browserSession-class       package:rtracklayer       R Documentation

_C_l_a_s_s "_b_r_o_w_s_e_r_S_e_s_s_i_o_n"

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

     An object representing a genome browser session. Each session
     corresponds to a set of loaded 'trackSet' instances and a set of
     'browserView' instances. Note that this is a virtual class; a
     concrete implementation is provided by each backend driver.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     A virtual Class: No objects may be created from it. See
     'browserSession' for obtaining an instance of an implementation
     for a particular genome browser.

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

     This specifies the API implemented by each browser backend. Note
     that a backend is not guaranteed to support all operations.

     '_b_r_o_w_s_e_r_V_i_e_w(_o_b_j_e_c_t, _s_e_g_m_e_n_t =         _g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t), _t_r_a_c_k = _t_r_a_c_k_s(_o_b_j_e_c_t), ...)' 
          Constructs a 'browserView' of 'segment' for this session.

     '_b_r_o_w_s_e_r_V_i_e_w_s(_o_b_j_e_c_t, ...)' Gets the 'browserView' instances
          belonging to this session.

     '_a_c_t_i_v_e_V_i_e_w(_o_b_j_e_c_t, ...)' Returns the 'browserView' that is
          currently active in the session.

     '_g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t, ...)' Gets the 'genomeSegment' representing
          the segment of the genome currently displayed by the browser
          (i.e. the segment shown by the active view) or a default
          value (possibly 'NULL') if no views exist.

     '_g_e_n_o_m_e_S_e_q_u_e_n_c_e(_o_b_j_e_c_t, _s_e_g_m_e_n_t =         _g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t), ...)' 
          gets a genomic sequence of 'segment' from this session.

     '_l_a_y_S_e_q_u_e_n_c_e(_o_b_j_e_c_t, ...)' Loads a sequence into the session.

     '_l_a_y_T_r_a_c_k(_o_b_j_e_c_t, _t_r_a_c_k, _n_a_m_e = _d_e_p_a_r_s_e(_s_u_b_s_t_i_t_u_t_e(_t_r_a_c_k)),         _v_i_e_w = _T_R_U_E, ...)' 
          Loads one or more 'track's into the session and optionally
          open a 'view' of the track.

     '_t_r_a_c_k_S_e_t(_o_b_j_e_c_t, _s_e_g_m_e_n_t = _g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t),         _n_a_m_e, ...)' 
          Gets features in 'segment' in the track stored as 'name' as a
          'trackSet'.

     '_t_r_a_c_k_s(_o_b_j_e_c_t, ...)' Gets the names of the tracks stored in this
          session. 

     '_c_l_o_s_e(_c_o_n, ...)' Close this session. 

     '_s_h_o_w(_o_b_j_e_c_t, ...)' Output a textual description of this session.

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

     Michael Lawrence

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

     'browserSession' for obtaining implementations of this class for a
     particular genome browser.

