#include <stdio.h>
#define TRUE 1
#define FALSE 0
#define MAX_LINE 20000

char cluster_id[480], ref_locus[480], msp_locus_1[480], msp_locus_2[480];
char sub_locus_1[480], sub_locus_2[480], sub_cluster_id[480];
FILE *fp;
int ref_true = FALSE;
int not_msp = TRUE;
int sub_true = FALSE;
float msp_score = -1;
float sub_score;

main(argc, argv)
int *argc;
char *argv[];
{
	int no_id = FALSE;
	int new_id = FALSE;
	int do_stdin = TRUE;
	int n = 1;
	char next_char, new_cluster_id[480], cluster[MAX_LINE];
	double atof();

	argv++;
	while (*argv) {
		if (!strcmp(*argv, "-n")) {
			no_id = TRUE;
			argv++;
		}
		if (!strcmp(*argv, "-m")) {
			not_msp = FALSE;
			argv++;
		}
		else if (!strcmp(*argv, "-i")) {
			argv++;
			if (!*argv) {
				fprintf(stderr, "ERROR: cluster ID not found !!\n", *argv);
				exit(1);
			}
			strcpy(new_cluster_id, *argv);
			new_id = TRUE;
			argv++;
		}
		else if (!strcmp(*argv, "-r")) {
			argv++;
			if (!*argv) {
				fprintf(stderr, "ERROR: ref_locus not found !!\n", *argv);
				exit(1);
			}
			strcpy(ref_locus, *argv);
			ref_true = TRUE;
			argv++;
		}		  
		else if (!strcmp(*argv, "-s")) {
			argv++;
			strcpy(sub_locus_1, *argv);
			argv++;
			sub_score = ((float) atof(*argv));
			argv++;
			strcpy(sub_locus_2, *argv);
			argv++;
			strcpy(sub_cluster_id, *argv);
			sub_true = TRUE;
			argv++;
		}		  
		else {
			do_stdin = FALSE;
			if (!(fp = fopen(*argv, "r"))) {
				fprintf(stderr, "ERROR: input file %s not found !!\n", *argv);
				exit(1);
			}
			argv++;
		}
	}

	if (do_stdin)
		fp = stdin;

	if (no_id || new_id) {
		while ((next_char = getc(fp)) != -1) {
			ungetc(next_char, fp);
			if (next_char == '(') {
				if (new_id)
					printf("%s.%d\t", new_cluster_id, n);
				read_node();
				printf("\n");
				getc(fp);  /* get CR */
				n++;
			}
			else {
				if (new_id)
					printf("%s.%d\t", new_cluster_id, n);
				fgets(cluster, MAX_LINE, fp);
				printf("%s", cluster);
				n++;
			}
		}
	} 
	else {
		while (fscanf(fp, "%s ", cluster_id) != EOF) {
			printf("%s\t", cluster_id);
			next_char = getc(fp);
			ungetc(next_char, fp);
			if (next_char == '(') {
				read_node();
				if (not_msp)
					printf("\n");
				else {
					printf("%s\t%.2f\t%s\n",
					msp_locus_1, msp_score, msp_locus_2);
					msp_score = -1;
				}
			}
			else {
				fgets(cluster, MAX_LINE, fp);
				printf("%s", cluster);
			}			    
		}
	}
}


read_node()
{
	char locus_1[60], locus_2[60], next_char_1, next_char_2;
	float score;

	getc(fp); /* get open paren */
	next_char_1 = getc(fp);
	if (next_char_1 == '(' ) {
	    if (not_msp)
		    printf("(");
		ungetc(next_char_1, fp);
		read_node();
		fscanf(fp, "%f ", &score);
		if (not_msp)
			printf(" %.2f ", score);
		next_char_2 = getc(fp);
		if (next_char_2 == '(' ) {
			ungetc(next_char_2, fp);
			read_node();
			getc(fp); /* get closed paren */
			if (not_msp)
				printf(")");
		} 
		else {
			ungetc(next_char_2, fp);
			fscanf(fp, "%[^)]", locus_2);
			getc(fp);  /* get closed paren */
			if (not_msp)
				printf("%s)", locus_2);
			fflush(stdout);
		}
	} 
	else {
		ungetc(next_char_1, fp);
		fscanf(fp, "%s ", locus_1);
		fscanf(fp, "%f ", &score);
		next_char_2 = getc(fp);
		if (next_char_2 == '(' ) {
			ungetc(next_char_2, fp);
			if (not_msp) {
				printf("(%s ", locus_1);
				printf("%.2f ", score);
				fflush(stdout);
			}
			read_node();
			getc(fp); /* get closed paren */
			if (not_msp)
				printf(")");
		} 
		else {
			ungetc(next_char_2, fp);
			fscanf(fp, "%[^)]", locus_2);
			getc(fp);  /* get closed paren */
			if (not_msp) {
				if (ref_true && !strcmp(locus_2, ref_locus))
					printf("(%s %.2f %s)",locus_2, score, locus_1);
				else if (sub_true &&
						 !strcmp(locus_1, sub_locus_1) &&
						 !strcmp(locus_2, sub_locus_2) &&
						 (score == sub_score) )
				    printf("%s", sub_cluster_id);
				else
				    printf("(%s %.2f %s)",locus_1, score, locus_2);
				fflush(stdout);
			}
			else if (score > msp_score) {
				msp_score = score;
				strcpy(msp_locus_1, locus_1);
				strcpy(msp_locus_2, locus_2);
			}
		}
	}
}