Delila Program: malopt

malopt program

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

{version = 1.09; (* of malopt.p 1996 March 22}

(* begin module describe.malopt *)
   malopt: 2d plot of optimal alignments

   malopt(optalign: in, maloptp: in, xyin: out, output: out)

   optalign:  output of malign

   maloptp:  parameters to control this program.  Lines:
       1: doclasses: integer number of classes to process
       2: colorbound: highest distance of the color scale
       3: xrectangle, yrectangle: size of rectangles of colors.
          Values of 1 and 1 give nice squares that just fit together.
          Values of 0.9 and 0.9 squares that don't touch each other.
          (This would allow more precise location of particluar
           pieces of data.)

   xyin:  input to xyplo.  Columns:
       1: x class
       2: y class
       3: x H, uncertainty in bits
       4: y H, uncertainty in bits
       5: x rectangle width
       6: y rectangle height
       7: distance from x class to y class
       8: hue for color computed from the distance
       9: saturation for color
      10: brightness for color

       A color scale is put on the left side of the graph,
       running from 0 to colorbound.
       The lower right triangle of the graph gives the distances
       according to these colors.

   output: messages to the user

   How can we look at all the classes produced by malign?  We can first
   normalize each alignment vector by subtracting the first value from all
   other values.  Then we can ask what the distance is between all classes.
   These data are put into xyin for plotting by the xyplo program.

   The distances are computed and reported to xyin.  The distances are also
   linearly transformed to give a color scale.  The user can define the upper
   bound of the color scale, to be able to look at details for smaller
   distances.  Distances larger than this "colorbound" are set to black.



see also
   malign.p, maloptp, xyplo.p, xyplop.malopt

   Thomas Dana Schneider


technical notes
   See xyplo for notes on color.

(* end module describe.malopt *)
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