/* sample program for invoking robust.c */
#include <stdio.h>
#define DIGIT 		10.0	/* all parameters are accurate to the tenth */

main(argc, argv)
int argc;
char *argv[];
{
	double atof();
	char *ckalloc();
	char *seq1, *seq2;
	int M, N;		/* lengths of sequences */
	long low, up, ms, G, H, W[128][128];
	long *S;		/* conversion operations */
	int i, j;
	long c;

	if (argc != 6)
		fatalf("%s seq1 seq2 ms(<0) g(>=0) h(>0)",argv[0]);
	M = get_seq(argv[1], &seq1);
	N = get_seq(argv[2], &seq2);
	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.");

	/* 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: length = %d\n",argv[1],M);
	printf("%s: length = %d\n",argv[2],N);
	printf("mismatch = %.1f, gap_open = %.1f, gap_ext = %.1f\n\n",ms/DIGIT,G/DIGIT,H/DIGIT);

	S = (long *)ckalloc((M+N)*sizeof(long));
	c = ALIGN(seq1-1,seq2-1,M,N,W,G,H,S);
	printf("\nOptimal cost = %.1f\n",
		((float)c)/DIGIT);
	DISPLAY(seq1-1,seq2-1,M,N,S,1,1);
	ROBUST(seq1-1,seq2-1,M,N,S,c);
	exit(0);
}

/* get_seq - read a sequence */
int get_seq(file_name, seqptr)
char *file_name, **seqptr;
{
	FILE *qp, *ckopen();
	char *p, *fgets(), *ckalloc();
	int c, n;
		
	qp = ckopen(file_name, "r");
	for (n=0; (c=getc(qp)) != EOF;)
		if (c != '\n') ++n;
	*seqptr = ckalloc(n+1);
	rewind(qp);
	p = *seqptr;
	while((c=getc(qp)) != EOF) 
		if (c != '\n') *p++ = c;
	*p = '\0';
	return p - *seqptr;
}