BioAlphabet-class         package:Biostrings         R Documentation

_C_l_a_s_s "_B_i_o_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 _b_i_o_l_o_g_y

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

     Each object of class "BioAlphabet" represents a particular
     alphabet used to represent some biological 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. 

     '_g_a_p': Object of class '"character"', the gap character in the
          alphabet. 

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

     _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 alphabet object. for
          the given letters. If one of the letters is not the gap
          character '-', then it is added as the first letter. An
          encoding also created which is stored in the 'mapping' slot. 

     _g_a_p_l_e_t_t_e_r(_x) <- _v_a_l_u_e Change the letter representing gaps in 'x'
          of class "BioPatternAlphabet" to 'value' which must be a
          single letter not in the base alphabet of 'x'.

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

     Saikat DebRoy

_S_e_e _A_l_s_o:

     'NucleotideAlphabet-class' and 'AminoAcidAlphabet-class', for two
     subclasses of the '"BioAlphabet"' class.

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

     new("NucleotideAlphabet", letters=c('A', 'G', 'C', 'T'))
     new("NucleotideAlphabet", letters=c('-', 'A', 'G', 'C', 'T'))

