AAString-class {Biostrings} | R Documentation |
An AAString object allows efficient storage and manipulation of a long amino acid sequence.
The AAString class is a direct XString subtype (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).
This alphabet contains all letters from the
Single-Letter Amino Acid Code (see ?AMINO_ACID_CODE
)
+ the stop ("*"
), the gap ("-"
) and the hard masking
("+"
) letters.
It is stored in the AA_ALPHABET
constant (character vector).
The alphabet
method also returns
AA_ALPHABET
when applied to an AAString
object and is provided for convenience only.
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, check=TRUE)
:
Tries to convert x
into an AAString object by reading
nchar
letters starting at position start
in x
.
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.
H. Pages
AMINO_ACID_CODE
,
letter
,
XString-class,
alphabetFrequency
AA_ALPHABET a <- AAString("MARKSLEMSIR*") length(a) alphabet(a)