XStringViews-constructors {Biostrings} | R Documentation

## Basic functions for creating or modifying XStringViews objects

### Description

A set of basic functions for creating or modifying XStringViews objects.

### Usage

      views(subject, start=NA, end=NA)
      adjacentViews(subject, width, gapwidth=0)
      XStringViews(x, subjectClass, collapse="")
      trim(x, use.names=TRUE)
      subviews(x, start=NA, end=NA, width=NA, use.names=TRUE)

### Arguments

`subject` | An XString object or a single string.
`start` | An integer vector containing the start positions of the views.
`end` | An integer vector containing the end positions of the views.
`width` | An integer vector containing the widths of the views.
`gapwidth` | An integer vector containing the widths of the gaps between the views.
`x` | An XString object or a character vector for `XStringViews`. An XStringViews object for `trim` and `subviews`.
`subjectClass` | The class to be given to the subject of the XStringViews object created and returned by the function. Must be the name of one of the direct XString subtypes i.e. `"BString"`, `"DNAString"`, `"RNAString"` or `"AAString"`.
`collapse` | An optional character string to be inserted between the views of the XStringViews object created and returned by the function.
`use.names` | [TODO]

### Details

The `views` function returns an XStringViews object containing views on `subject` with start and end positions given in the `start` and `end` vectors.

The `adjacentViews` function returns an XStringViews object containing views on `subject` with widths given in the `width` vector and separated by gaps of width `gapwidth`. The first view starts at position 1.

The `XStringViews` constructor will try to create an XStringViews object from the value passed to its `x` argument. If `x` itself is an XStringViews object, the returned object is obtained by coercing its subject to the class specified by `subjectClass`. If `x` is an XString object, the returned object is made of a single view that starts at the first letter and ends at the last letter of `x` (in addition `x` itself is coerced to the class specified by `subjectClass` when specified). If `x` is a character vector, the returned object has one view per character string in `x` (and its subject is an instance of the class specified by `subjectClass`).

### Value

All these functions return an XStringViews object `y` with the following number of views (`length(y)`): `max(length(start), length(end)` for the `views` function and `length(width)` for the `adjacentViews` function. For the `XStringViews` constructor, `length(y)` is `1` when `x` is an XString object and `length(x)` otherwise.

### See Also

XStringViews-class, XString-class, `gaps`

### Examples

      ## 'start' and 'end' are recycled
      views("abcdefghij", 2:1, 4)
      views("abcdefghij", 5:7, )
      views("abcdefghij", , 5:7)

      ## Views can be "out of limits"
      views("abcdefghij", 2:0, 4)

      ## Views on a DNAString object
      v12 <- views(DNAString("TAATAATG"), -2:9, 0:11)

      ## Creating adjacent views
      v3 <- adjacentViews("abcdefghij", 4:2, gapwidth=1)

      XStringViews(v12, subjectClass="RNAString")
      XStringViews(AAString("MARKSLEMSIR*"))
      XStringViews("abcdefghij", subjectClass="BString")

      ## Applying gaps() to an XStringViews object
      v2 <- views("abCDefgHIJK", start=c(8, 3), end=c(14, 4))
      gaps(v2)

[Package Biostrings version 2.8.18 Index]