BioPatternAlphabet-class     package:Biostrings     R Documentation

_C_l_a_s_s _r_e_p_r_e_s_e_n_t_i_n_g _a_l_p_h_a_b_e_t_s _u_s_e_d _i_n _p_a_t_t_e_r_n_s _f_o_r _m_a_t_c_h_i_n_g
_b_i_o_l_o_g_i_c_a_l _s_e_q_u_e_n_c_e_s

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

     Each object of class "BioPatternAlphabet" represents an alphabet
     for patterns that is used to match a specific type of biological
     sequence.

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

     Objects can be created by calls of the form
     'new("BioPatternAlphabet", baseAlphabet, letters)' where 'letters'
     is a named character vector with the names being single letters
     not in the base alphabet and the value corresponding to each name
     are strings made of letters from the base alphabet. Each such name
     value pair defines a new letter in the pattern alphabet which
     matches all the letters in its value string.

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

     '_b_a_s_e_A_l_p_h_a_b_e_t': Object of class '"BioAlphabet"', the base alphabet
          that for the letters matched by members of this pattern
          alphabet. 

     '_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. 

_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 "BioPatternAlphabet" return a new uninitialized
          "BioString" object for that alphabet with length
          'length.string'. See 'BioString-class' for more details.

     _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'.

     _i_n_i_t_i_a_l_i_z_e(._O_b_j_e_c_t, ...) Method to initialize an object of class
          "BioPatternAlphabet". Usually used indirectly via a call to
          'new'

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

     Saikat DebRoy

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

     'BioAlphabet-class'

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

     dnaAlph <- new("BioPatternAlphabet",
                    DNAAlphabet(), c(N="AGCT",
                                     B="CGT",
                                     D="AGT",
                                     H="ACT",
                                     K="GT",
                                     M="AC",
                                     R="AG",
                                     S="CG",
                                     V="ACG",
                                     W="AT",
                                     Y="CT"))
     dnaAlph

