/* Function: p7_hmmcache_Sizeof()
* Synopsis: Returns total size of a profile cache, in bytes.
*
* Purpose: Calculate and return the size of a profile cache,
* in bytes.
*
* The cache contains both standard and vectorized
* profiles. Very roughly, for a total number of consensus
* positions M, we consume M*560 bytes; 276 in a standard
* profile, and 284 in a vectorized one. This is a lot, and
* a target of future optimization.
*/
size_t
p7_hmmcache_Sizeof(P7_HMMCACHE *cache)
{
size_t n = sizeof(P7_HMMCACHE);
int i;
n += sizeof(char) * (strlen(cache->name) + 1);
n += esl_alphabet_Sizeof(cache->abc);
n += sizeof(P7_OPROFILE *) * cache->lalloc; /* cache->omlist */
n += sizeof(P7_PROFILE *) * cache->lalloc; /* cache->gmlist */
for (i = 0; i < cache->n; i++)
{
n += p7_oprofile_Sizeof(cache->omlist[i]);
n += p7_profile_Sizeof (cache->gmlist[i]);
}
return n;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
float ftol = 1e-4; /* floating-point tolerance for checking parameters against expected probs or summing to 1 */
char errbuf[eslERRBUFSIZE];
/* Read in one HMM; sets alphabet to the HMM's alphabet */
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
p7_hmmfile_Close(hfp);
/* Set up a null model */
bg = p7_bg_Create(abc);
/* Allocate and configure a profile from HMM and null model */
gm = p7_profile_Create(hmm->M, abc);
p7_profile_Config(gm, hmm, bg);
p7_profile_SetLength(gm, 400); /* 400 is arbitrary here; this is whatever your target seq length L is */
printf("profile memory consumed: %" PRId64 " bytes\n", (int64_t) p7_profile_Sizeof(gm));
/* Debugging tools allow dumping, validating the object */
if (p7_profile_Validate(gm, errbuf, ftol) != eslOK) p7_Fail("profile validation failed\n %s\n", errbuf);
if (esl_opt_GetBoolean(go, "--vv"))
p7_profile_Dump(stdout, gm);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
/* Function: p7_oprofile_Sizeof()
* Synopsis: Return the allocated size of a <P7_OPROFILE>.
* Incept: SRE, Wed Mar 2 10:39:54 2011 [Janelia]
*
* Purpose: Returns the allocated size of a <P7_OPROFILE>,
* in bytes.
*/
size_t
p7_oprofile_Sizeof(P7_OPROFILE *om)
{
return p7_profile_Sizeof(om);
}
