BString-class {Biostrings}R Documentation

The BString class

Description

The BString class is a general container for storing a big string (a long sequence of characters) and to make its manipulation easy and efficient. The DNAString, RNAString and AAString classes are direct BString derivations with the more specific purpose of storing a DNA sequence (DNAString), a RNA sequence (RNAString) or a sequence of amino acids (AAString).

Details

The 2 main differences between a BString object and a standard character vector are: (1) the data stored in a BString object are not copied on object duplication and (2) a BString can only store a single string (see the BStringViews for an efficient way to store a collection of big strings in a single object). A BString object can be used to store any non-empty string based on a single-byte character set.

Accesor methods

In the code snippets below, x is a BString (or derived) object and i is a numeric vector.

letter(x, i): [TODO: Document me]

Constructor-like functions and generics

In the code snippet below, src can be a character vector or a BString (or derived) object.

BString(src): [TODO: Document me]

Standard generic methods

In the code snippets below, x, object, e1 and e2 are BString (or derived) objects, and i is a numeric vector.

length(x) or nchar(x): Used to get the length of a BString, i.e., its number of letters
x[i]: [TODO: Document me]
e1 == e2: [TODO: Document me]
e1 != e2: [TODO: Document me]
as.character(x): [TODO: Document me]
toString(x): [TODO: Document me]

Other functions and generics

In the code snippets below, x is a BString (or derived) object and first and last are single numerics.

subBString(x, first, last): [TODO: Document me]

Author(s)

H. Pages

See Also

DNAString-class, RNAString-class, AAString-class BStringViews-class

Examples

  b <- BString("I am a BString object")
  length(b)

[Package Biostrings version 2.2.1 Index]