prototype = prototype(elementType = "Ranges"),
prototype = prototype(elementType = "IRanges"),
prototype = prototype(elementType = "IRanges",
prototype = prototype(elementType = "NormalIRanges"),
return("at least one element of object is not normal")
setGeneric(".SEW<-", signature="x",  # not exported
function(x, FUN, check=TRUE, value) standardGeneric(".SEW<-"))
if (!identical(lapply(x, names), lapply(value, names)) &&
value <- split(value, factor(space(x), names(x)))
stop("'value' must extend class IntegerList or integer")
x[[i]] <- FUN(x[[i]], check = check, value = value[[i]])
.SEW(x, FUN = "start<-", check = check) <- value
.SEW(x, FUN = "end<-", check = check) <- value
.SEW(x, FUN = "width<-", check = check) <- value
FUN(x@unlistData, check = check, value = value)
space <- factor(rep.int(space, elementLengths(x)), space)
stop("'value' must be a single string or NULL")
.Call2("CompressedIRangesList_isNormal", x, TRUE, PACKAGE = "IRanges"))
.Call2("SimpleIRangesList_isNormal", x, PACKAGE = "IRanges"))
RangesList <- function(..., universe = NULL)
stop("'universe' must be a single string or NULL")
if (length(ranges) == 1 && is.list(ranges[[1L]]))
stop("all elements in '...' must be Ranges objects")
IRangesList <- function(..., universe = NULL, compress = TRUE)
(is(ranges[[1L]], "LogicalList") || is(ranges[[1L]], "RleList"))) {
!is(ranges[[1L]], "Ranges") && !is(ranges[[2L]], "Ranges")) {
stop("'compress' must be TRUE when passing the 'start' and 'end' arguments")
ans_start <- IntegerList(ranges[["start"]], compress = TRUE)
ans_end <- IntegerList(ranges[["end"]], compress = TRUE)
stop("'start' and 'end' are not compatible")
stop("all elements in '...' must be IRanges objects")
rangesListSingleSquareBracket <- function(x, i, j, ..., drop)
stop("'[' subsetting by RangesList is defunct.\n",
if (!all(sapply(sapply(args, universe), identical, universe(x))))
stop("all RangesList objects to merge must have the same universe")
names <- spaces <- unique(do.call(c, spaceList))
if (!all(unlist(lapply(args, length)) == length(x)))
stop("if any RangesList objects to merge are missing names, ",
function(x, y, ...) .RangesList.merge(x, ...)
function(x, y, ...) .RangesList.merge(y, ...)
function(x, y, ...) .RangesList.merge(x, y, ...)
cat(classNameForDisplay(x), " of length ", x_len, "\n",
if (x_len >= 3L && cumsumN[3L] <= 20L) {
} else if (x_len >= 2L && cumsumN[2L] <= 20L) {
as.data.frame.RangesList <- function(x, row.names=NULL, optional=FALSE, ...)
.as.list.CompressedNormalIRangesList <- function(x, use.names = TRUE)
function(x, recursive = TRUE, use.names = TRUE)
x <- newList("SimpleIRangesList", lapply(x, as, "IRanges"))
stop("cannot coerce a non-logical 'RleList' or a logical 'RleList' ",
"with NAs to a CompressedIRangesList object")
ranges <- as(unlist(from, use.names = FALSE), "IRanges")
"with NAs to a SimpleIRangesList object")
"with NAs to a CompressedNormalIRangesList object")
"with NAs to a SimpleNormalIRangesList object")
stop("'x' must be a CompressedNormalIRangesList object")
function(x, ..., na.rm) CompressedNormalIRangesList.max(x, TRUE))
function(x, ..., na.rm) CompressedNormalIRangesList.min(x, TRUE))