AASequence-class         package:pairseqsim         R Documentation

"_A_A_S_e_q_u_e_n_c_e" _O_b_j_e_c_t _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _a _p_r_o_t_e_i_n _S_e_q_u_e_n_c_e

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

     Object representation of a protein Sequence

_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("AASequence",
     sequence, info, alphabet)'. or by call to
     'AASequence("PROTINSEQUENCEHERE",info="my prot seq")'

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

     '._D_a_t_a': Object of class '"character"' the sequence

     '_i_n_f_o': Object of class '"character"' the info 

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

     Class '"character"', directly.

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

     _f_r_e_q_u_e_n_c_y 'signature(x = "AASequence")': returns the amino acid
          frequencies 

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "AASequence")': internal 

     _r_e_a_d_F_a_s_t_a 'signature(object = "AASequence")': read FASTA file
          format

     _s_a_l_i_g_n 'signature(obj1 = "AASequenceList", obj2 = "AASequence")':
          see: 'salign-methods'

     _s_a_l_i_g_n 'signature(obj1 = "AASequence", obj2 = "AASequenceList")':
          see: 'salign-methods'

     _s_a_l_i_g_n 'signature(obj1 = "AASequence", obj2 = "AASequence")': see:
          'salign-methods'

     _s_e_l_f_a_l_i_g_n 'signature(object = "AASequence", sub = "Submatrix")':
          Computes Smith-Waterman score of the alignment of the
          sequence with itself.

     _s_h_o_w 'signature(object = "AASequence")': 

     _t_e_s_t_a_l_i_g_n 'signature(obj1 = "AASequence", obj2 = "AASequence")':
          internal, see: 'testalign-methods'

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

     Witold E. Wolski

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

     'salign-methods','readFasta-methods'

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

     seq1<-new("AASequence","MEDQVGFGFRPNDEEL",info="seq1")
     seq2<-AASequence("seq2","VAISEVNICSY")

