NucleotideAlphabet-class     package:Biostrings     R Documentation

_C_l_a_s_s "_N_u_c_l_e_o_t_i_d_e_A_l_p_h_a_b_e_t" _r_e_p_r_e_s_e_n_t_s _a_l_p_h_a_b_e_t_s _u_s_e_d _i_n _D_N_A _o_r _R_N_A

_D_e_s_c_r_i_p_t_i_o_n:

     Each object of class "NucleotideAlphabet" represents a nucleotide
     alphabet. Usually this is the RNA or DNA alphabet and consists of
     'A', 'C', 'G', 'T' for DNA and 'A', 'C', 'G', 'U' for RNA along
     with '-' which represents a gap in the sequence.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     A virtual Class: No objects may be created from it.

_S_l_o_t_s:

     '_l_e_t_t_e_r_s': Object of class '"character"' representing the letters
          of the alphabet. Usually roman upper case letters are used.
          The one exception is the gap character which is always '-'.

     '_m_a_p_p_i_n_g': Object of class '"integer"' representing the encoding
          used to represent these objects internally. 

_E_x_t_e_n_d_s:

     Class '"BioAlphabet"', directly.

_M_e_t_h_o_d_s:

     _B_i_o_S_t_r_i_n_g_N_e_w_V_a_l_u_e_s(_a_l_p_h_a_b_e_t, _l_e_n_g_t_h._s_t_r_i_n_g) Given 'alphabet' of
          class "NucleotideAlphabet" return a new uninitialized
          "BioString" object for that alphabet with length
          'length.string'. See 'BioString-class' for more details.

     _i_n_i_t_i_a_l_i_z_e(._O_b_j_e_c_t, _l_e_t_t_e_r_s) Initialize an nucleotide alphabet
          object for the given letters. If one of the letters is not
          the gap character '-', then it is added as the first letter.
          With the gap character, the length of the alphabet should be
          five. An encoding also created which is stored in the
          'mapping' slot. 

_A_u_t_h_o_r(_s):

     Saikat DebRoy

_E_x_a_m_p_l_e_s:

     myDNAAlph <- new("NucleotideAlphabet", letters=c('A', 'G', 'C', 'T'))
     myDNAAlph
     BioStringNewValues(myDNAAlph, 20)

