AAString-class {Biostrings} | R Documentation

## AAString objects

### Description

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

### Usage

    AAString(x="", start=1, nchar=NA)

    ## Predefined constants:
    AA_ALPHABET       # full Amino Acid alphabet
    AA_STANDARD       # first 20 letters only
    AA_PROTEINOGENIC  # first 22 letters only

### Arguments

`x` | A single string.
`start, nchar` | Where to start reading from in `x` and how many letters to read.

### Details

The AAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with an AAString object (inheritance).

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

### The Amino Acid alphabet

This alphabet contains all letters from the Single-Letter Amino Acid Code (see `?AMINO_ACID_CODE`) plus `"*"` (the stop letter), `"-"` (the gap letter), `"+"` (the hard masking letter), and `"."` (the not a letter or not available letter). It is stored in the `AA_ALPHABET` predefined constant (character vector).

The `alphabet()` function returns `AA_ALPHABET` when applied to an AAString object.

### Constructor-like functions and generics

In the code snippet below, `x` can be a single string (character vector of length 1) or a BString object.

  `AAString(x="", start=1, nchar=NA)`: Tries to convert `x` into an AAString object by reading `nchar` letters starting at position `start` in `x`.

### Accessor methods

In the code snippet below, `x` is an AAString object.

  `alphabet(x)`: If `x` is an AAString object, then return the Amino Acid alphabet (see above). See the corresponding man pages when `x` is a BString, DNAString or RNAString object.

### Author(s)

H. Pagès

### See Also

`AMINO_ACID_CODE`, `letter`, XString-class, `alphabetFrequency`

### Examples

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

[Package Biostrings version 2.62.0 Index]