Delila Program: matrix

# matrix program

## By downloading this code you agree to the Source Code Use License (PDF). Pascal source code: matrix.p (wget instructions) Instructions on compiling MacOS binary: matrix Alphabetic List of Delila Programs Delila Programs by Most Recent Update Please report broken links delilabundle.zip = All Programs and MacOS Binaries Copyright Statement for Delila Programs

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

```{   version = 3.29; (* of matrix 2016 Jan 12}

(* 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 *)
{This manual page was created by makman 1.45}

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