PFAM-class            package:AnnBuilder            R Documentation

_C_l_a_s_s "_P_F_A_M" _a _s_u_b-_c_l_a_s_s _o_f _p_u_b_R_e_p_o _t_o _h_a_n_d_l_e _d_a_t_a _f_r_o_m _h_t_t_p://_w_w_w._s_a_n_g_e_r._a_c._u_k/_S_o_f_t_w_a_r_e/_P_f_a_m/

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

     This class is a sub-class of pubRepo that is implemented
     specifically to parse the data <URL:
     ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz>

_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("PFAM", ...)'. A
     constructor (PFAM) is available and should be used to instatiate
     objects of 'PFAM'

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

     '_s_r_c_U_r_l': Object of class '"character", from class "pubRepo"' a
          character string for the surce url where data will be
          downloaded/processed

     '_f_r_o_m_W_e_b': Object of class '"logical"' for inficating whether the
          source file should be accessed through the web or locally

_E_x_t_e_n_d_s:

     Class '"pubRepo"', directly.

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

     _p_a_r_s_e_D_a_t_a 'signature(object = "PFAM")': A method to parse a source
          file using a specified parser

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

     Ting-Yuan Liu

_R_e_f_e_r_e_n_c_e_s:

     <URL:
     ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz>

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

     'pubRepo-class'

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

     ## Not run: 
     ## create PFAM class
     pfamObj <- PFAM(srcUrl="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz",
                     fromWeb=TRUE)
     tableList <- parseData(pfamObj)
     ## End(Not run)

