palCon-class              package:cosmo              R Documentation

_C_l_a_s_s "_p_a_l_C_o_n" ~~~

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

     This class defines a global constraint when palindromic patterns
     are known to be found in the motif.

_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('palCon','
      '    int1       = ...., # Object of class numeric'
      '    int2       = ...., # Object of class numeric'
      '    errBnd     = ...., # Object of class numeric'
      '  )' or by: '  makePalCon('
      '    int1       = ...., # Object of class numeric'
      '    int2       = ...., # Object of class numeric'
      '    errBnd     = ...., # Object of class numeric'
      '  )'

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

     '_i_n_t_1': Object of class '"numeric"' first palindromic interval 

     '_i_n_t_2': Object of class '"numeric"' second palindromic interval 

     '_e_r_r_B_n_d': Object of class '"numeric"' error tolerated in
          mismatches

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

     No methods defined with class "palCon" in the signature.

_N_o_t_e:

     ~~further notes~~

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

     Fabian Gallusser, fgallusser@berkeley.edu

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

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

     'shapeCon', 'subMotifCon', 'posFreqCon', 'boundCon',
     'shapeDiffCon' 'makeConSet'

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

     set=makeConSet(3,c("B","V","B"),c(4,NA,4))
     palcon=makePalCon(1,3,0.5)
     set=addCon(set,list(palcon),NA)

