# Copyright (C) 2000, 2001, 2002, 2011, 2018 James R Barcelona @barce ,
# All Rights Reserved.
# Permission is granted to copy and modify this program for
# non-commercial purposes, so long as this copyright notice is
# preserved.  This software is distributed without warranty.
# Commercial users must contact the author for licensing terms.

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 *                                       *
 *               DNA Hash                *
 *                                       *
 *****************************************/

DNA Hash is a set of programs that:
	(1) Create permutations of DNA sequences
	(2) Model the steganographic method of encryption
		using DNA sequences.

Just type make to build.

Currently part (1) is finished, but part (2) is almost 
there

genperms - useful when creating a list of DNA sequences
mapped to alphanumeric characters.

	usage: ./genperms -p length
		where length is the length of the DNA sequence

driver - a sample of what the DNAHash classes can do. It takes
a message and encrypts it into DNA sequences, and then decrypts it.

Edit the "Strings Message" variable as you see fit in the file, mdriver.cc.

	usage: ./mdriver
		mdriver will encrypt and then decrypt the Strings Message.
 
Primers, the markers for where the encrypted sequence
starts and ends, are finally implemented!

mdriver - (STILL NEEDS WORK) the driver for the message class.

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 *                                       *
 *            Historical Notes           *
 *                                       *
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11 March 2002

Mdriver now implements primers, but doesn't "mirror" the process
of using primers to find a message in a batch of DNA. This mirrorring
will be the next process. Also, argument handlers need to be added
to mdriver.

12 May 2001

Genperms now takes an argument -p which is the length of
the string for permutations.

25 August 2000

Genperms is a program that generates permutations of the
DNA base pairs.


12 August 2000

Primer class has been added, as well as two new functions, encode and
decode, which will be put into a message class later on.

Base pairs >3 are supported.

The driver reads a string from a file called message and encodes that string.

4 August 2000
A dnakey file consists of a char followed by a base pair sequence.

For example:
A
CCG
B
CCA
C
CCT

Currently the hash class supports base pair sequences of 3 chars.

# $Header: /usr/local/cvsroot/dnahash/README,v 1.3 2001/05/13 03:06:34 barce Exp $