/*
 *       Copyright 1991 Steven Smith at the Harvard Genome Lab.
 *       All rights reserved.
 */
#include "Flatio.c"

int main(ac, av)
int ac;
char **av;
{
	struct data_format data[10000];
	int Match = 2, Mismatch = 8;
	int i, j, k, l, numseqs, mis, Case = 32;
	int slen, pcnt, pos;
	int UT = FALSE;
	char c;
	if (ac < 3) {
		fprintf(stderr,
			"usage: %s search_string %%mismatch [-case] [-match "
			"color] [-mismatch color]\n",
			av[0]);
		fprintf(stderr, "		[-u=t]\n");
		exit(0);
	}
	for (j = 3; j < ac; j++) {
		if (strcmp("-case", av[j]) == 0) Case = 0;
		if (strcmp("-match", av[j]) == 0)
			sscanf(av[j + 1], "%d", &Match);
		if (strcmp("-u=t", av[j]) == 0) UT = TRUE;
		if (strcmp("-mismatch", av[j]) == 0)
			sscanf(av[j + 1], "%d", &Mismatch);
	}
	numseqs = ReadFlat(stdin, data, 10000);

	slen = strlen(av[1]);
	sscanf(av[2], "%d", &pcnt);
	pcnt *= slen;
	pcnt /= 100;

	if (UT)
		for (j = 0; j <= strlen(av[1]); j++) {
			if (av[1][j] == 't') av[1][j] = 'u';
			if (av[1][j] == 'T') av[1][j] = 'U';
		}

	for (i = 0; i < numseqs; i++) {
		if (UT)
			for (j = 0; data[i].nuc[j] != '\0'; j++) {
				if (data[i].nuc[j] == 't')
					data[i].nuc[j] = 'u';
				else if (data[i].nuc[j] == 'T')
					data[i].nuc[j] = 'U';
			}
		printf("name:%s\n", data[i].name);
		printf("length:%d\n", strlen(data[i].nuc));
		printf("start:\n");
		for (j = 0; j < data[i].length; j++) {
			mis = 0;
			for (k = 0, pos = j; k < slen && pos < data[i].length;
			     k++, pos++) {
				c = data[i].nuc[pos];
				for (; (c == ' ' || c == '-' || c == '~') &&
				       pos < data[i].length;)
					c = data[i].nuc[++pos];
				c |= Case;

				if (data[i].type == '#') {
					if (CompIUP(c, (av[1][k] | Case)) ==
					    FALSE)
						mis++;
				}
				else {
					if (c != (av[1][k] | Case)) mis++;
				}
			}
			if (k == slen && mis <= pcnt) {
				for (k = j; k < pos; k++) printf("%d\n", Match);
				j = pos - 1;
			}
			else
				printf("%d\n", Mismatch);
		}
	}
	exit(0);
}

int CompIUP(a, b)
char a, b;
{
	static int tmatr[16] = {'-', 'a', 'c', 'm', 'g', 'r', 's', 'v',
				't', 'w', 'y', 'h', 'k', 'd', 'b', 'n'};

	static int matr[128] = {
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0,    0,
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0,    0,
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0x00, 0,
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0,    0,
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0,    0,
	    0,	  0,	0,    0, 0,    0,    0,	   0,	 0,    0,    0x01,
	    0xe,  0x02, 0x0d, 0, 0,    0x04, 0x0b, 0,	 0,    0x0c, 0,
	    0x03, 0x0f, 0,    0, 0,    0x05, 0x06, 0x08, 0x08, 0x07, 0x09,
	    0x00, 0xa,	0,    0, 0,    0,    0,	   0,	 0,    0x01, 0x0e,
	    0x02, 0x0d, 0,    0, 0x04, 0x0b, 0,	   0,	 0x0c, 0,    0x03,
	    0x0f, 0,	0,    0, 0x05, 0x06, 0x08, 0x08, 0x07, 0x09, 0x00,
	    0x0a, 0,	0,    0, 0,    0x00, 0};

	int testa, testb;

	if (a & 32 != b & 32) return (FALSE);

	testa = matr[(int)a];
	testb = matr[(int)b];
	return (testa & testb);
}