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:

     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".

     'matchPDict' function returns an MIndex object.

_A_c_c_e_s_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.

