/* sample program for invoking sub.c */
#include <stdio.h>
#include "sub.h"

main(int argc, char *argv[])
{
	double atof();
	char *ckalloc();
	FILE *qp, *ckopen();
	char *seq1, *seq2;
	char *name1, *name2;
	int from1, to1, from2, to2;
	int M, N;		/* lengths of sequences */
	long low, up, ms, G, H, W[128][128], CUT_OFF;
	int *L, *R;
	int i, j;
	int c;

	if (argc != 7)
		fatalf("%s seq1 seq2 ms(<0) g(>=0) h(>0) cut_off",argv[0]);
	M = get_seq(argv[1], &seq1, &name1, &from1, &to1);
	N = get_seq(argv[2], &seq2, &name2, &from2, &to2);
	ms = DIGIT * atof(argv[3]);
	if (ms > 0)
		fatal("The mismatch weight should be nonpositive.");
	G = DIGIT * atof(argv[4]);
	if (G < 0)
		fatal("The gap-open penalty should be nonnegative.");
	H = DIGIT * atof(argv[5]);
	if (H < 0)
		fatal("The gap-extend penalty should be positive.");
	CUT_OFF = DIGIT * atof(argv[6]);

	/* set up match and mismatch weights */
	for (i = 0; i < 128; i++)
	   for (j = 0; j < 128; j++)
		if (i == j)
		   W[i][j] = DIGIT;
		else
		   W[i][j] = ms;

	printf("%s[%d,%d]: length = %d\n",name1,from1,to1,M);
	printf("%s[%d,%d]: length = %d\n",name2,from2,to2,N);
	printf("mismatch = %.1f, gap_open = %.1f, gap_ext = %.1f, cut_off = %.1f\n\n",ms/DIGIT,G/DIGIT,H/DIGIT,CUT_OFF/DIGIT);

	c = ALL_SUB(seq1-1,seq2-1,M,N,W,G,H,CUT_OFF);
	if (c == -1) printf("No alignment is of score >= cut_off\n");
	exit(0);
}