.show_vframe_header <- function(iW, startW, endW, widthW)
{
cat(format("", width=iW+1),
format("start", width=startW, justify="right"), " ",
format("end", width=endW, justify="right"), " ",
format("width", width=widthW, justify="right"), "\n",
sep="")
}
XStringViews.show_vframe_line <- function(x, i, iW, startW, endW, widthW)
{
start <- start(x)[i]
end <- end(x)[i]
width <- end - start + 1
snippetWidth <- getOption("width") - 6 - iW - startW - endW - widthW
cat(format(paste("[", i,"]", sep=""), width=iW, justify="right"), " ",
format(start, width=startW, justify="right"), " ",
format(end, width=endW, justify="right"), " ",
format(width, width=widthW, justify="right"), " ",
"[", XStringViews.get_snippet(subject(x), start, end, snippetWidth), "]\n",
sep="")
}
XStringViews.show_vframe <- function(x)
{
nhead <- get_showHeadLines()
ntail <- get_showTailLines()
cat("\nviews:")
lx <- length(x)
if (lx == 0)
cat(" NONE\n")
else {
cat("\n")
iW <- nchar(as.character(lx)) + 2 # 2 for the brackets
startMax <- max(start(x))
startW <- max(nchar(startMax), nchar("start"))
endMax <- max(end(x))
endW <- max(nchar(endMax), nchar("end"))
widthMax <- max(width(x))
widthW <- max(nchar(widthMax), nchar("width"))
XStringViews.show_vframe_header(iW, startW, endW, widthW)
if (lx <= nhead + ntail +1) {
for (i in seq_len(lx))
XStringViews.show_vframe_line(x, i, iW, startW, endW, widthW)
} else {
if (nhead > 0)
for (i in seq_len(nhead))
XStringViews.show_vframe_line(x, i, iW, startW, endW,
widthW)
cat(format("...", width=iW, justify="right"),
" ",
format("...", width=startW, justify="right"),
" ",
format("...", width=endW, justify="right"),
" ",
format("...", width=widthW, justify="right"),
" ...\n", sep="")
if (ntail > 0)
for (i in (lx-ntail+1L):lx)
XStringViews.show_vframe_line(x, i, iW, startW, endW,
widthW)
}
}
}
setMethod("show", "XStringViews",
function(object)
{
subject <- subject(object)
lsub <- length(subject)
cat(" Views on a ", lsub, "-letter ", class(subject), " subject", sep="")
cat("\nsubject:", toSeqSnippet(subject, getOption("width") - 9))
XStringViews.show_vframe(object)
}
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Equality.
###
### Assume that 'start1', 'end1', 'start2', 'end2' are single integers
### and that start1 <= end1 and start2 <= end2.
XStringViews.view1_equal_view2 <- function(x1, start1, end1, x2, start2, end2)
{
one <- as.integer(1)
w1 <- end1 - start1 + one
w2 <- end2 - start2 + one
if (w1 != w2)
return(FALSE)
lx1 <- length(x1)
isBlank1 <- end1 < one || start1 > lx1
lx2 <- length(x2)
isBlank2 <- end2 < one || start2 > lx2
if (isBlank1 && isBlank2)
return(TRUE)
if (isBlank1 || isBlank2)
return(FALSE)
# Left margin
LmarginSize1 <- start1 < one
LmarginSize2 <- start2 < one
if (LmarginSize1 != LmarginSize2)
return(FALSE)
if (LmarginSize1) {
# Both views have a left margin
if (start1 != start2)
return(FALSE)
start1 <- one
start2 <- one
}
# Right margin
RmarginSize1 <- end1 > lx1
RmarginSize2 <- end2 > lx2
if (RmarginSize1 != RmarginSize2)
return(FALSE)
if (RmarginSize1) {
# Both views have a right margin
if (end1 - lx1 != end2 - lx2)
return(FALSE)
end1 <- lx1
end2 <- lx2
}
# At this point, we can trust that 1 <= start1 <= end1 <= lx1
# and that 1 <= start2 <= end2 <= lx2.
subseq(x1, start=start1, end=end1) == subseq(x2, start=start2, end=end2)
}
### 'x' and 'y' must be XStringViews objects.
### Returns a logical vector of length max(length(x), length(y)).
### Recycle its arguments.
XStringViews.equal <- function(x, y)
{
lx <- length(x)
ly <- length(y)
if (lx < ly) {
tmp <- x
x <- y
y <- tmp
tmp <- lx
lx <- ly
ly <- tmp
}
if (ly == 0)
return(logical(0))
# Now we are sure that lx >= ly >= 1
ans <- logical(lx)
j <- 1
for (i in seq_len(lx)) {
ans[i] <- XStringViews.view1_equal_view2(
subject(x), start(x)[i], end(x)[i],
subject(y), start(y)[j], end(y)[j])
# Recycle
if (j < ly) j <- j + 1 else j <- 1
}
if (j != 1)
warning(paste("longer object length",
"is not a multiple of shorter object length"))
ans
}
### These methods are called if at least one side of the "==" (or "!=")
### operator is an XStringViews object. They have precedence over the
### corresponding methods defined for XString objects, i.e. they will
### be called if one side is an XStringViews object and the other side
### is an XString object.
### Typical use:
### v <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11)
### v == v[4]
### v == v[1]
### v2 <- Views(DNAString("G"), start=1, end=3)
### v == v2
### Also works if one side is an XString object:
### v == DNAString("ATG")
### RNAString("AUG") == v
### Whitespace matters:
### v == "TG"
### But this doesn't work neither ("TG " can't be converted to a DNAString
### object):
### v == "TG "
setMethod("==", signature(e1="XStringViews", e2="XStringViews"),
function(e1, e2)
{
if (!comparable_seqtypes(seqtype(e1), seqtype(e2))) {
class1 <- class(subject(e1))
class2 <- class(subject(e2))
stop("comparison between XStringViews objects with subjects of ",
"class \"", class1, "\" and \"", class2, "\" ",
"is not supported")
}
XStringViews.equal(e1, e2)
}
)
setMethod("==", signature(e1="XStringViews", e2="XString"),
function(e1, e2)
{
if (!comparable_seqtypes(seqtype(e1), seqtype(e2))) {
class1 <- class(subject(e1))
class2 <- class(e2)
stop("comparison between an XStringViews object with a subject of ",
"class \"", class1, "\" and a \"", class2, "\" instance ",
"is not supported")
}
XStringViews.equal(e1, as(e2, "Views"))
}
)
setMethod("==", signature(e1="XStringViews", e2="character"),
function(e1, e2)
{
if (!is(subject(e1), "BString"))
stop("comparison between an XStringViews object with a subject of ",
"class \"", class(subject(e1)), "\" and a character vector ",
"is not supported")
if (length(e2) == 0 || any(e2 %in% c("", NA)))
stop("comparison between an XStringViews object and a character ",
"vector of length 0 or with empty strings or NAs ",
"is not supported")
XStringViews.equal(e1, as(BStringSet(e2), "Views"))
}
)
setMethod("==", signature(e1="XString", e2="XStringViews"),
function(e1, e2) e2 == e1
)
setMethod("==", signature(e1="character", e2="XStringViews"),
function(e1, e2) e2 == e1
)
setMethod("!=", signature(e1="XStringViews", e2="XStringViews"),
function(e1, e2) !(e1 == e2)
)
setMethod("!=", signature(e1="XStringViews", e2="XString"),
function(e1, e2) !(e1 == e2)
)
setMethod("!=", signature(e1="XStringViews", e2="character"),
function(e1, e2) !(e1 == e2)
)
setMethod("!=", signature(e1="XString", e2="XStringViews"),
function(e1, e2) !(e1 == e2)
)
setMethod("!=", signature(e1="character", e2="XStringViews"),
function(e1, e2) !(e1 == e2)
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Other methods.
###
setMethod("as.character", "XStringViews",
function(x, use.names=TRUE, check.limits=TRUE)
{
if (!isTRUEorFALSE(check.limits))
stop("'check.limits' must be TRUE or FALSE")
if (check.limits)
out.of.limits <- "error"
else
out.of.limits <- "warning"
y <- fromXStringViewsToStringSet(x, out.of.limits=out.of.limits,
use.names=use.names)
as.character(y)
}
)
setMethod("as.matrix", "XStringViews",
function(x, use.names=TRUE)
{
## TODO: Supress this warning in BioC 2.12.
msg <- c("as.matrix() on an XStringViews object 'x' has changed ",
"behavior: now the\n views in 'x' must be of equal width ",
"and each view is converted into a row of\n",
" single characters. To achieve the old behavior, ",
"do 'as.matrix(ranges(x))'.\n To supress this warning, do ",
"'suppressWarnings(as.matrix(x))'.\n This warning will be ",
"removed in BioC 2.12.")
warning(msg)
y <- fromXStringViewsToStringSet(x, out.of.limits="error",
use.names=use.names)
as.matrix(y)
}
)
setMethod("toString", "XStringViews",
function(x, ...)
{
toString(as.character(x), ...)
}
)
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