int main (int argc, char **argv)
{
struct uio_info_t *info_list, *p;
program_name = argv[0];
decode_switches (argc, argv);
if (opt_help)
usage(0);
if (opt_version)
version(0);
info_list = uio_find_devices(uio_filter);
if (!info_list)
printf("No UIO devices found.\n");
p = info_list;
while (p) {
uio_get_all_info(p);
if (opt_verbose) uio_get_device_attributes(p);
if (opt_mmap) uio_mmap_test(p);
show_uio_info(p);
p = p->next;
}
uio_free_info(info_list);
exit (0);
}
int
main (int argc, char **argv)
{
int i;
program_name = argv[0];
i = decode_switches (argc, argv);
/* do the work */
exit (0);
}
int main (int argc, char **argv)
{
struct uio_info_t *info_list, *p;
program_name = argv[0];
decode_switches (argc, argv);
if (uio_offset < 0) {
fprintf(stderr, "Negative offsets are not supported.\n");
usage (-EINVAL);
}
if (opt_help)
usage(0);
if (opt_version)
version(0);
info_list = uio_find_devices(uio_filter);
if (!info_list)
printf("No UIO devices found.\n");
p = info_list;
while (p) {
char dev_name[16];
int fd;
uio_get_all_info(p);
uio_get_device_attributes(p);
snprintf(dev_name,sizeof(dev_name),"/dev/uio%d",p->uio_num);
fd = open(dev_name,O_RDWR);
if (fd<0) {
close(fd);
p = p->next;
continue;
}
uio_single_mmap(p,uio_map,fd);
if (opt_read) uio_read(p);
if (opt_write) uio_write(p);
close(fd);
p = p->next;
}
uio_free_info(info_list);
exit (0);
}
/*============================*/
int main (int argc, char *argv[]) {
int tmp;
char *line;
loc_min *LM;
int *tm;
int i;
char signal[100]="", what[100]="", stuff[100]="";
/* Parse command line */
program_name = argv[0];
opt.kT = -300;
opt.MOVESET = "";
opt.minh = 0.0000001;
opt.label = 0; /* normally, use numbers for minima */
GRAPH = NULL;
/* Try to parse head to determine graph-type */
decode_switches (argc, argv);
if (args_info.inputs_num > 0) {
opt.INFILE = fopen(args_info.inputs[0], "r");
if (opt.INFILE==NULL) nrerror("can't open file");
} else {
opt.INFILE = stdin;
}
line = get_line(opt.INFILE);
if (line == NULL) {
fprintf(stderr,"Error in input file\n");
exit(123);
}
opt.seq = (char *) space(strlen(line) + 1);
sscanf(line,"%s %d %99s %99s %99s", opt.seq, &tmp, signal, what, stuff);
if(strcmp(stuff, "\0")!=0 && strncmp(what, "Q", 1)==0) { /* lattice proteins*/
memset(opt.seq, 0, strlen(line)+1);
strcpy(opt.seq, stuff);
}
if ((!opt.poset)&&(strcmp(signal,"::")!=0)) {
int r, dim;
/* in this case we have a poset file !!!! */
r=sscanf(signal,"P:%d",&dim);
if(r<1) {
fprintf(stderr,
"Warning: obscure headline in input file\n");
dim = 0;
}
if(dim>0) opt.poset = dim;
}
if (opt.poset) { /* in this case we have a poset file !!!! */
fprintf(stderr,
"!!! Input data are a poset with %d objective functions\n",
opt.poset);
/* we have a SECIS design file */
if ( ((GRAPH != NULL) && (strstr(GRAPH, "SECIS") != NULL))
||(strncmp(what, "SECIS", 5) == 0) )
{
#if HAVE_SECIS_EXTENSION
int len, max_m, min_as;
char *sec_structure, *protein_sequence;
if (sscanf(what,"SECIS,%d,%d", &max_m, &min_as) < 2) {
fprintf(stderr,
"Error in input format for SECIS design !"
"expected format: SECIS,INT,INT\n"
"got: `%s'",
what);
exit(EXIT_FAILURE);
}
free(line);
line = get_line(opt.INFILE);
len = strlen(line);
sec_structure = (char*)calloc(len+1, sizeof(char));
protein_sequence = (char*)calloc(len+1, sizeof(char));
sscanf(line,"%s %s", sec_structure, protein_sequence);
if (opt.want_verbose)
fprintf(stderr,
"\nGraph is SECIS design with the following parameters:\n"
"Structure: %s\n"
"Constraints: %s\n"
"Protein sequence: %s\n"
"Max. number of mutations : %d\n"
"Min. alignment score (aa): %d\n\n",
sec_structure,
opt.seq,
protein_sequence,
max_m,
min_as);
initialize_SECIS(opt.seq, sec_structure, protein_sequence,
max_m, min_as);
free(sec_structure);
free(protein_sequence);
#else
fprintf(stderr,
"You need to reconfigure barriers with the --with-secis"
" option\nto use barriers SECIS design extension\n");
exit(EXIT_FAILURE);
#endif
}
}
free(line);
if (GRAPH==NULL)
if(strlen(what)) GRAPH = what;
if (GRAPH==NULL) GRAPH="RNA";
opt.GRAPH=GRAPH;
LM = barriers(opt);
if (opt.INFILE != stdin) fclose(opt.INFILE);
tm = make_truemin(LM);
if(opt.poset) mark_global(LM);
print_results(LM,tm,opt.seq);
fflush(stdout);
if (!opt.want_quiet) ps_tree(LM,tm,0);
if (opt.rates || opt.microrates) {
compute_rates(tm,opt.seq);
if (!opt.want_quiet) ps_tree(LM,tm,1);
print_rates(tm[0], "rates.out");
}
if (opt.poset) mark_global(LM);
for (i = 0; i < args_info.path_given; ++i) {
int L1, L2;
sscanf(args_info.path_arg[i], "%d=%d", &L1, &L2);
if ((L1>0) && (L2>0)) {
FILE *PATH = NULL;
char tmp[30];
path_entry *path;
path = backtrack_path(L1, L2, LM, tm);
(void) sprintf(tmp, "path.%03d.%03d.txt", L1, L2);
PATH = fopen (tmp, "w");
if (PATH == NULL) nrerror("couldn't open path file");
print_path(PATH, path, tm);
/* fprintf(stderr, "%llu %llu\n", 0, MAXIMUM); */
fclose (PATH);
fprintf (stderr, "wrote file %s\n", tmp);
free (path);
}
}
/* memory cleanup */
free(opt.seq);
free(LM);
free(tm);
#if WITH_DMALLOC
kill_hash(); /* freeing the hash takes unacceptably long */
#endif
cmdline_parser_free(&args_info);
exit(0);
}
int
main (int argc, char * argv[])
{
int i, trim_len_fw, trim_len_rev;
//struct reads_info ** ri_left;
//struct reads_info ** ri_right;
// int cnt_reads_left;
// int cnt_reads_right;
int read_size;
char * out[4];
FILE * fd[4];
int ass;
double uncalled_forward, uncalled_reverse;
struct user_args sw;
struct emp_freq * ef;
struct block_t fwd_block;
struct block_t rev_block;
char two_piece;
int elms;
if (!decode_switches (argc, argv, &sw))
{
/* TODO: Validate reads names */
usage ();
return (EXIT_FAILURE);
}
ef = (struct emp_freq *)malloc (sizeof(struct emp_freq));
ef->freqa = ef->freqc = ef->freqg = ef->freqt = ef->total = ef->pa = ef->pc = ef->pg = ef->pt = ef->q = 0.25;
init_scores(sw->phred_base, ef);
/* read the two fastq files containing the left-end and right-end reads */
//ri_left = read_fastq(sw.fastq_left, &cnt_reads_left);
//ri_right = read_fastq(sw.fastq_right, &cnt_reads_right);
//if (!validate_input (cnt_reads_left, cnt_reads_right))
// {
// return (EXIT_FAILURE);
// }
// read_size = strlen (ri_left[0]->data);
/* TODO: THIS IS WRONG!!!! TO GET EMPIRICAL FREQUENCIES WE NEED TO READ THE WHOLE FILE :-( */
//ef = get_emp_freq (cnt_reads_right, read_size, fwd_block.reads, rev_block.reads);
/* reverse the right ends */
/* allocate memory for the assembled results */
/*
ai = (struct asm_info *) malloc (cnt_reads_left * sizeof(struct asm_info));
for (i = 0; i < cnt_reads_left; ++i)
{
ai[i].data = (char *) malloc ((2 * read_size + 1) * sizeof(char));
ai[i].quality_score = (char *) malloc ((2 * read_size + 1) * sizeof(char));
}
*/
init_fastq_reader (sw.fastq_left, sw.fastq_right, sw.memory, &fwd_block, &rev_block);
/* construct output file names */
out[0] = makefilename (sw.outfile, ".assembled.fastq");
out[1] = makefilename (sw.outfile, ".unassembled.forward.fastq");
out[2] = makefilename (sw.outfile, ".unassembled.reverse.fastq");
out[3] = makefilename (sw.outfile, ".discarded.fastq");
fd[0] = fopen (out[0], "w");
fd[1] = fopen (out[1], "w");
fd[2] = fopen (out[2], "w");
fd[3] = fopen (out[3], "w");
while (1)
{
elms = get_next_reads (&fwd_block, &rev_block);
if (!elms) break;
read_size = strlen (fwd_block.reads[0]->data);
// printf ("%d elms (Seq)\n", elms);
//#pragma omp parallel shared(fwd_block.reads, rev_block.reads, ai) private(i, ass, uncalled, kassian_result)
#pragma omp parallel private(i, ass)
{
/* flags[i] = 1 (assembled) 0 (discarded) 2 (unassembled) */
#pragma omp for schedule (guided)
for (i = 0; i < elms; ++ i)
{
mstrrev (rev_block.reads[i]->data);
mstrcpl (rev_block.reads[i]->data);
mstrrev (rev_block.reads[i]->qscore);
if (sw.emp_freqs == 0)
{
ass = assembly (fwd_block.reads[i], rev_block.reads[i], &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
else
{
ass = assembly_ef (fwd_block.reads[i], rev_block.reads[i], ef, &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
}
}
for ( i = 0; i < elms; ++ i)
{
two_piece = *(fwd_block.reads[i]->data - 1);
*(fwd_block.reads[i]->data - 1) = 0;
if (*(fwd_block.reads[i]->qscore - 1) == 1) /* assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
fprintf (fd[0], "%s\n", fwd_block.reads[i]->header);
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->data);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->data);
fprintf (fd[0], "%s\n", rev_block.reads[i]->data);
}
fprintf (fd[0], "+\n");
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->qscore);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->qscore);
fprintf (fd[0], "%s\n", rev_block.reads[i]->qscore);
}
}
else /* not assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
trim_len_fw = trim (fwd_block.reads[i], &sw, read_size, &uncalled_forward);
trim_len_rev = trim_cpl (rev_block.reads[i], &sw, read_size, &uncalled_reverse);
if (trim_len_fw < sw.min_trim_len || trim_len_rev < sw.min_trim_len || uncalled_forward >= sw.max_uncalled || uncalled_reverse >= sw.max_uncalled)
{ /* discarded reads*/
/* Maybe consider printing the untrimmed sequences */
fprintf (fd[3], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[3], "%s\n", rev_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
else /* unassembled reads*/
{
fprintf (fd[1], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[2], "%s\n", rev_block.reads[i]->header);
fprintf (fd[1], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[2], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
}
}
}
free (ef);
free (out[0]);
free (out[1]);
free (out[2]);
free (out[3]);
destroy_reader ();
/* TODO: Fix those file closings */
fclose (fd[0]);
fclose (fd[1]);
fclose (fd[2]);
fclose (fd[3]);
return (0);
}
int
main (int argc, char **argv)
{
int i;
struct xs_handle *xs;
xs_transaction_t th;
char *path;
int fd;
fd_set set;
int er;
char **vec;
unsigned int num_strings;
char * buf;
unsigned int len;
char *program;
char **arguments;
int arguments_count;
pid_t pid;
int j;
char *last_value = NULL;
int status;
program_name = argv[0];
i = decode_switches (argc, argv);
if (argc - i < 1)
usage(1);
path = argv[i++];
if (argc - i > 0)
{
program = argv[i++];
arguments_count = argc - i;
arguments = malloc(sizeof(char*) * (argc - i + 2));
arguments[0] = program;
for (j=0; j<arguments_count; j++)
arguments[j + 1] = argv[i + j];
arguments[j + 1] = NULL;
} else
{
program = NULL;
arguments = NULL;
arguments_count = 0;
}
if (want_verbose) {
printf("Path: %s\n", path);
if (program)
{
printf("Program: %s", program);
for (i=1; i<arguments_count + 1; i++)
printf(" %s", arguments[i]);
printf("\n");
}
}
/* Get a connection to the daemon */
xs = xs_daemon_open();
if ( xs == NULL ) xs = xs_domain_open();
if ( xs == NULL ) {
error("Unable to connect to XenStore");
exit(1);
}
/* Create a watch on /local/domain/0/mynode. */
er = xs_watch(xs, path, "token");
if ( er == 0 ) {
error("Unable to create watch");
exit(1);
}
/* We are notified of read availability on the watch via the
* file descriptor.
*/
fd = xs_fileno(xs);
while (1)
{
FD_ZERO(&set);
FD_SET(fd, &set);
/* Poll for data. */
if ( select(fd + 1, &set, NULL, NULL, NULL) > 0
&& FD_ISSET(fd, &set))
{
/* num_strings will be set to the number of elements in vec
* (typically, 2 - the watched path and the token) */
vec = xs_read_watch(xs, &num_strings);
if ( !vec ) {
error("Unable to read watch");
continue;
}
if (want_verbose)
printf("Path changed: %s\n", vec[XS_WATCH_PATH]);
/* Prepare a transaction and do a read. */
th = xs_transaction_start(xs);
buf = xs_read(xs, th, vec[XS_WATCH_PATH], &len);
xs_transaction_end(xs, th, false);
if (buf)
{
if (last_value && strcmp(buf, last_value) == 0) {
if (want_verbose)
printf("Value did not change\n");
continue;
}
if (want_verbose)
printf("New value: %s\n", buf);
if (program) {
pid = fork();
if (pid == 0) {
setenv("XENSTORE_WATCH_PATH", vec[XS_WATCH_PATH], 1);
setenv("XENSTORE_WATCH_VALUE", buf, 1);
for (i=0; arguments[i]; i++) {
if (strcmp(arguments[i], "%v") == 0)
arguments[i] = buf;
else if (strcmp(arguments[i], "%p") == 0)
arguments[i] = vec[XS_WATCH_PATH];
}
execvp(program, arguments);
error("Unable to start program");
exit(1);
} else {
waitpid(pid, &status, 0);
}
} else {
if (!want_verbose)
printf("%s\n", buf);
}
if (last_value)
free(last_value);
last_value = buf;
}
}
}
/* Cleanup */
close(fd);
xs_daemon_close(xs);
free(path);
exit(0);
}
int main(int argc, char *argv[])
{
int num;
char *dir, **cmd;
#ifdef HAVE_LIBCAP
cap_t caps;
cap_value_t capv[7];
int flags;
#else
cap_user_header_t head;
cap_user_data_t data;
__u32 mask;
#endif
uid = 0;
gid = 0;
#if 0
euid = geteuid();
egid = getegid();
#endif
num = decode_switches(argc, argv);
dir = argv[num++];
cmd = argv + num;
if (dir == NULL)
usage(EXIT_FAILURE);
if (chdir(dir))
die(dir);
if (chroot(dir))
die("chroot");
#ifdef HAVE_LIBCAP
if (captxt != NULL) {
if ((caps = cap_from_text(captxt)) == NULL)
die("cap_from_text");
} else {
if ((caps = cap_get_proc()) == NULL)
die("cap_get_proc");
capv[0] = CAP_SETPCAP; /* give caps to non-chrooted tasks */
capv[1] = CAP_SYS_MODULE; /* hijack syscalls like chroot() */
capv[2] = CAP_SYS_RAWIO; /* raw disk access (needed?) */
capv[3] = CAP_SYS_CHROOT; /* can't have this, obviously... */
capv[4] = CAP_SYS_PTRACE; /* control other, non-caged tasks */
capv[5] = CAP_SYS_ADMIN; /* mount proc and mess with kmem */
#ifdef CAP_MKNOD
capv[6] = CAP_MKNOD; /* create block devices */
flags = 7;
#else
flags = 6;
#endif /* CAP_MKNOD */
if (cap_set_flag(caps, CAP_EFFECTIVE, flags, capv, CAP_CLEAR))
die("cap_set_flag");
if (cap_set_flag(caps, CAP_PERMITTED, flags, capv, CAP_CLEAR))
die("cap_set_flag");
if (cap_set_flag(caps, CAP_INHERITABLE, flags, capv, CAP_CLEAR))
die("cap_set_flag");
}
if (cap_set_proc(caps))
die("cap_set_proc");
cap_free(&caps);
#else
if ((head = malloc(8)) == NULL)
die("malloc()");
if ((data = malloc(3 * 4)) == NULL)
die("malloc()");
head->pid = 0;
head->version = _LINUX_CAPABILITY_VERSION;
if (capget(head, data))
die("capget");
mask = (1 << CAP_SETPCAP); /* give caps to non-chrooted tasks */
mask |= (1 << CAP_SYS_MODULE); /* hijack syscalls such as chroot() */
mask |= (1 << CAP_SYS_RAWIO); /* raw disk access (needed?) */
mask |= (1 << CAP_SYS_CHROOT); /* can't have this, obviously... */
mask |= (1 << CAP_SYS_PTRACE); /* control other, non-caged tasks */
mask |= (1 << CAP_SYS_ADMIN); /* mount proc and mess with kmem */
#ifdef CAP_MKNOD
mask |= (1 << CAP_MKNOD); /* create block devices */
#endif /* CAP_MKNOD */
data->permitted &= ~mask;
data->effective &= ~mask;
data->inheritable &= ~mask;
if (capset(head, data))
die("capset()");
#endif /* HAVE_LIBCAP */
if ((gid) && (setgid(gid)))
die("setgid");
if ((uid) && (setuid(uid)))
die("setuid");
execvp(cmd[0], cmd);
die(cmd[0]);
}
int
main (int argc, char **argv)
{
int i;
char *p;
edg_wll_GssStatus gss_stat;
int ret;
FILE *pidf;
#ifndef IL_NOTIFICATIONS
p = strdup(argv[0]);
program_name = basename(p);
if (strcmp(program_name, "glite-lb-proxy-interlogd") == 0) {
file_prefix = DEFAULT_PROXY_PREFIX;
socket_path = DEFAULT_PROXY_SOCKET;
pidfile = DEFAULT_PROXY_PIDFILE;
}
free(p);
#endif
program_name = argv[0];
setlinebuf(stdout);
setlinebuf(stderr);
if ((p = getenv("EDG_WL_INTERLOG_TIMEOUT"))) TIMEOUT = atoi(p);
i = decode_switches (argc, argv);
if(glite_common_log_init()) {
fprintf(stderr, "glite_common_log_init() failed, exiting.\n");
exit(EXIT_FAILURE);
}
/* parse config file, if any */
if(conf_file != NULL) {
config = load_conf_file(conf_file);
}
/* check for reasonable queue lengths */
if((queue_size_low == 0 && queue_size_high > 0) ||
(queue_size_low > queue_size_high)) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "max queue length -Q must be greater than low queue length -q, both or none must be specified!");
exit(EXIT_FAILURE);
}
/* force -b if we do not have log server */
if(log_server == NULL) {
log_server = strdup(DEFAULT_LOG_SERVER);
bs_only = 1;
}
/* initialize error reporting */
if(init_errors()) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to initialize error message subsystem. Exiting.");
exit(EXIT_FAILURE);
}
if (signal(SIGPIPE, SIG_IGN) == SIG_ERR
|| signal(SIGABRT, handle_signal) == SIG_ERR
|| signal(SIGTERM, handle_signal) == SIG_ERR
|| signal(SIGINT, handle_signal) == SIG_ERR) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to setup signal handlers: %s, exiting.",
strerror(errno));
exit(EXIT_FAILURE);
}
/* just try it before deamonizing to be able to complain aloud */
if (!(pidf = fopen(pidfile,"w"))) {
perror(pidfile);
exit(EXIT_FAILURE);
}
fclose(pidf);
if(!debug &&
(daemon(0,0) < 0)) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to daemonize itself: %s, exiting.",
strerror(errno));
exit(EXIT_FAILURE);
}
pidf = fopen(pidfile,"w");
assert(pidf); /* XXX */
fprintf(pidf,"%d\n",getpid());
fclose(pidf);
umask(S_IRWXG | S_IRWXO);
#ifdef LB_PERF
/* this must be called after installing signal handlers */
glite_wll_perftest_init(NULL, /* host */
NULL, /* user */
NULL, /* test name */
event_source,
njobs);
#endif
if(input_queue_attach() < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to initialize input queue: %s",
error_get_msg());
exit(EXIT_FAILURE);
}
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Initialized input queue.");
/* initialize output queues */
if(queue_list_init(log_server) < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to initialize output event queues: %s",
error_get_msg());
exit(EXIT_FAILURE);
}
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Initialized event queues.");
if(lazy_close)
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, " using lazy mode when closing connections, timeout %d",
default_close_timeout);
/* get credentials */
if (CAcert_dir)
setenv("X509_CERT_DIR", CAcert_dir, 1);
if(edg_wll_gss_initialize()) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to initialize GSS.");
exit(EXIT_FAILURE);
}
ret = edg_wll_gss_watch_creds(cert_file,&cert_mtime);
if (ret < 0)
glite_common_log(LOG_CATEGORY_SECURITY,LOG_PRIORITY_WARN,"edg_wll_gss_watch_creds failed, unable to access credentials\n");
cred_handle = malloc(sizeof(*cred_handle));
if(cred_handle == NULL) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to allocate structure for credentials.");
exit(EXIT_FAILURE);
}
cred_handle->creds = NULL;
cred_handle->counter = 0;
ret = edg_wll_gss_acquire_cred(cert_file, key_file, GSS_C_INITIATE, &cred_handle->creds, &gss_stat);
if (ret) {
char *gss_err = NULL;
if (ret == EDG_WLL_GSS_ERROR_GSS)
edg_wll_gss_get_error(&gss_stat, "edg_wll_gss_acquire_cred_gsi()", &gss_err);
glite_common_log(LOG_CATEGORY_SECURITY, LOG_PRIORITY_FATAL, "Failed to load GSI credential: %s",
(gss_err) ? gss_err : "edg_wll_gss_acquire_cred_gsi() failed");
if (gss_err)
free(gss_err);
if(gss_stat.minor_status != 0) {
exit(EXIT_FAILURE);
} else {
glite_common_log(LOG_CATEGORY_SECURITY, LOG_PRIORITY_WARN, "Continuing unauthenticated (yet).");
}
}
if(cred_handle && cred_handle->creds) {
glite_common_log(LOG_CATEGORY_SECURITY, LOG_PRIORITY_INFO, "Using certificate %s", cred_handle->creds->name);
}
/* parse config, initialize plugins */
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Initializing plugins:\n");
if(config) {
char *s = strstr(config, "[interlogd]");
char *p;
char name[MAXPATHLEN+1];
if(s) {
/* next line */
s = strchr(s, '\n');
if(s) s++;
while(s) {
if(*s == 0 || *s == '[')
break;
/* parse line */
p = strchr(s, '\n');
if(p) {
*p = 0;
}
/* XXX possible overflow by long line in config file */
ret = sscanf(s, " plugin =%s", name);
if(p) *p = '\n';
if(ret > 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, " loading plugin %s\n", name);
if(plugin_mgr_init(name, config) < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_ERROR, "Failed to load plugin %s: %s\n", name, error_get_msg());
}
}
s = p + 1;
}
}
}
#ifndef PERF_EMPTY
/* find all unsent events waiting in files */
#ifdef LB_PERF
if(norecover) {
if(event_store_init(file_prefix) < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to initialize event stores: %s",
error_get_msg());
exit(EXIT_FAILURE);
}
} else
#endif
{
pthread_t rid;
if(pthread_create(&rid, NULL, recover_thread, NULL) < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Failed to start recovery thread: %s", strerror(errno));
exit(EXIT_FAILURE);
}
pthread_detach(rid);
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Started recovery thread.");
}
#endif
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Using %d threads for parallel delivery.", parallel);
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Entering main loop.");
/* do the work */
if(loop() < 0) {
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_FATAL, "Fatal error: %s", error_get_msg());
if (killflg) {
input_queue_detach();
unlink(pidfile);
exit(EXIT_FAILURE);
}
}
glite_common_log(LOG_CATEGORY_CONTROL, LOG_PRIORITY_INFO, "Done!");
input_queue_detach();
unlink(pidfile);
exit (0);
}
}
if (buf != NULL)
free(buf);
}
/* Начало работы фильтра. Обработка аргументов коммандной строки */
/* Получение имени комманды. */
program_name = argv[0];
/* Инициализация функции аварийной очистки. */
init_cleanup(program_name);
push_cleanup(cleanup);
/* Разбор аргуентов командной строки. */
opt_r = decode_switches (argc, argv, EXIT_FAILURE, long_options, option_vars, &usage_header, &usage_params);
/* Проверка наличия параметров изображения. */
if (!width || !height || !hres || !vres) {
fprintf(stderr, "%s: WIDTH, HEIGHT, HRES & VRES should be specified.\n", program_name);
/* Выход с признаком ошибки, если были переданы не все параметры. */
exit(EXIT_FAILURE);
}
/* Инициализация счётчика цветовых каналов и размера отсчёта в соответствие с
* цветовой схемой изображения.
*/
if (is_cmyk) {
ss = 4; /* 4 байта для CMYK */
c0 = 0; /* 4 цвета, с 0 */
cN = 3; /* по 3 */
int main ( int argc, char ** argv)
{
struct TSwitch sw;
char * out_file;
unsigned int MAXnumgaps; //input argument
double gap_open_pen; //input argument
double gap_extend_pen; //input argument
unsigned int scoring_matrix; //input argument
unsigned int MAXgap;
unsigned int num_mat; //input argument + 1
double MAXscore; //to be computed
unsigned int MINnumgaps; //to be computed
unsigned int istart; //where to start backtracing
unsigned int jstart; //where to start backtracing
unsigned int iend; //where to end backtracing
unsigned int jend; //where to end backtracing
unsigned int * gaps_pos; //position of the gap(s)
unsigned int * gaps_len; //len of the gap(s)
unsigned int * where; //where is the gap(s): text [1] or pattern [2]
struct TSeq * t; //text t
unsigned int n; //length of text
struct TSeq * p; //pattern p
unsigned int m; //length of pattern
unsigned int L; //local alignment
double *** G; //dynamic programming matrix
int *** H; //backtracing matrix
unsigned int swap; //swap the text and the pattern in case m < n
unsigned int i, j;
/* checks the arguments */
i = decode_switches ( argc, argv, &sw );
if ( i < 5 || ! sw . seq_a || ! sw . seq_b )
{
usage ();
return ( 1 );
}
else
{
gap_open_pen = - sw . gap_open_pen; //the penalties should have a negative value
gap_extend_pen = - sw . gap_extend_pen;
out_file = sw . out_file;
L = sw . L;
if ( ! strcmp ( "EDNAFULL", sw . matrix ) ) scoring_matrix = 0;
else if ( ! strcmp ( "EBLOSUM62", sw . matrix ) ) scoring_matrix = 1;
else
{
fprintf ( stderr, "Error: scoring matrix argument should be `EDNAFULL' for nucleotide sequences or `EBLOSUM62' for protein sequences!!!\n" );
return ( 1 );
}
if ( L > 1 )
{
fprintf (stderr, "Error: wrong argument with L: should be either 0 (semi-global) or 1 (local)\n" );
return ( 1 );
}
}
/* reads the text */
t = read_fasta_file ( sw . seq_a );
if ( ! t )
{
fprintf (stderr, "Error: cannot read file %s!!!\n", sw . seq_a );
return ( 1 );
}
if ( ! t -> header ) t -> header = strdup ( "Seq A" );
/* reads the pattern */
p = read_fasta_file ( sw . seq_b );
if ( ! p )
{
fprintf( stderr, "Error: cannot read file %s!!!\n", sw . seq_b );
return ( 1 );
}
if ( ! p -> header ) p -> header = strdup ( "Seq B" );
/* calculate text's and pattern's length */
n = strlen ( t -> data );
m = strlen ( p -> data );
/* checks the lengths of text and pattern and swaps if needed */
if ( m > n )
{
swap_txt_pat ( &t, &n, &p, &m );
swap = 1;
}
else
swap = 0;
/* checks the max num of gaps: MAXnumgaps < n */
MAXnumgaps = ( sw . max_num_gaps <= -1 ) ? 2 : sw . max_num_gaps;
if( MAXnumgaps >= n )
{
fprintf ( stderr, "Error: the max gap length should be less than the length of the text!!!\n" );
return ( 1 );
}
if ( L == 1 ) num_mat = MAXnumgaps + 1;
else num_mat = MAXnumgaps;
MAXgap = ( sw . max_gap <= -1 ) ? n - 1 : sw . max_gap;
if( MAXgap >= n )
{
fprintf ( stderr, "Error: the max gap length should be less than the length of the text!!!\n" );
return ( 1 );
}
/* 3d dynamic memory allocation for matrices G and H*/
if( ( G = ( double *** ) malloc ( ( num_mat ) * sizeof( double ** ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
for ( i = 0; i < num_mat; i ++ )
{
if( ( G[i] = ( double ** ) malloc ( ( n + 1 ) * sizeof( double * ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
if( ( G[i][0] = ( double * ) calloc ( ( n + 1 ) * ( m + 1 ), sizeof( double ) ) ) == NULL )
{
fprintf( stderr, "G could not be allocated\n" );
return 0;
}
for ( j = 1; j < n + 1; j++ )
G[i][j] = ( void * ) G[i][0] + j * ( m + 1 ) * sizeof( double );
}
if( ( H = ( int *** ) malloc ( ( num_mat ) * sizeof( int ** ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
for ( i = 0; i < num_mat; i ++ )
{
if( ( H[i] = ( int ** ) malloc ( ( n + 1 ) * sizeof( int * ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
if( ( H[i][0] = ( int * ) calloc ( ( n + 1 ) * ( m + 1 ), sizeof( int ) ) ) == NULL )
{
fprintf( stderr, "H could not be allocated\n" );
return 0;
}
for ( j = 1; j < n + 1; j++ )
H[i][j] = ( void* ) H[i][0] + j * ( m + 1 ) * sizeof( int );
}
/* dynamic programming algorithm */
if ( L == 0 )
{
if ( MAXgap == n - 1 )
{
if ( ! ( dp_algorithm( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen ) ) )
{
fprintf ( stderr, "Error: dp_algorithm() failed!!!\n" );
return ( 1 );
}
}
else
{
if ( ! ( dp_algorithm_pruned( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen, MAXgap ) ) )
{
fprintf ( stderr, "Error: dp_algorithm_pruned() failed!!!\n" );
return ( 1 );
}
}
}
else
{
if ( MAXgap == n - 1 )
{
if ( ! ( dp_algorithm_lcl( G, MAXnumgaps, H, t -> data, n, p -> data, m, scoring_matrix, gap_open_pen, gap_extend_pen ) ) )
{
fprintf ( stderr, "Error: dp_algorithm() failed!!!\n" );
return ( 1 );
}
}
else
{
fprintf ( stderr, "Error: option `- m' is only for global alignment!!!\n" );
return ( 1 );
}
}
MINnumgaps = 0; //to be computed
/* finds the optimal alignment based on the matrices scores */
if ( L == 0 ) opt_solution ( G, MAXnumgaps, n, m, &MAXscore, &istart, &MINnumgaps );
if ( L == 1 ) opt_solution_lcl ( G, MAXnumgaps, n, m, &MAXscore, &istart, &jstart, &MINnumgaps );
if( ( gaps_pos = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "gaps_pos could not be allocated\n" );
return 0;
}
if( ( gaps_len = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "gaps_pos could not be allocated\n" );
return 0;
}
if( ( where = ( unsigned int * ) calloc ( MINnumgaps, sizeof( unsigned int ) ) ) == NULL )
{
fprintf( stderr, "where could not be allocated\n" );
return 0;
}
/* computes the position of the gap */
if ( L == 0 ) backtracing ( H[MINnumgaps - 1], m, n, istart, gaps_pos, MINnumgaps, gaps_len, where );
if ( L == 1 ) backtracing_lcl ( G[MINnumgaps], m, n, H[MINnumgaps], istart, jstart, gaps_pos, MINnumgaps, gaps_len, where, &iend, &jend );
#if 0
int s;
for ( s = 0; s < num_mat; s++ )
{
for(i = 0; i < n+1; i++) //Matrix G output
{
for(j = 0; j < m+1; j++)
{
fprintf( stderr,"%d\t", (int) G[s][i][j] );
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
#if 1
for(i = 0; i < n+1; i++) //Matrix H output
{
for(j = 0; j < m+1; j++)
{
fprintf( stderr,"%d\t", H[s][i][j]);
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
#endif
}
if ( L == 1 ) fprintf( stderr,"\n[%d,%d]-->[%d,%d]\n", istart, jstart, iend, jend );
#endif
/* outputs the results */
if ( L == 0 )
if ( ! ( results ( out_file, t, n, p, m, MAXscore, gaps_pos, MINnumgaps, gaps_len, where, swap, scoring_matrix, gap_open_pen, gap_extend_pen, L ) ) )
{
fprintf(stderr, "Error: results() failed!!!\n");
return ( 1 );
}
if ( L == 1 )
if ( ! ( results_lcl ( out_file, t, n, p, m, MAXscore, gaps_pos, MINnumgaps, gaps_len, where, istart, iend, jstart, jend, swap, scoring_matrix, gap_open_pen, gap_extend_pen, L ) ) )
{
fprintf(stderr, "Error: results() failed!!!\n");
return ( 1 );
}
for ( i = 0; i < num_mat; i++ )
{
free ( G[i][0] );
free ( G[i] );
free ( H[i][0] );
free ( H[i] );
}
free ( G );
free ( H );
free ( gaps_pos );
free ( gaps_len );
free ( where );
free ( t -> header );
free ( p -> header );
free ( t );
free ( p );
free ( sw . out_file );
free ( sw . matrix );
return ( 0 );
}
