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 |
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 convertx
into an AAString object by readingnchar
letters starting at positionstart
inx
.
Accessor methods
In the code snippet below, x
is an AAString object.
-
alphabet(x)
: Ifx
is an AAString object, then return the Amino Acid alphabet (see above). See the corresponding man pages whenx
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)