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\name{XDoubleViews-class}
\docType{class}
% Classes:
\alias{class:XDoubleViews}
\alias{XDoubleViews-class}
\alias{XDoubleViews}
% Constructors:
\alias{Views,XDouble-method}
\alias{Views,numeric-method}
% Methods:
\alias{show,XDoubleViews-method}
\alias{==,XDoubleViews,XDoubleViews-method}
\alias{==,XDoubleViews,XDouble-method}
\alias{==,XDoubleViews,numeric-method}
\alias{==,XDouble,XDoubleViews-method}
\alias{==,numeric,XDoubleViews-method}
\title{The XDoubleViews class}
\description{
The XDoubleViews class is the basic container for storing a set of views
(start/end locations) on the same XDouble object.
}
\details{
An XDoubleViews object contains a set of views (start/end locations) on the
same \link{XDouble} object called "the subject numeric vector" or simply
"the subject".
Each view is defined by its start and end locations: both are integers such
that start <= end.
An XDoubleViews object is in fact a particular case of a
\link[IRanges]{Views} object (the XDoubleViews class contains the
\link[IRanges]{Views} class) so it can be manipulated in a similar manner:
see \code{?\link[IRanges]{Views}} for more information.
Note that two views can overlap and that a view can be "out of limits"
i.e. it can start before the first element of the subject or/and end
after its last element.
}
\section{Other methods}{
In the code snippets below,
\code{x}, \code{object}, \code{e1} and \code{e2} are XDoubleViews objects,
and \code{i} can be a numeric or logical vector.
\describe{
\item{\code{x[[i]]}:}{
Extract a view as an \link{XDouble} object.
\code{i} must be a single numeric value (a numeric vector of length 1).
Can't be used for extracting a view that is "out of limits" (raise an
error). The returned object has the same \link{XDouble} subtype as
\code{subject(x)}.
}
\item{\code{e1 == e2}:}{
A vector of logicals indicating the result of the view by
view comparison. The views in the shorter of the two XDoubleViews
object being compared are recycled as necessary.
}
\item{\code{e1 != e2}:}{
Equivalent to \code{!(e1 == e2)}.
}
}
}
\author{
P. Aboyoun for the \code{XIntegerViews*} code, which was adapted to work
over \code{XDouble}'s by S. Lianoglou
}
\seealso{
\link{view-summarization-methods},
\link[IRanges]{Views-class},
\link{XDouble-class},
\link{XIntegerViews-class}
}
\examples{
## One standard way to create an XDoubleViews object is to use
## the Views() constructor:
subject <- as(rnorm(6), "XDouble")
v4 <- Views(subject, start=3:0, end=5:8)
v4
subject(v4)
length(v4)
start(v4)
end(v4)
width(v4)
## Attach a comment to views #3 and #4:
names(v4)[3:4] <- "out of limits"
names(v4)
## A more programatical way to "tag" the "out of limits" views:
idx <- start(v4) < 1 | end(v4) > length(subject(v4))
names(v4)[idx] <- "out of limits"
## Extract a view as an XDouble object:
v4[[2]]
## It is an error to try to extract an "out of limits" view:
\dontrun{
v4[[3]] # Error!
}
## Here the first view doesn't even overlap with the subject:
subject <- as(c(97, 97, 97, 45, 45, 98), "XDouble")
Views(subject, start=-3:4, end=-3:4 + c(3:6, 6:3))
## Some fast view* functionalities:
x <- rnorm(55)
bounds <- IRanges(c(1, 11, 35, 20), width=c(5, 10, 15, 28))
v <- Views(x, bounds)
val <- viewMins(v)
expect <- sapply(1:length(bounds), function(i) {
min(x[start(bounds)[i]:end(bounds[i])])
})
stopifnot(all(val == expect))
}
\keyword{methods}
\keyword{classes}
|
