Views objects
The Views virtual class is a general container for storing a set of views on an arbitrary Vector object, called the "subject".
Its primary purpose is to introduce concepts and provide some facilities that can be shared by the concrete classes that derive from it.
Some direct subclasses of the Views class are: RleViews, XIntegerViews (defined in the XVector package), XStringViews (defined in the Biostrings package), etc...
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL):
This constructor is a generic function with dispatch on argument
subject. Specific methods must be defined for the subclasses
of the Views class. For example a method for
XString subjects is defined
in the Biostrings package that returns an
XStringViews
object. There is no default method.
The treatment of the start, end and width
arguments is the same as with the IRanges constructor,
except that, in addition, Views allows start to be an
IntegerRanges object. With this feature,
Views(subject, IRanges(my_starts, my_ends, my_widths, my_names))
and Views(subject, my_starts, my_ends, my_widths, my_names)
are equivalent (except when my_starts is itself a
IntegerRanges object).
In the code snippets below, from is a Views object:
as(from, "IRanges"): Creates an IRanges object
containing the view locations in from.
All the accessor-like methods defined for IRanges objects
work on Views objects. In addition, the following accessors are defined
for Views objects:
subject(x):
Return the subject of the views.
x[i]: Select the views specified by i.
x[[i]]:
Extracts the view selected by i as an object of the same class
as subject(x). Subscript i can be a single integer
or a character string.
The result is the subsequence of subject(x) defined by
window(subject(x), start=start(x)[i], end=end(x)[i])
or an error if the view is "out of limits" (i.e. start(x)[i] < 1
or end(x)[i] > length(subject(x))).
c(x, ..., ignore.mcols=FALSE): Concatenate Views objects.
They must have the same subject.
trim(x, use.names=TRUE):
Equivalent to
restrict(x, start=1L, end=length(subject(x)), keep.all.ranges=TRUE,
use.names=use.names).
subviews(x, start=NA, end=NA, width=NA, use.names=TRUE):
start, end, and width arguments must be vectors
of integers, eventually with NAs, that contain coordinates relative
to the current ranges. Equivalent to
trim(narrow(x, start=start, end=end, width=width, use.names=use.names)).
successiveViews(subject, width, gapwidth=0, from=1):
Equivalent to Views(subject, successiveIRanges(width, gapwidth, from)).
See ?successiveIRanges for a description of the width,
gapwidth and from arguments.
Hervé Pagès
Some direct subclasses of the Views class: RleViews-class, XIntegerViews-class, XDoubleViews-class, XStringViews-class.
showClass("Views") # shows (some of) the known subclasses
## Create a set of 4 views on an XInteger subject of length 10:
subject <- Rle(3:-6)
v1 <- Views(subject, start=4:1, end=4:7)
## Extract the 2nd view:
v1[[2]]
## Some views can be "out of limits"
v2 <- Views(subject, start=4:-1, end=6)
trim(v2)
subviews(v2, end=-2)
## See ?`XIntegerViews-class` in the XVector package for more examples.Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.