Views-class {IRanges} | R Documentation

## Views objects

### Description

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...

### Constructor

  `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).

### Coercion

In the code snippets below, `from` is a Views object:

  `as(from, "IRanges")`: Creates an `IRanges` object containing the view locations in `from`.

### Accessor-like methods

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.

### Subsetting

  `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))`).

### Concatenation

  `c(x, ..., ignore.mcols=FALSE)`: Concatenate `Views` objects. They must have the same subject.

### Other methods

  `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.

### Author(s)

Hervé Pagès

### See Also

IRanges-class, Vector-class, IRanges-utils, XVector.

Some direct subclasses of the Views class: RleViews-class, XIntegerViews-class, XDoubleViews-class, XStringViews-class.

`findOverlaps`.

### Examples

    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.

[Package IRanges version 2.22.2 Index]