AAString-class          package:Biostrings          R Documentation

_T_h_e _A_A_S_t_r_i_n_g _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_D_e_t_a_i_l_s:

     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).

_T_h_e _A_A_S_t_r_i_n_g _a_l_p_h_a_b_e_t:

     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.

_C_o_n_s_t_r_u_c_t_o_r-_l_i_k_e _f_u_n_c_t_i_o_n_s _a_n_d _g_e_n_e_r_i_c_s:

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

      'AAString(src)': [TODO: Document me]

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

     'BString', 'AMINO_ACID_CODE', 'BStringViews'

_E_x_a_m_p_l_e_s:

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