Delila Program: matrix

matrix program

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

{      version = 3.28; (* of matrix 1987 feb 13 *)}

(* begin module describe.matrix *)
(*
name
      matrix: dot matrices for helices between two books

synopsis
      matrix(xbook: in, ybook: in, hlist: in, mlist: out,
             matrixp: in, output: out)

files
      xbook: a book from the delila system

      ybook: a book from the delila system.  If you want to look for
         structures in one sequence, then use the program copy to make
         a copy of xbook in ybook.

      hlist: the helix listing for xbook and ybook made by program helix

      mlist: the matrices listed out.  Sequences from the x book are printed
         vertically, while those from the y book are horizontal.
         helices are printed as a set of numbers:
            1 means gt base pair
            2 means at base pair
            3 means gc base pair
         if mlist is wider than your printer, use the split program.

      matrixp: parameters to control the mlist
         If matrixp is empty, default values are used. otherwise, the first
         line contains one number.  If this number is a positive integer,
         it specifies the minimum length helix in base pairs from hlist to
         record in mlist;
         if this number is a negative real number, it specifies the maximum
         energy in kcal of the helixes written in mlist.

      output: messages to the user

description
      Matrix produces a dot matrix for the two books.  Only helices
      of some length (or longer) or of some maximum energy (or less) are
      printed.  The helices are made using program helix.

documentation
      delman.use.comparison
      J. V. Maizel, Jr. and R. P. Lenk PNAS 78: 7665-7609 (1981)

see also
      helix, dotmat, split, keymat

author
      Thomas D. Schneider

bugs
      none known

technical notest
      The constant maxarray defines the maximum area that the program
      can handle.

*)
(* end module describe.matrix *)
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