/*-------------------------------------------------------------

Copyright (C) 2000 Peter Clote. 
All Rights Reserved.

Permission to use, copy, modify, and distribute this
software and its documentation for NON-COMMERCIAL purposes
and without fee is hereby granted provided that this
copyright notice appears in all copies.


THE AUTHOR AND PUBLISHER MAKE NO REPRESENTATIONS OR
WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS
AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED
BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
THIS SOFTWARE OR ITS DERIVATIVES.

-------------------------------------------------------------*/


/*************************************************
   dotter0.c
   P. Clote

Outputs a text file of coordinates of the form
   n-i  j+1
for each i,j such that a[i] = b[j], when given
2 sequences a[0],...,a[n-1] and b[0],...,b[m-1].
The idea is that in producing a dot plot for the sequences,
sequence a appears down the left side and sequence b at the
top, with a dot at each position where the character in a matches
the character in b.

Suppose the output is saved in a file "out".
Then use gnuplot with command
   plot "out" with points
produces a screen image of the dot plot of the two sequences.
*************************************************/


#include <stdio.h>
#include <string.h>
#include <stdlib.h>

#define N 1000
#define M 1000
   // N,M upper bounds on length of sequences a,b resp.



main(int argc, char *argv[]) {
   char *a, *b;
   int n,m,i,j;
   char s[N][M];
   if ( argc != 3 )
      error("Usage: %s string1 string 2.\n");

   a = argv[1];
   b = argv[2];
   n = strlen(a);
   m = strlen(b);
   for (i=0;i<n;i++)
      for (j=0;j<m;j++)
         if (a[i] == b[j])
            printf("%d %d\n",j+1,n-i);
}


/*---------------------------------------------------------------
Sample run:

% a.out
GCGGGGGTCGCCAAGCCAGGTCAAAGGCGCCAGATTGAGGGTCUGGTCCCGTAGGGGTTCGCGGGTTCAAATCCCGTCCCCCGCA
CGCGGGGTACCGGGCTTGGTAGCCCGGGGCGGACTTCAGATCCGTCGAGGGCGAGAGCCCTCGGGGTTCGATTCCCCCCCTGCGC
> out  

Here the 2 sequences are actually tRNA's from M. jannaschii.
---------------------------------------------------------------*/