AAString-class          package:Biostrings          R Documentation

AAString objects

Description:

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

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') + 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.

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. Pages

See Also:

     'AMINO_ACID_CODE', 'letter', XString-class, 'alphabetFrequency'

Examples:

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

