CONSTANT = ON;		  argv++;		  strcat(Pattern, argv[0]);		  if(argc > 1 && argv[1][0] == '-') {			fprintf(stderr, "%s: -k should be the last option in the command\n", Progname);			exit(2);		  }		  break;       case 'l' : FILENAMEONLY = ON;                  break;       case 'n' : LINENUM = ON;  /* output prefixed by line no*/                  break;       case 'v' : INVERSE = ON;  /* output no-matched lines */                  break;       case 't' : OUTTAIL = ON;  /* output from tail of delimiter */                  break;       case 'B' : BESTMATCH = ON;                  break;       case 'w' : WORDBOUND = ON;/* match to words */		  if(WHOLELINE) {			fprintf(stderr, "%s: illegal option combination\n", Progname);			exit(2);		  }                  break;       case 'y' : NOPROMPT = ON;		  break;       case 'I' : I = atoi(argv[0]+2);  /* Insertion Cost */	          JUMP = ON;                  break;       case 'S' : S = atoi(argv[0]+2);  /* Substitution Cost */                  JUMP = ON;                  break;       case 'D' : DD = atoi(argv[0]+2); /* Deletion Cost */                  JUMP = ON;                  break;       case 'G' : FILEOUT = ON; 		  COUNT = ON;		  break;       default  : if (isdigit(c)) {		    APPROX = ON;                    D = atoi(argv[0]+1);                    if (D > MaxError) {                      fprintf(stderr,"%s: the maximum number of errors is %d \n", Progname, MaxError);                      exit(2);                    }                  } else {                    fprintf(stderr, "%s: illegal option  -%c\n",Progname, c);		    usage();                  }       } /* switch(c) */  } /* while (--argc > 0 && (*++argv)[0] == '-') */  if (FILENAMEONLY && NOFILENAME) {    fprintf(stderr, "%s: -h and -l options are mutually exclusive\n",Progname);  }  if (COUNT && (FILENAMEONLY || NOFILENAME)) {      FILENAMEONLY = OFF;       if(!FILEOUT) NOFILENAME = OFF;  }  if (!(PAT_FILE) && Pattern[0] == '\0') { /* Pattern not set with -e option */    if (argc == 0) usage();    strcpy(Pattern, *argv);     argc--;    argv++;  }  Numfiles = 0;    fd = 3; /* make sure it's not 0 */  if (argc == 0)  /* check Pattern against stdin */    fd = 0;  else {    if (!(Textfiles = (CHAR **)malloc(argc * sizeof(CHAR *) ))) {      fprintf(stderr, "%s: malloc failure (you probably don't have enough memory)\n", Progname);      exit(2);    }    while (argc--)  { /* one or more filenames on command line -- put                          the valid filenames in a array of strings */    /*      if ((filetype = check_file(*argv)) != ISASCIIFILE) {	if(filetype == NOSUCHFILE) fprintf(stderr,"%s: %s: no such file or directory\n",Progname,*argv);        argv++;*/            if ((filetype = check_file(*argv)) == NOSUCHFILE) {	if(filetype == NOSUCHFILE) fprintf(stderr,"%s: %s: no such file or directory\n",Progname,*argv);        argv++;      } else { /* file is ascii*/        if (!(Textfiles[Numfiles] = (CHAR *)malloc((strlen(*argv)+1)))) {          fprintf(stderr, "%s: malloc failure (you probably don't have enough memory)\n", Progname);          exit(2);        }        strcpy(Textfiles[Numfiles++], *argv++);	   } /* else */     } /* while (argc--) */  } /* else */  checksg(Pattern, D);       /* check if the pattern is simple */  strcpy(OldPattern, Pattern);  if (SGREP == 0) {      preprocess(D_pattern, Pattern);      strcpy(old_D_pat, D_pattern);      M = maskgen(Pattern, D);  }  else M = strlen(OldPattern);  if (PAT_FILE)  prepf(fp);  if (Numfiles > 1) FNAME = ON;  if (NOFILENAME) FNAME = 0;  num_of_matched = 0;  compat(); /* check compatibility between options */  if (fd == 0) {    if(FILENAMEONLY) {       fprintf(stderr, "%s: -l option is not compatible with standard input\n", Progname);       exit(2);      }    if(PAT_FILE) mgrep(fd);    else {    	if(SGREP) sgrep(OldPattern, strlen(OldPattern), fd, D);   	else      bitap(old_D_pat, Pattern, fd, M, D);    }    if (COUNT) {	if(INVERSE && PAT_FILE) printf("%d\n", total_line-num_of_matched);	else printf("%d\n", num_of_matched);    }  }   else {    for (i = 0; i < Numfiles; i++, close(fd), num_of_matched = 0) {      	strcpy(CurrentFileName, Textfiles[i]);      	if ((fd = open(Textfiles[i], 0)) <= 0) {            fprintf(stderr, "%s: can't open file %s\n",Progname, Textfiles[i]);      	} 	else { 	     	if(PAT_FILE) mgrep(fd);	     	else {             		if(SGREP) sgrep(OldPattern, strlen(OldPattern), fd, D);             		else      bitap(old_D_pat, Pattern, fd, M, D);	        }        	if (num_of_matched) NOMATCH = OFF;        	if (COUNT && !FILEOUT) {			if(INVERSE && PAT_FILE) { 		    		if(FNAME) printf("%s: %d\n", CurrentFileName, total_line - num_of_matched);				else printf("%d\n", total_line - num_of_matched);			}			else { 		    		if(FNAME) printf("%s: %d\n", CurrentFileName, num_of_matched);				else printf("%d\n", num_of_matched);			}        	}  /* if COUNT */		if(FILEOUT && num_of_matched) {			file_out(CurrentFileName);		}      	} /* else */    }  /* for i < Numfiles */    if(NOMATCH && BESTMATCH) {	if(WORDBOUND || WHOLELINE || LINENUM || INVERSE) { 		SGREP = 0;	      		preprocess(D_pattern, Pattern);      		strcpy(old_D_pat, D_pattern);      		M = maskgen(Pattern, D);	}	COUNT=ON; D=1;	while(D<M && D<=MaxError && num_of_matched == 0) {    		for (i = 0; i < Numfiles; i++, close(fd)) {      			strcpy(CurrentFileName, Textfiles[i]);      			if ((fd = open(Textfiles[i], 0)) > 0) {	     			if(PAT_FILE) mgrep(fd);	     			else {             		    		if(SGREP) sgrep(OldPattern,strlen(OldPattern),fd,D);             		    		else bitap(old_D_pat,Pattern,fd,M,D);      				}			}    		}  /* for i < Numfiles */		D++;	} /* while */	if(num_of_matched > 0) {		D--; COUNT = 0;		if(NOPROMPT) goto GO_AHEAD;		if(D==1) fprintf(stderr, "best match has 1 error, ");		else fprintf(stderr, "best match has %d errors, ", D);		fflush(stderr);		if(num_of_matched == 1) fprintf(stderr,"there is 1 match, output it? (y/n)");		else fprintf(stderr,"there are %d matches, output them? (y/n)", num_of_matched);		scanf("%c",&c);		if(c != 'y') goto CONT;GO_AHEAD:    		for (i = 0; i < Numfiles; i++, close(fd)) {      			strcpy(CurrentFileName, Textfiles[i]);      			if ((fd = open(Textfiles[i], 0)) > 0) {	     			if(PAT_FILE) mgrep(fd);	     			else {             		    		if(SGREP) sgrep(OldPattern,strlen(OldPattern),fd,D);             		    		else bitap(old_D_pat,Pattern,fd,M,D);				}      			}    		}  /* for i < Numfiles */		NOMATCH = 0;	}   } }CONT: if(EATFIRST) {      printf("\n");      EATFIRST = OFF; } if(num_of_matched) NOMATCH = OFF; if(NOMATCH) exit(1); exit(0);} /* end of main() */	   file_out(fname)char *fname;{int num_read;int fd;int i, len;CHAR buf[4097];	if(FNAME) {		len = strlen(fname);		putchar('\n');		for(i=0; i< len; i++) putchar(':');		putchar('\n');		printf("%s\n", CurrentFileName);		len = strlen(fname);		for(i=0; i< len; i++) putchar(':');		putchar('\n');		fflush(stdout);	}	fd = open(fname, 0);	while((num_read = read(fd, buf, 4096)) > 0) 		write(1, buf, num_read);}usage(){    	fprintf(stderr, "usage: %s [-#cdehiklnpstvwxBDGIS] [-f patternfile] pattern [files]\n", Progname);  	printf("\n");		fprintf(stderr, "summary of frequently used options:\n");	fprintf(stderr, "-#: find matches with at most # errors\n");	fprintf(stderr, "-c: output the number of matched records\n");	fprintf(stderr, "-d: define record delimiter\n");	fprintf(stderr, "-h: do not output file names\n");	fprintf(stderr, "-i: case-insensitive search, e.g., 'a' = 'A'\n");	fprintf(stderr, "-l: output the names of files that contain a match\n");	fprintf(stderr, "-n: output record prefixed by record number\n");	fprintf(stderr, "-v: output those records containing no matches\n");	fprintf(stderr, "-w: pattern has to match as a word, e.g., 'win' will not match 'wind'\n");	fprintf(stderr, "-B: best match mode. find the closest matches to the pattern\n"); 	fprintf(stderr, "-G: output the files that contain a match\n"); 	printf("\n");	    	exit(2);}checksg(Pattern, D) CHAR *Pattern; int D;{                            char c;  int i, m;  m = strlen(Pattern);  if(!(PAT_FILE) && m <= D) {      fprintf(stderr, "%s: size of pattern must be greater than number of errors\n", Progname);      exit(2);  }  SIMPLEPATTERN = ON;  for (i=0; i < m; i++)   {      switch(Pattern[i])      {         case ';' : SIMPLEPATTERN = OFF; break;         case ',' : SIMPLEPATTERN = OFF; break;         case '.' : SIMPLEPATTERN = OFF; break;         case '*' : SIMPLEPATTERN = OFF; break;         case '-' : SIMPLEPATTERN = OFF; break;         case '[' : SIMPLEPATTERN = OFF; break;         case ']' : SIMPLEPATTERN = OFF; break;         case '(' : SIMPLEPATTERN = OFF; break;         case ')' : SIMPLEPATTERN = OFF; break;         case '<' : SIMPLEPATTERN = OFF; break;         case '>' : SIMPLEPATTERN = OFF; break;         case '^' : if(D > 0) SIMPLEPATTERN = OFF; 		    break;         case '$' : if(D > 0) SIMPLEPATTERN = OFF; 		    break;         case '|' : SIMPLEPATTERN = OFF; break;         case '#' : SIMPLEPATTERN = OFF; break;         case '\\' : SIMPLEPATTERN = OFF; break;         default  : break;      }  }  if (CONSTANT) SIMPLEPATTERN = ON;  if (SIMPLEPATTERN == OFF) return;  if (NOUPPER && D) return;       if (JUMP == ON) return;  if (I == 0) return;  if (LINENUM) return;  if (DELIMITER) return;     if (INVERSE) return;  if (WORDBOUND && D > 0) return;    if (WHOLELINE && D > 0) return;    if (SILENT) return;     /* REMINDER: to be removed */  SGREP = ON;  if(m >= 16) DNA = ON;  for(i=0; i<m; i++) {	c = Pattern[i];	if(c == 'a' || c == 'c' || c == 't' || c == 'g' ) ;	else DNA = OFF;  }  return;}output (buffer, i1, i2, j)  register CHAR *buffer; int i1, i2, j;{register CHAR *bp, *outend;	if(i1 > i2) return;        num_of_matched++;        if(COUNT)  return;        if(SILENT) return;	if(OUTTAIL) {              i1 = i1 + D_length;              i2 = i2 + D_length;        }        if(DELIMITER) j = j+1;        if(FIRSTOUTPUT) {           if (buffer[i1] == '\n')  {               i1++;               EATFIRST = ON;           }           FIRSTOUTPUT = 0;        }        if(TRUNCATE) {           fprintf(stderr, "WARNING!!!  some lines have been truncated in output record #%d\n", num_of_matched-1);        }        while(buffer[i1] == '\n' && i1 <= i2) {	   printf("\n");           i1++;        }        if(FNAME == ON) printf("%s: ", CurrentFileName);        if(LINENUM) printf("%d: ", j-1); 	bp = buffer + i1;	outend = buffer + i2;	while(bp <= outend) putchar(*bp++);}/* end of main.c */