int main(int argc, char **argv) {
int format = TT_ANY, r, prec = 0, version = 3, silent = 0;
int compress_mode = -1;
char *inf = NULL;
char *outf = NULL;
mFILE *ofp = mstdout();
int normalise = 0;
for (argc--, argv++; argc > 0; argc--, argv++) {
if (strcmp(*argv, "-8") == 0) {
prec = 1;
} else if (strcmp(*argv, "-2") == 0) {
version = 2;
} else if (strcmp(*argv, "-3") == 0) {
version = 3;
} else if (strcmp(*argv, "-normalise") == 0) {
normalise = 1;
} else if (strcmp(*argv, "-s") == 0) {
silent = 1;
} else if (strcasecmp(*argv, "-abi") == 0) {
format = TT_ABI;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-alf") == 0) {
format = TT_ALF;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-scf") == 0) {
format = TT_SCF;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-ztr") == 0) {
format = TT_ZTR;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-any") == 0) {
format = TT_ANY;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-output") == 0) {
outf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-compress") == 0) {
compress_mode = compress_str2int(*++argv);
argc--;
} else {
break;
}
}
/* if no args left than input file must have been specified */
if (!argc && !inf)
usage();
/* if outfile set, then using original syntax, so don't expect
any extra args */
if (argc && outf)
usage();
if (!silent) {
printf("makeSCF v3.06\n");
printf("Copyright (c) MRC Laboratory of Molecular Biology, 2001. All rights reserved.\n");
}
set_scf_version(version);
if(!argc) {
/* original calling syntax */
if (outf) {
ofp = mfopen(outf, "wb+");
if (NULL == ofp) {
perror(outf);
return 1;
}
}
r = convert(inf, ofp, outf, format, prec, compress_mode, normalise);
mfclose(ofp);
return r;
}
/* else */ {
/* new calling syntax, handling multiple files */
int result=0;
for (; argc > 0; argc--, argv++) {
if (inf) {
/* got infile, so get outfile and process */
outf= *argv;
ofp = mfopen(outf, "wb+");
if (NULL == ofp) {
perror(outf);
if(!result) result=1;
continue;
}
r = convert(inf, ofp, outf, format, prec, compress_mode,
normalise);
mfclose(ofp);
if(!result) /* keep track of the first error */
result=r;
/* now need to get another infile */
inf=NULL;
} else {
/* need infile */
inf= *argv;
}
}
return result;
}
}
int main(int argc, char **argv) {
struct opts opts;
opts.in_format = TT_ANY;
opts.out_format = TT_ZTR;
opts.scale = 0;
opts.sub_background = 0;
opts.normalise = 0;
opts.name = NULL;
opts.compress_mode = -1;
opts.dots = 0;
opts.fofn = NULL;
opts.passed = NULL;
opts.failed = NULL;
opts.error = NULL;
for (argc--, argv++; argc > 0; argc--, argv++) {
if (**argv != '-')
break;
if (strcmp(*argv, "-scale") == 0) {
opts.scale = atoi(*++argv);
argc--;
} else if (strcmp(*argv, "-fofn") == 0) {
opts.fofn = *++argv;
argc--;
} else if (strcmp(*argv, "-passed") == 0) {
opts.passed = *++argv;
argc--;
} else if (strcmp(*argv, "-failed") == 0) {
opts.failed = *++argv;
argc--;
} else if (strcmp(*argv, "-error") == 0) {
opts.error = *++argv;
fprintf(stderr,"* Detected error argument %s\n", opts.error);
argc--;
} else if (strcmp(*argv, "-subtract_background") == 0) {
opts.sub_background = 1;
} else if (strcmp(*argv, "-normalise") == 0) {
opts.normalise = 1;
} else if (strcmp(*argv, "-dots") == 0) {
opts.dots = 1;
} else if (strcmp(*argv, "-in_format") == 0) {
argv++;
argc--;
if (TT_UNK == (opts.in_format = trace_type_str2int(*argv)))
opts.in_format = atoi(*argv);
} else if (strcmp(*argv, "-name") == 0) {
opts.name = *++argv;
argc--;
} else if (strcmp(*argv, "-out_format") == 0) {
argv++;
argc--;
if (TT_UNK == (opts.out_format = trace_type_str2int(*argv)))
opts.out_format = atoi(*argv);
} else if (strcasecmp(*argv, "-compress") == 0) {
opts.compress_mode = compress_str2int(*++argv);
argc--;
} else if (strcmp(*argv, "-abi_data") == 0) {
int c1, c2, c3, c4;
argc--;
if (4 == sscanf(*++argv, "%d,%d,%d,%d", &c1, &c2, &c3, &c4)) {
abi_set_data_counts(c1, c2, c3, c4);
} else {
usage();
}
} else if (strcmp(*argv, "--") == 0) {
break;
} else {
usage();
}
}
if (argc == 2) {
/* Old syntax, for backwards compatibility */
if (TT_UNK == (opts.in_format = trace_type_str2int(argv[0])))
opts.in_format = atoi(argv[0]);
if (TT_UNK == (opts.out_format = trace_type_str2int(argv[1])))
opts.out_format = atoi(argv[1]);
} else if (argc != 0) {
usage();
}
// Added by SAK: Allow redirection of error output to file, due to problems with Java exec
if( NULL != opts.error){
int fd;
fprintf(stderr,"* Redirecting stderr to %s\n", opts.error);
close(2); // close fd with stderr
fd = creat(opts.error, -1 );
if(fd == -1){
exit(-1);
}
}
if (!opts.fofn) {
return convert(stdin, stdout, "(stdin)", "(stdout)", &opts);
} else {
FILE *fpin, *fpout;
FILE *fppassed = NULL, *fpfailed = NULL;
char *infname, *outfname;
int ret, ret_all = 0;
char line[8192], line2[8192];
FILE *fofn_fp;
if (NULL == (fofn_fp = fopen(opts.fofn, "r"))) {
perror(opts.fofn);
return -1;
}
if (opts.passed && NULL == (fppassed = fopen(opts.passed, "w"))) {
perror(opts.passed);
return -1;
}
if (opts.failed && NULL == (fpfailed = fopen(opts.failed, "w"))) {
perror(opts.failed);
return -1;
}
while (fgets(line, 8192, fofn_fp) != NULL) {
int i, j, len;
time_t ret_time; // SAK
/* Find input and output name, escaping spaces as needed */
len = strlen(line);
outfname = NULL;
for (i = j = 0; i < len; i++) {
if (line[i] == '\\' && i != len-1) {
line2[j++] = line[++i];
} else if (line[i] == ' ') {
line2[j++] = 0;
outfname = &line2[j];
} else if (line[i] != '\n') {
line2[j++] = line[i];
}
}
line2[j] = 0;
infname = line2;
/* Open input and output files */
if (NULL == (fpin = fopen(infname, "rb"))) {
char buf[2048];
sprintf(buf, "ERROR %s", infname);
perror(buf);
if (opts.dots) {
fputc('!', stdout);
fflush(stdout);
}
if (fpfailed)
fprintf(fpfailed, "%s\n", infname);
continue;
}
if (outfname) {
if (NULL == (fpout = fopen(outfname, "wb+"))) {
char buf[2048];
sprintf(buf, "ERROR %s", outfname);
perror(buf);
fclose(fpin);
if (opts.dots) {
fputc('!', stdout);
fflush(stdout);
}
if (fpfailed)
fprintf(fpfailed, "%s\n", infname);
continue;
}
} else {
outfname = "(stdout)";
fpout = stdout;
}
/* Convert */
ret = convert(fpin, fpout, infname, outfname, &opts);
ret_time = time(NULL); // SAK
ret_all |= ret;
if (opts.dots) {
fputc(ret ? '!' : '.', stdout);
fflush(stdout);
}
if (ret) {
if (fpfailed)
fprintf(fpfailed, "%s %s", infname, ctime(&ret_time)); // SAK
} else {
if (fppassed)
fprintf(fppassed, "%s %s", infname, ctime(&ret_time)); // SAK
}
/* Tidy up */
fclose(fpin);
if (fpout != stdout)
fclose(fpout);
}
if(ret_all)
fprintf(stderr,"* ret_all = %d\n", ret_all);
fclose(fofn_fp);
return ret_all;
}
return 0;
}
