matchPattern           package:Biostrings           R Documentation

_S_t_r_i_n_g _s_e_a_r_c_h_i_n_g _f_u_n_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generic that finds all matches of a pattern in a BString.
     Currently only the ``shift-or'' algorithm is available.

_U_s_a_g_e:

       matchPattern(pattern, subject, algorithm="shift-or", mismatch=0, fixed=NA)
       countPattern(pattern, subject, algorithm="shift-or", mismatch=0, fixed=NA)
       mismatch(pattern, x, fixed=NA)

_A_r_g_u_m_e_n_t_s:

 pattern: The pattern string. 

 subject: A BString (or DNAString or RNAString) object containing the
          subject string. 

algorithm: One of the following: '"boyer-moore"', '"forward-search"' or
          '"shift-or"' (currently, only '"shift-or"' is available). 

mismatch: The number of mismatches allowed. If non-zero a fuzzy string
          searching algorithm is used for matching. 

   fixed: A logical.  If 'TRUE', 'pattern' is a string to be matched as
          is. 

       x: A BStringViews object (typically, one returned by
          code{matchPattern(pattern, subject)}). 

_D_e_t_a_i_l_s:

_V_a_l_u_e:

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s: