Delila Program: rsgra

rsgra program

Documentation for the rsgra program is below, with links to related programs in the "see also" section.

{   version = 5.13; (* of rsgra.p 2021 Aug 27}

(* begin module describe.rsgra *)
   rsgra: rsequence graph

   rsgra(rsdata: in, picture: out, rsgrap, wave: in, marks: in,
         output: out)

   rsdata: data file from rseq program

   picture: graph of rsequence in PostScript

   rsgrap: parameters to control the program.
      first line: two integers that define the from-to range to display

   wave: parameters to control the program.  empty file means no cosine
      wave, otherwise the parameters of the wave are given one per line:
      extreme: char;  h or l, the extreme high or low point on the curve
         defined by the wavelocation and wavebit
      wavelocation: real; the location in bases of the extreme
      wavebit: real; the location in bits of the extreme
      waveamplitude: real; the amplitude of the wave in bits
      wavelength: real; the wave length of the wave in bases

   marks: an empty file or a set of integers, one per line that are the
      locations of bases that should be specially marked on the graph.
      If the first line of the file begins with the letter 'b' and is
      followed by a real number, then this number defines the location of
      a bar to be placed on the graph immediately after the position given.

   output: messages to the user

description    Rsgra generates a graph of Rsequence versus position l.
The user may overlay a cosine wave on the graph, to signify    the
orientation of the major grove, for example.

   See the discussion about the REMOVE feature in makelogo.p.

see also
   rseq.p, makelogo.p

   Thomas D. Schneider


   2007 Feb 9: Adobe Readers look at PostScript files and if the file
   contains a 90 rotate, the reader TURNS THE WHOLE PAGE.  Stupid.  To
   avoid this, break 90 degree rotations into two 45 degree rotations.
   Amazingly simple way to fool an idiotic program.

   But it doesn't work.  So the rotation is not done now.

   For the same reason, the marks file cannot be empty.
   Use a large negative value to avoid having marks.

(* end module describe.rsgra *)
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