argoSession-class        package:rtracklayer        R Documentation

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

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

     An object representing a session in the Argo genome browser.

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

     Objects may be created by calls of the form
     'browserSession("argo", name, jar)' where 'name' is the name of
     the session in Argo and 'jar' is the path to the installed Argo
     jar file.

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


     '_j_r_e_f': Object of class '"jobjRef"' holding the reference to the
          low-level Argo object. 

     '_s_e_q_c_a_c_h_e': Object of class '"environment"' that caches sequence
          objects after lookup from UCSC. 

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

     Class '"browserSession"', directly.

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


     '_a_c_t_i_v_e_V_i_e_w(_o_b_j_e_c_t)' Obtains the currently active 'browserView'
          for this session. 

     '_a_c_t_i_v_e_V_i_e_w<-(_o_b_j_e_c_t)' Sets the currently active view for this
          session.

     '_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, _s_e_g_m_e_n_t, _T_R_U_E),         ...)' 
          Creates a 'browserView' of 'segment' with visible tracks
          named in 'track'. Parameters in '...' correspond to slots in
          the 'genomeSegment' class and override those in 'segment'.

     '_b_r_o_w_s_e_r_V_i_e_w_s(_o_b_j_e_c_t)' Gets a list of the 'browserView' instances
          for this session. 

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

     '_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)' Gets the genome sequence in
          'segment'. 

     '_l_a_y_S_e_q_u_e_n_c_e(_o_b_j_e_c_t, _s_e_q_u_e_n_c_e, _n_a_m_e, _l_a_b_e_l =         _n_a_m_e)' Stores
          'sequence' under 'name', labeled as 'label' in the user
          interface. 

     '_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)' 
          Stores 'track' under 'name', opening a view of the track if
          'view' is 'TRUE'.

     '_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)' 
          Obtains a 'trackSet' named 'name' from 'segment'.

     '_t_r_a_c_k_s(_o_b_j_e_c_t, _s_e_g_m_e_n_t = _N_U_L_L, _v_i_s_i_b_l_e =         _F_A_L_S_E)' Gets the
          names of tracks in 'segment'. If 'visible' is 'TRUE', only
          the visible tracks are returned. Note that in Argo tracks are
          visible on a global, not per-session nor per-view, basis. 

_N_o_t_e:

     In order to use this backend, the Argo jar file must be manually
     downloaded from the URL in the references. The call to
     'browserSession' must then pass the path to the jar file as the
     'jar' parameter. By default, the path is the 'java' directory of
     the 'rtracklayer' package.

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

     Michael Lawrence

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

     The Argo genome browser: <URL:
     http://www.broad.mit.edu/annotation/argo/>

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

     'browserSession' for creating instances of this class.

