BStringViews-constructors     package:Biostrings     R Documentation

_B_a_s_i_c _f_u_n_c_t_i_o_n_s _f_o_r _c_r_e_a_t_i_n_g _B_S_t_r_i_n_g_V_i_e_w_s _o_b_j_e_c_t_s

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

     A set of basic functions for creating BStringViews objects.

_U_s_a_g_e:

       views(subject, start=NA, end=NA)
       adjacentViews(subject, width, gapwidth=0)
       BStringViews(src, subjectClass, collapse="")

_A_r_g_u_m_e_n_t_s:

 subject: A BString (or derived) object or a single string. 

   start: An integer vector containing the start positions of the
          views. 

     end: An integer vector containing the end positions of the views. 

   width: An integer vector containing the widths of the views. 

gapwidth: An integer vector containing the widths of the gaps between
          the views. 

     src: A BString (or derived) object or a character vector. 

subjectClass: The class to be given to the subject of the BStringViews
          object created and returned by the function. Must be
          '"BString"' or one of its subclasses: '"DNAString"',
          '"RNAString"' or '"AAString"'. 

collapse: An optional character string to be inserted between the views
          of the BStringViews object created and returned by the
          function. 

_D_e_t_a_i_l_s:

     The 'views' function returns a BStringViews object containing
     views on 'subject' with start and end positions given in the
     'start' and 'end' vectors.

     The 'adjacentViews' function returns a BStringViews object
     containing views on 'subject' with widths given in the 'width'
     vector and separated by gaps of width 'gapwidth'. The first view
     starts at position 1.

     The 'BStringViews' constructor will try to create a BStringViews
     object from the value passed to its 'src' argument. If 'src'
     itself is a BStringViews object, the returned object is obtained
     by coercing its subject to the class specified by 'subjectClass'.
     If 'src' is a BString object, the returned object is made of a
     single view that starts at the first letter and ends at the last
     letter of 'src' (in addition 'src' itself is coerced to the class
     specified by 'subjectClass' when specified). If 'src' is a
     character vector, the returned object has one view per character
     string in 'src' (and its subject is an instance of the class
     specified by 'subjectClass').

_V_a_l_u_e:

     All these functions return a BStringViews object 'y' with the
     following number of views ('length(y)'): 'max(length(start),
     length(end)' for the 'views' function and 'length(width)' for the
     'adjacentViews' function. For the 'BStringViews' constructor,
     'length(y)' is '1' when 'src' is a BString object and
     'length(src)' otherwise.

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

     BStringViews-class, BString, DNAString, RNAString

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

       ## 'start' and 'end' are recycled
       views("abcdefghij", 2:1, 4)
       views("abcdefghij", 5:7, )
       views("abcdefghij", , 5:7)

       ## Views can be "out of limits"
       views("abcdefghij", 2:0, 4)

       ## Views on a DNAString object
       v12 <- views(DNAString("TAATAATG"), -2:9, 0:11)

       ## Creating adjacent views
       v3 <- adjacentViews("abcdefghij", 4:2, gapwidth=1)

       BStringViews(v12, subjectClass="RNAString")
       BStringViews(AAString("MARKSLEMSIR*"))
       BStringViews("abcdefghij", subjectClass="BString")

