Delila Program: waveplot

waveplot program

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

{   version = 1.09; (* of waveplot.p 2012 Nov 21}

(* begin module describe.waveplot *)
(*
name
   waveplot: plot sites around the wave of B-form DNA

synopsis
   waveplot(searchfeatures: in, waveplotp: in, xyin: out, output: out)

files

   searchfeatures:  output of the search program containing the
   locations of a pattern along a sequence.

   xyin:  input to the xyplo program for plotting

   waveplotp:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      The parameters are like those in live:

      zerobase: integer; to set the phase of the wave by.
      wavelength: integer; The wave length in bases.  Usually 10.6.

      riconsensus: integer; Maximum value to divide Ri by to normalize
      color saturation.  If it is 0 or less, the saturation is set to
      1.0.

      These variables are from live but maybe not needed:
      wavevertical: integer; amount to shift colored wave vertically
      waveheight: integer; height of colored wave

   output: messages to the user

description

   When one identifies a set of sites, how are they oriented in
   physical space around the DNA relative to each other?  A zero
   coordinate is chosen by the user.  All sites that are exact
   multiples of 10.6 bp have the same orientation as a site at this
   coordinate.  The orientation of other sites is determined by
   repeatedly subtracting 10.6 bases per DNA twist from a coordinate
   until the value is above the zero coordinate but below 10.6.  The
   actual distance can be changed from 10.6 to whatever value the user
   desires.

examples

documentation

see also

   The program that generates searchfeatures search.p

   A program that generates marks for lister maps
    that are colors rotating through the spectrum.
    The wavelength can be adjusted as here. live.p

   Program to plot the data xyplo.p
   Example xyplop file for xyplo: waveplot.xyplop

author

   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.waveplot *)
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