int
main(
int argc,
char ** argv)
{
int c;
char *command;
application_argument_t argument;
int i;
#ifdef GNUTAR
gnutar_path = GNUTAR;
#else
gnutar_path = NULL;
#endif
gnutar_directory = NULL;
gnutar_onefilesystem = 1;
gnutar_atimepreserve = 1;
gnutar_checkdevice = 1;
gnutar_sparse = 1;
gnutar_no_unquote = 0;
exit_handling = NULL;
/* initialize */
/*
* Configure program for internationalization:
* 1) Only set the message locale for now.
* 2) Set textdomain for all amanda related programs to "amanda"
* We don't want to be forced to support dozens of message catalogs.
*/
setlocale(LC_MESSAGES, "C");
textdomain("amanda");
if (argc < 2) {
printf("ERROR no command given to amgtar\n");
error(_("No command given to amgtar"));
}
/* drop root privileges */
if (!set_root_privs(0)) {
if (strcmp(argv[1], "selfcheck") == 0) {
printf("ERROR amgtar must be run setuid root\n");
}
error(_("amgtar must be run setuid root"));
}
safe_fd(3, 2);
set_pname("amgtar");
/* Don't die when child closes pipe */
signal(SIGPIPE, SIG_IGN);
#if defined(USE_DBMALLOC)
malloc_size_1 = malloc_inuse(&malloc_hist_1);
#endif
add_amanda_log_handler(amanda_log_stderr);
add_amanda_log_handler(amanda_log_syslog);
dbopen(DBG_SUBDIR_CLIENT);
startclock();
dbprintf(_("version %s\n"), version());
config_init(CONFIG_INIT_CLIENT, NULL);
//check_running_as(RUNNING_AS_DUMPUSER_PREFERRED);
//root for amrecover
//RUNNING_AS_CLIENT_LOGIN from selfcheck, sendsize, sendbackup
/* parse argument */
command = argv[1];
argument.config = NULL;
argument.host = NULL;
argument.message = 0;
argument.collection = 0;
argument.calcsize = 0;
argument.tar_blocksize = NULL;
argument.level = NULL;
init_dle(&argument.dle);
while (1) {
int option_index = 0;
c = getopt_long (argc, argv, "", long_options, &option_index);
if (c == -1) {
break;
}
switch (c) {
case 1: argument.config = stralloc(optarg);
break;
case 2: argument.host = stralloc(optarg);
break;
case 3: argument.dle.disk = stralloc(optarg);
break;
case 4: argument.dle.device = stralloc(optarg);
break;
case 5: argument.level = g_slist_append(argument.level,
GINT_TO_POINTER(atoi(optarg)));
break;
case 6: argument.dle.create_index = 1;
break;
case 7: argument.message = 1;
break;
case 8: argument.collection = 1;
break;
case 9: argument.dle.record = 1;
break;
case 10: gnutar_path = stralloc(optarg);
break;
case 11: gnutar_listdir = stralloc(optarg);
break;
case 12: if (optarg && strcasecmp(optarg, "NO") == 0)
gnutar_onefilesystem = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
gnutar_onefilesystem = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad ONE-FILE-SYSTEM property value (%s)]\n"), get_pname(), optarg);
break;
case 13: if (optarg && strcasecmp(optarg, "NO") == 0)
gnutar_sparse = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
gnutar_sparse = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad SPARSE property value (%s)]\n"), get_pname(), optarg);
break;
case 14: if (optarg && strcasecmp(optarg, "NO") == 0)
gnutar_atimepreserve = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
gnutar_atimepreserve = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad ATIME-PRESERVE property value (%s)]\n"), get_pname(), optarg);
break;
case 15: if (optarg && strcasecmp(optarg, "NO") == 0)
gnutar_checkdevice = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
gnutar_checkdevice = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad CHECK-DEVICE property value (%s)]\n"), get_pname(), optarg);
break;
case 16: if (optarg)
argument.dle.include_file =
append_sl(argument.dle.include_file, optarg);
break;
case 17: if (optarg)
argument.dle.include_list =
append_sl(argument.dle.include_list, optarg);
break;
case 18: argument.dle.include_optional = 1;
break;
case 19: if (optarg)
argument.dle.exclude_file =
append_sl(argument.dle.exclude_file, optarg);
break;
case 20: if (optarg)
argument.dle.exclude_list =
append_sl(argument.dle.exclude_list, optarg);
break;
case 21: argument.dle.exclude_optional = 1;
break;
case 22: gnutar_directory = stralloc(optarg);
break;
case 23: if (optarg)
normal_message =
g_slist_append(normal_message, optarg);
break;
case 24: if (optarg)
ignore_message =
g_slist_append(ignore_message, optarg);
break;
case 25: if (optarg)
strange_message =
g_slist_append(strange_message, optarg);
break;
case 26: if (optarg)
exit_handling = stralloc(optarg);
break;
case 27: argument.calcsize = 1;
break;
case 28: argument.tar_blocksize = stralloc(optarg);
break;
case 29: if (optarg && strcasecmp(optarg, "NO") == 0)
gnutar_no_unquote = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
gnutar_no_unquote = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad No_UNQUOTE property value (%s)]\n"), get_pname(), optarg);
break;
case ':':
case '?':
break;
}
}
argument.argc = argc - optind;
argument.argv = argv + optind;
if (argument.config) {
config_init(CONFIG_INIT_CLIENT | CONFIG_INIT_EXPLICIT_NAME | CONFIG_INIT_OVERLAY,
argument.config);
dbrename(get_config_name(), DBG_SUBDIR_CLIENT);
}
if (config_errors(NULL) >= CFGERR_ERRORS) {
g_critical(_("errors processing config file"));
}
re_table = build_re_table(init_re_table, normal_message, ignore_message,
strange_message);
for(i=0;i<256;i++)
exit_value[i] = 1; /* BAD */
exit_value[0] = 0; /* GOOD */
exit_value[1] = 0; /* GOOD */
if (exit_handling) {
char *s = exit_handling;
while (s) {
char *r = strchr(s, '=');
if (r) {
int j = atoi(s);
if (j >= 0 && j < 256) {
r++;
if (strncasecmp(r, "GOOD", 4) == 0) {
exit_value[j] = 0;
}
}
}
s = strchr(s+1, ' ');
}
}
gnutar_listdir = getconf_str(CNF_GNUTAR_LIST_DIR);
if (strlen(gnutar_listdir) == 0)
gnutar_listdir = NULL;
if (gnutar_path) {
dbprintf("GNUTAR-PATH %s\n", gnutar_path);
} else {
dbprintf("GNUTAR-PATH is not set\n");
}
if (gnutar_listdir) {
dbprintf("GNUTAR-LISTDIR %s\n", gnutar_listdir);
} else {
dbprintf("GNUTAR-LISTDIR is not set\n");
}
if (gnutar_directory) {
dbprintf("DIRECTORY %s\n", gnutar_directory);
}
dbprintf("ONE-FILE-SYSTEM %s\n", gnutar_onefilesystem? "yes":"no");
dbprintf("SPARSE %s\n", gnutar_sparse? "yes":"no");
dbprintf("NO-UNQUOTE %s\n", gnutar_no_unquote? "yes":"no");
dbprintf("ATIME-PRESERVE %s\n", gnutar_atimepreserve? "yes":"no");
dbprintf("CHECK-DEVICE %s\n", gnutar_checkdevice? "yes":"no");
{
amregex_t *rp;
for (rp = re_table; rp->regex != NULL; rp++) {
switch (rp->typ) {
case DMP_NORMAL : dbprintf("NORMAL %s\n", rp->regex); break;
case DMP_IGNORE : dbprintf("IGNORE %s\n", rp->regex); break;
case DMP_STRANGE: dbprintf("STRANGE %s\n", rp->regex); break;
case DMP_SIZE : dbprintf("SIZE %s\n", rp->regex); break;
case DMP_ERROR : dbprintf("ERROR %s\n", rp->regex); break;
}
}
}
if (strcmp(command, "support") == 0) {
amgtar_support(&argument);
} else if (strcmp(command, "selfcheck") == 0) {
amgtar_selfcheck(&argument);
} else if (strcmp(command, "estimate") == 0) {
amgtar_estimate(&argument);
} else if (strcmp(command, "backup") == 0) {
amgtar_backup(&argument);
} else if (strcmp(command, "restore") == 0) {
amgtar_restore(&argument);
} else if (strcmp(command, "validate") == 0) {
amgtar_validate(&argument);
} else {
dbprintf("Unknown command `%s'.\n", command);
fprintf(stderr, "Unknown command `%s'.\n", command);
exit (1);
}
return 0;
}
int main(int argc, char **argv)
{
const char *hmmfile; /* file to read HMMs from */
FILE *fp; /* output file handle */
HMMFILE *hmmfp; /* opened hmmfile for reading */
struct plan7_s *hmm; /* HMM to generate from */
int L; /* length of a sequence */
int i; /* counter over sequences */
char *ofile; /* output sequence file */
int nseq; /* number of seqs to sample */
int seed; /* random number generator seed */
int be_quiet; /* TRUE to silence header/footer */
int do_alignment; /* TRUE to output in aligned format */
int do_consensus; /* TRUE to do a single consensus seq */
AjBool ajselex;
AjBool ajcons;
AjPFile inf=NULL;
AjPFile outf=NULL;
AjPStr instr=NULL;
AjPStr outstr=NULL;
#ifdef MEMDEBUG
unsigned long histid1, histid2, orig_size, current_size;
orig_size = malloc_inuse(&histid1);
fprintf(stderr, "[... memory debugging is ON ...]\n");
#endif
/***********************************************
* Parse command line
***********************************************/
nseq = 10;
be_quiet = FALSE;
do_alignment = FALSE;
do_consensus = FALSE;
ofile = NULL;
embInitPV("ohmmemit",argc,argv,"HMMER",VERSION);
ajselex = ajAcdGetBoolean("selex");
ajcons = ajAcdGetBoolean("consensus");
nseq = ajAcdGetInt("number");
seed = ajAcdGetInt("seed");
inf = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
if(!seed)
seed = time ((time_t *) NULL);
if(ajselex)
do_alignment=TRUE;
else
do_alignment=FALSE;
if(ajcons)
do_consensus=TRUE;
else
do_consensus=FALSE;
instr = ajStrNewC((char *)ajFileGetNameC(inf));
outstr = ajStrNewC((char *)ajFileGetNameC(outf));
hmmfile = ajStrGetPtr(instr);
sre_srandom(seed);
if (do_alignment && do_consensus)
ajFatal("Sorry, -selex and -consensus are incompatible.\n");
if (nseq != 10 && do_consensus)
ajWarn("-consensus overrides -number (# of sampled seqs)");
/***********************************************
* Open HMM file (might be in HMMERDB or current directory).
* Read a single HMM from it.
***********************************************/
if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL)
ajFatal("Failed to open HMM file %s\n", hmmfile);
if (!HMMFileRead(hmmfp, &hmm))
ajFatal("Failed to read any HMMs from %s\n", hmmfile);
HMMFileClose(hmmfp);
if (hmm == NULL)
ajFatal("HMM file %s corrupt or in incorrect format? Parse failed",
hmmfile);
/* Configure the HMM to shut off N,J,C emission: so we
* do a simple single pass through the model.
*/
Plan7NakedConfig(hmm);
Plan7Renormalize(hmm);
/***********************************************
* Open the output file, or stdout
***********************************************/
fp = ajFileGetFileptr(outf);
/***********************************************
* Show the options banner
***********************************************/
be_quiet=TRUE;
if (! be_quiet)
{
printf("HMM file: %s\n", hmmfile);
if (! do_consensus)
{
printf("Number of seqs: %d\n", nseq);
printf("Random seed: %d\n", seed);
}
printf("- - - - - - - - - - - - - - - - - - - - - - - - - "
"- - - - - - -\n\n");
}
/***********************************************
* Do the work.
* If we're generating an alignment, we have to collect
* all our traces, then output. If we're generating unaligned
* sequences, we can emit one at a time.
***********************************************/
if (do_consensus)
{
char *seq;
SQINFO sqinfo; /* info about sequence (name/desc) */
EmitConsensusSequence(hmm, &seq, NULL, &L, NULL);
strcpy(sqinfo.name, "consensus");
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
WriteSeq(fp, kPearson, seq, &sqinfo);
free(seq);
}
else if (do_alignment)
{
struct p7trace_s **tr;
char **dsq;
SQINFO *sqinfo;
char **aseq;
AINFO ainfo;
float *wgt;
dsq = MallocOrDie(sizeof(char *) * nseq);
tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq);
sqinfo = MallocOrDie(sizeof(SQINFO) * nseq);
wgt = MallocOrDie(sizeof(float) * nseq);
FSet(wgt, nseq, 1.0);
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &(dsq[i]), &L, &(tr[i]));
sprintf(sqinfo[i].name, "seq%d", i+1);
sqinfo[i].len = L;
sqinfo[i].flags = SQINFO_NAME | SQINFO_LEN;
}
P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, FALSE,
&aseq, &ainfo);
/* Output the alignment */
WriteSELEX(fp, aseq, &ainfo, 50);
if (ofile != NULL && !be_quiet)
printf("Alignment saved in file %s\n", ofile);
/* Free memory
*/
for (i = 0; i < nseq; i++)
{
P7FreeTrace(tr[i]);
free(dsq[i]);
}
FreeAlignment(aseq, &ainfo);
free(sqinfo);
free(dsq);
free(wgt);
free(tr);
}
else /* unaligned sequence output */
{
struct p7trace_s *tr;
char *dsq;
char *seq;
SQINFO sqinfo;
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &dsq, &L, &tr);
sprintf(sqinfo.name, "seq%d", i+1);
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
seq = DedigitizeSequence(dsq, L);
WriteSeq(fp, kPearson, seq, &sqinfo);
P7FreeTrace(tr);
free(dsq);
free(seq);
}
}
ajFileClose(&outf);
FreePlan7(hmm);
SqdClean();
#ifdef MEMDEBUG
current_size = malloc_inuse(&histid2);
if (current_size != orig_size)
malloc_list(2, histid1, histid2);
else
fprintf(stderr, "[No memory leaks.]\n");
#endif
ajStrDel(&instr);
ajStrDel(&outstr);
ajFileClose(&inf);
ajFileClose(&outf);
embExit();
return 0;
}
/*ARGSUSED*/ int
main( int argc,
char ** argv[] )
{
union dbmalloptarg m;
unsigned long oldsize;
char *s;
unsigned long size;
char *t;
char *u;
// make sure we have both chain checking and fill area enabled
m.i = 1;
dbmallopt(MALLOC_CKCHAIN, &m);
m.i = 3;
dbmallopt(MALLOC_FILLAREA, &m);
// test leak detection software
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Testing malloc_inuse()...");
oldsize = malloc_inuse((unsigned long *) 0);
s = malloc(ALLOCSIZE);
size = malloc_inuse((unsigned long *) 0);
if (size != (oldsize + ALLOCSIZE))
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "\toldsize = %lu, size = %lu - should be %lu\n",
oldsize, size, oldsize + ALLOCSIZE);
}
else
{
fprintf(stderr, "OK\n");
}
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Testing malloc_mark()...");
malloc_mark(s);
size = malloc_inuse((unsigned long *) 0);
if (size != oldsize)
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "\tsize = %lu, should be %lu\n", size, oldsize);
}
else
{
fprintf(stderr, "OK\n");
}
// test new malloc_size function
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Testing malloc_size()...");
size = malloc_size(s);
if (size != ALLOCSIZE)
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "\tsize = %lu, should be %d\n", size, ALLOCSIZE);
}
else
{
fprintf(stderr, "OK\n");
}
// test memalign
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Testing memalign()...");
s = memalign((SIZETYPE) BIG_ALIGN, (SIZETYPE) 10);
t = memalign((SIZETYPE) BIG_ALIGN, (SIZETYPE) 20);
if ((s == NULL) || ((((SIZETYPE) s) & (BIG_ALIGN - 1)) != 0)
|| ((((SIZETYPE) t) & (SMALL_ALIGN - 1)) != 0))
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "\ts = 0x%lx(align=%d), t = 0x%lx(align=%d)\n",
s, BIG_ALIGN, t, SMALL_ALIGN);
}
else
{
fprintf(stderr, "OK\n");
}
s = memalign((SIZETYPE) 4096, (SIZETYPE) 10);
t = malloc(20);
s = malloc(10);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from strcpy() - out of bounds\n");
fflush(stderr);
strncpy(s, " ", 11);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from memset() - out of bounds (beyond)\n");
fflush(stderr);
memset(t, ' ', 21);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from free() - overrun\n");
fflush(stderr);
free(t);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from free() - double free\n");
fflush(stderr);
free(t);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "NO error from bzero\n");
fflush(stderr);
bzero(s, 10);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from bzero() - out of bounds\n");
fflush(stderr);
bzero(s, 11);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from free() - overrun\n");
fflush(stderr);
free(s);
u = malloc(1);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from memset() - out of bounds (before)\n");
fflush(stderr);
memset(u - 2, ' ', 3);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from free() - underrun\n");
fflush(stderr);
free(u);
s = malloc(10);
t = malloc(500); /* do this to make sure memset doesnt core */
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from memset() - out of bounds\n");
fflush(stderr);
memset(s, '1', 100);
fprintf(stderr, "-------------------------------------\n");
fprintf(stderr, "Error from malloc() - chain broken\n");
fflush(stderr);
t = malloc(10);
return (0);
}
int
main(
int argc,
char ** argv)
{
int c;
char *command;
application_argument_t argument;
#ifdef STAR
star_path = STAR;
#else
star_path = NULL;
#endif
star_tardumps = "/etc/tardumps";
star_dle_tardumps = 0;
star_onefilesystem = 1;
star_sparse = 1;
star_directory = NULL;
/* initialize */
/*
* Configure program for internationalization:
* 1) Only set the message locale for now.
* 2) Set textdomain for all amanda related programs to "amanda"
* We don't want to be forced to support dozens of message catalogs.
*/
setlocale(LC_MESSAGES, "C");
textdomain("amanda");
if (argc < 2) {
printf("ERROR no command given to amstar\n");
error(_("No command given to amstar"));
}
/* drop root privileges */
if (!set_root_privs(0)) {
if (strcmp(argv[1], "selfcheck") == 0) {
printf("ERROR amstar must be run setuid root\n");
}
error(_("amstar must be run setuid root"));
}
safe_fd(3, 2);
set_pname("amstar");
/* Don't die when child closes pipe */
signal(SIGPIPE, SIG_IGN);
#if defined(USE_DBMALLOC)
malloc_size_1 = malloc_inuse(&malloc_hist_1);
#endif
add_amanda_log_handler(amanda_log_stderr);
add_amanda_log_handler(amanda_log_syslog);
dbopen(DBG_SUBDIR_CLIENT);
startclock();
dbprintf(_("version %s\n"), VERSION);
config_init(CONFIG_INIT_CLIENT, NULL);
//check_running_as(RUNNING_AS_DUMPUSER_PREFERRED);
//root for amrecover
//RUNNING_AS_CLIENT_LOGIN from selfcheck, sendsize, sendbackup
/* parse argument */
command = argv[1];
argument.config = NULL;
argument.host = NULL;
argument.message = 0;
argument.collection = 0;
argument.calcsize = 0;
argument.level = NULL;
argument.command_options = NULL;
init_dle(&argument.dle);
opterr = 0;
while (1) {
int option_index = 0;
c = getopt_long (argc, argv, "", long_options, &option_index);
if (c == -1)
break;
switch (c) {
case 1: argument.config = stralloc(optarg);
break;
case 2: argument.host = stralloc(optarg);
break;
case 3: argument.dle.disk = stralloc(optarg);
break;
case 4: argument.dle.device = stralloc(optarg);
break;
case 5: argument.level = g_slist_append(argument.level,
GINT_TO_POINTER(atoi(optarg)));
break;
case 6: argument.dle.create_index = 1;
break;
case 7: argument.message = 1;
break;
case 8: argument.collection = 1;
break;
case 9: argument.dle.record = 1;
break;
case 10: star_path = stralloc(optarg);
break;
case 11: star_tardumps = stralloc(optarg);
break;
case 12: if (optarg && strcasecmp(optarg, "NO") == 0)
star_dle_tardumps = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
star_dle_tardumps = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad STAR-DLE-TARDUMP property value (%s)]\n"), get_pname(), optarg);
break;
case 13: if (optarg && strcasecmp(optarg, "YES") != 0) {
/* This option is required to be YES */
/* star_onefilesystem = 0; */
}
break;
case 14: if (optarg && strcasecmp(optarg, "NO") == 0)
star_sparse = 0;
else if (optarg && strcasecmp(optarg, "YES") == 0)
star_sparse = 1;
else if (strcasecmp(command, "selfcheck") == 0)
printf(_("ERROR [%s: bad SPARSE property value (%s)]\n"), get_pname(), optarg);
break;
case 15: argument.calcsize = 1;
break;
case 16: if (optarg)
normal_message =
g_slist_append(normal_message, optarg);
break;
case 17: if (optarg)
ignore_message =
g_slist_append(ignore_message, optarg);
break;
case 18: if (optarg)
strange_message =
g_slist_append(strange_message, optarg);
break;
case 19: if (optarg)
argument.dle.include_list =
append_sl(argument.dle.include_list, optarg);
break;
case 20: if (optarg)
argument.dle.exclude_list =
append_sl(argument.dle.exclude_list, optarg);
break;
case 21: if (optarg)
star_directory = stralloc(optarg);
break;
case 22: argument.command_options =
g_slist_append(argument.command_options,
stralloc(optarg));
case 23: if (optarg)
argument.dle.exclude_file =
append_sl(argument.dle.exclude_file, optarg);
break;
case ':':
case '?':
break;
}
}
if (!argument.dle.disk && argument.dle.device)
argument.dle.disk = stralloc(argument.dle.device);
if (!argument.dle.device && argument.dle.disk)
argument.dle.device = stralloc(argument.dle.disk);
argument.argc = argc - optind;
argument.argv = argv + optind;
if (argument.config) {
/* overlay this configuration on the existing (nameless) configuration */
config_init(CONFIG_INIT_CLIENT | CONFIG_INIT_EXPLICIT_NAME | CONFIG_INIT_OVERLAY,
argument.config);
dbrename(get_config_name(), DBG_SUBDIR_CLIENT);
}
if (config_errors(NULL) >= CFGERR_ERRORS) {
g_critical(_("errors processing config file"));
}
re_table = build_re_table(init_re_table, normal_message, ignore_message,
strange_message);
if (strcmp(command, "support") == 0) {
amstar_support(&argument);
} else if (strcmp(command, "selfcheck") == 0) {
amstar_selfcheck(&argument);
} else if (strcmp(command, "estimate") == 0) {
amstar_estimate(&argument);
} else if (strcmp(command, "backup") == 0) {
amstar_backup(&argument);
} else if (strcmp(command, "restore") == 0) {
amstar_restore(&argument);
} else if (strcmp(command, "validate") == 0) {
amstar_validate(&argument);
} else {
fprintf(stderr, "Unknown command `%s'.\n", command);
exit (1);
}
return 0;
}
int main(int argc, char **argv)
{
const char *hmmfile; /* file to read HMMs from */
HMMFILE *hmmfp; /* opened hmmfile for reading */
const char *seqfile; /* file to read target sequence from */
char **rseq; /* raw, unaligned sequences */
SQINFO *sqinfo; /* info associated with sequences */
char **dsq; /* digitized raw sequences */
int nseq; /* number of sequences */
char **aseq; /* aligned sequences */
AINFO ainfo; /* alignment information */
float *wgt; /* per-sequence weights */
int i;
struct plan7_s *hmm; /* HMM to align to */
struct p7trace_s **tr; /* traces for aligned sequences */
int be_quiet; /* TRUE to suppress verbose banner */
int matchonly; /* TRUE to show only match state syms */
const char *outfile; /* optional alignment output file */
FILE *ofp; /* handle on alignment output file */
AjPFile ajwithali; /* name of additional alignment file to align */
AjPFile ajmapali; /* name of additional alignment file to map */
AjBool ajmatch=ajFalse;
AjPFile outf=NULL;
AjPStr outfname=NULL;
AjPFile inf=NULL;
AjPStr infname=NULL;
AjPSeqset seqset=NULL;
AjPStr ajseqfile=NULL;
char* mapali=NULL;
char* withali=NULL;
#ifdef MEMDEBUG
unsigned long histid1, histid2, orig_size, current_size;
orig_size = malloc_inuse(&histid1);
fprintf(stderr, "[... memory debugging is ON ...]\n");
#endif
/***********************************************
* Parse command line
***********************************************/
matchonly = FALSE;
outfile = NULL;
be_quiet = FALSE;
withali = NULL;
mapali = NULL;
embInitPV("ohmmalign",argc,argv,"HMMER",VERSION);
ajmatch = ajAcdGetBoolean("matchonly");
if(ajmatch)
matchonly=TRUE;
else
matchonly=FALSE;
ajmapali = ajAcdGetInfile("mapalifile");
if (ajmapali)
mapali = ajCharNewS(ajFileGetNameS(ajmapali));
ajFileClose(&ajmapali);
ajwithali = ajAcdGetInfile("withalifile");
if (ajwithali)
withali = ajCharNewS(ajFileGetNameS(ajwithali));
ajFileClose(&ajwithali);
be_quiet=TRUE;
outf = ajAcdGetOutfile("outfile");
outfname = ajStrNewC((char *)ajFileGetNameC(outf));
if(*ajStrGetPtr(outfname)>31)
ajFileClose(&outf);
outfile = ajStrGetPtr(outfname);
inf = ajAcdGetInfile("hmmfile");
infname = ajStrNewC((char *)ajFileGetNameC(inf));
ajFileClose(&inf);
hmmfile = ajStrGetPtr(infname);
seqset = ajAcdGetSeqset("sequences");
ajseqfile = ajStrNewC(ajStrGetPtr(seqset->Filename));
seqfile = ajStrGetPtr(ajseqfile);
/***********************************************
* Open HMM file (might be in HMMERDB or current directory).
* Read a single HMM from it.
*
* Currently hmmalign disallows the J state and
* only allows one domain per sequence. To preserve
* the S/W entry information, the J state is explicitly
* disallowed, rather than calling a Plan7*Config() function.
* this is a workaround in 2.1 for the 2.0.x "yo!" bug.
***********************************************/
if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL)
ajFatal("Failed to open HMM file %s\n", hmmfile);
if (!HMMFileRead(hmmfp, &hmm))
ajFatal("Failed to read any HMMs from %s\n", hmmfile);
HMMFileClose(hmmfp);
if (hmm == NULL)
ajFatal("HMM file %s corrupt or in incorrect format? Parse failed", hmmfile);
hmm->xt[XTE][MOVE] = 1.; /* only 1 domain/sequence ("global" alignment) */
hmm->xt[XTE][LOOP] = 0.;
P7Logoddsify(hmm, TRUE);
/* do we have the map we might need? */
if (mapali != NULL && ! (hmm->flags & PLAN7_MAP))
ajFatal("HMMER: HMM file %s has no map; you can't use --mapali.", hmmfile);
/***********************************************
* Open sequence file in current directory.
* Read all seqs from it.
***********************************************/
/*
if (! SeqfileFormat(seqfile, &format, NULL))
switch (squid_errno) {
case SQERR_NOFILE:
ajFatal("Sequence file %s could not be opened for reading", seqfile);
case SQERR_FORMAT:
default:
ajFatal("Failed to determine format of sequence file %s", seqfile);
}
if (! ReadMultipleRseqs(seqfile, format, &rseq, &sqinfo, &nseq))
ajFatal("Failed to read any sequences from file %s", seqfile);
*/
emboss_rseqs(seqset,&rseq,&sqinfo,&nseq);
/***********************************************
* Show the banner
***********************************************/
be_quiet=TRUE;
if (! be_quiet)
{
/* Banner(stdout, banner); */
printf( "HMM file: %s\n", hmmfile);
printf( "Sequence file: %s\n", seqfile);
printf("- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n");
}
/***********************************************
* Do the work
***********************************************/
/* Allocations and initializations.
*/
dsq = MallocOrDie(sizeof(char *) * nseq);
tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq);
/* Align each sequence to the model, collect traces
*/
for (i = 0; i < nseq; i++)
{
dsq[i] = DigitizeSequence(rseq[i], sqinfo[i].len);
if (P7ViterbiSize(sqinfo[i].len, hmm->M) <= RAMLIMIT)
(void) P7Viterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i]));
else
(void) P7SmallViterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i]));
}
/* Include an aligned alignment, if desired.
*/
if (mapali != NULL)
include_alignment(mapali, hmm, TRUE, &rseq, &dsq, &sqinfo, &tr, &nseq);
if (withali != NULL)
include_alignment(withali, hmm, FALSE, &rseq, &dsq, &sqinfo, &tr, &nseq);
/* Turn traces into a multiple alignment
*/
wgt = MallocOrDie(sizeof(float) * nseq);
FSet(wgt, nseq, 1.0);
P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, matchonly,
&aseq, &ainfo);
/***********************************************
* Output the alignment
***********************************************/
if (outfile != NULL && (ofp = fopen(outfile, "w")) != NULL)
{
WriteSELEX(ofp, aseq, &ainfo, 50);
printf("Alignment saved in file %s\n", outfile);
fclose(ofp);
}
else
WriteSELEX(stdout, aseq, &ainfo, 50);
/***********************************************
* Cleanup and exit
***********************************************/
for (i = 0; i < nseq; i++)
{
P7FreeTrace(tr[i]);
FreeSequence(rseq[i], &(sqinfo[i]));
free(dsq[i]);
}
FreeAlignment(aseq, &ainfo);
FreePlan7(hmm);
free(sqinfo);
free(rseq);
free(dsq);
free(wgt);
free(tr);
SqdClean();
ajStrDel(&outfname);
ajStrDel(&infname);
ajStrDel(&ajseqfile);
#ifdef MEMDEBUG
current_size = malloc_inuse(&histid2);
if (current_size != orig_size) malloc_list(2, histid1, histid2);
else fprintf(stderr, "[No memory leaks.]\n");
#endif
ajSeqsetDel(&seqset);
ajFileClose(&ajwithali);
ajFileClose(&ajmapali);
embExit();
return 0;
}
int
handle_command(char *buffer)
{
int rc = 1;
char *op;
int cmdtype;
static unsigned long mark;
if (ExtractArg(buffer, &op, &buffer) < 0)
{
return -1;
}
cmdtype = type_command(op);
switch (cmdtype)
{
case COMMAND_GET:
handle_get_command(buffer);
break;
case COMMAND_SET:
handle_set_command(buffer);
break;
case COMMAND_RESET:
handle_reset_command(buffer);
break;
case COMMAND_BYE:
handle_bye_command(buffer);
rc = 0;
break;
case COMMAND_CLI:
handle_cli_command(buffer);
break;
case COMMAND_MEMSTART:
#ifdef _DMALLOC_
dmalloc_message("starting new log");
mark = dmalloc_mark();
#elif _DBMALLOC_
if(malloc_chain_check(0)!=0)
{
int fd;
fd = open("/usr/local/nextone/logs/malloc.inuse", O_CREAT|O_RDWR
);
malloc_dump(fd );
close(fd);
}
orig_size = malloc_inuse(&histid1);
#endif
break;
case COMMAND_MEMSTOP:
#ifdef _DMALLOC_
dmalloc_log_changed(mark, 1, 0, 1);
dmalloc_message("end of log");
#elif _DBMALLOC_
current_size = malloc_inuse(&histid2);
if(current_size != orig_size)
{
int fd;
fd = open("/usr/local/nextone/logs/malloc.inuse", O_CREAT|O_RDWR
);
malloc_list(fd, histid1, histid2);
close(fd);
}
#endif
break;
case COMMAND_NONE:
default:
break;
}
return rc;
}
