AAString-class {Biostrings}R Documentation

The AAString class

Description

A AAString object allows efficient storage and manipulation of a long amino acid sequence.

Details

The AAString class derives directly from the BString class (with no additional slot). All functions and methods described in the BString man page also work with a AAString object (inheritance).

Unlike a BString object that allows storage of any non-empty string (based on a single-byte character set) a AAString object can only store a non-empty string based on the AAString alphabet (see below).

The AAString alphabet

This alphabet contains all letters from the Single-Letter Amino Acid Code (see AMINO_ACID_CODE) + the stop letter "*". It is stored in the AA_ALPHABET constant (character vector). The alphabet method also returns AA_ALPHABET when applied to a AAString object and is provided for convenience only.

Constructor-like functions and generics

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

AAString(src): Tries to convert src into an AAString object. src can be a single string (character vector of length 1) or a BString object.

Other functions and generics

In the code snippets below, x must be a BString (or derived) object.

alphabet(x): If x is of class AAString, return the AAString alphabet (see above). See the corresponding man pages when x is of class BString, DNAString or RNAString.

Author(s)

H. Pages

See Also

AMINO_ACID_CODE, subBString, letter, BString-class, BStringViews-class

Examples

  AA_ALPHABET
  a <- AAString("MARKSLEMSIR*")
  length(a)
  alphabet(a)

[Package Biostrings version 2.6.6 Index]