MIndex-class           package:Biostrings           R Documentation

_M_I_n_d_e_x _o_b_j_e_c_t_s

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

     The MIndex class is the basic container for storing the matches of
     a set of patterns in a subject sequence.

_D_e_t_a_i_l_s:

     THIS IS STILL WORK IN PROGRESS!

     An MIndex object contains the matches (start/end locations) of a
     set of patterns found in an XString object called "the subject
     string" or "the subject sequence" or simply "the subject".

     The 'matchPDict' function returns an MIndex object.

     MORE TO COME SOON...

_A_c_c_e_s_o_r _m_e_t_h_o_d_s:

     In the code snippets below, 'x' is an MIndex object.


      'length(x)': The number of patterns that matches are stored for.

      'names(x)': The names of the patterns that matches are stored
          for.

      'startIndex(x)': A list containing the starting positions of the
          matches for each pattern.

      'endIndex(x)': A list containing the ending positions of the
          matches for each pattern.

      'countIndex(x)': An integer vector containing the number of
          matches for each pattern.


_S_u_b_s_e_t_t_i_n_g _m_e_t_h_o_d_s:

     In the code snippets below, 'x' is an MIndex object.


      'x[[i]]': Extract the matches for the i-th pattern as an IRanges
          object.


_O_t_h_e_r _u_t_i_l_i_t_y _m_e_t_h_o_d_s _a_n_d _f_u_n_c_t_i_o_n_s:

     In the code snippets below, 'x' and 'mindex' are MIndex objects
     and 'subject' is the XString object containing the sequence in
     which the matches were found.


      'unlist(x, recursive=TRUE, use.names=TRUE)': Return all the
          matches in a single IRanges object. 'recursive' and
          'use.names' are ignored.

      'extractAllMatches(subject, mindex)': Return all the matches in a
          single XStringViews object.


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

     H. Pages

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

     'matchPDict', PDict-class, IRanges-class, XStringViews-class

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

       ## See ?matchPDict and ?`matchPDict-inexact` for some examples.

