static void
scan_thread(void *arg)
{
int i;
int count;
int workeridx;
WORKER_INFO *info;
ESL_THREADS *obj;
ESL_STOPWATCH *w;
P7_BG *bg = NULL; /* null model */
P7_PIPELINE *pli = NULL; /* work pipeline */
P7_TOPHITS *th = NULL; /* top hit results */
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
w = esl_stopwatch_Create();
esl_stopwatch_Start(w);
/* Convert to an optimized model */
bg = p7_bg_Create(info->abc);
/* Create processing pipeline and hit list */
th = p7_tophits_Create();
pli = p7_pipeline_Create(info->opts, 100, 100, FALSE, p7_SCAN_MODELS);
p7_pli_NewSeq(pli, info->seq);
/* loop until all sequences have been processed */
count = 1;
while (count > 0) {
int inx;
int blksz;
P7_OPROFILE **om;
/* grab the next block of sequences */
if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
inx = *info->inx;
blksz = *info->blk_size;
if (inx > *info->limit) {
blksz /= 5;
if (blksz < 1000) {
*info->limit = info->om_cnt * 2;
} else {
*info->limit = inx + (info->om_cnt - inx) * 2 / 3;
}
}
*info->blk_size = blksz;
*info->inx += blksz;
if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");
om = info->om_list + inx;
count = info->om_cnt - inx;
if (count > blksz) count = blksz;
/* Main loop: */
for (i = 0; i < count; ++i, ++om) {
p7_pli_NewModel(pli, *om, bg);
p7_bg_SetLength(bg, info->seq->n);
p7_oprofile_ReconfigLength(*om, info->seq->n);
p7_Pipeline(pli, *om, bg, info->seq, th);
p7_pipeline_Reuse(pli);
}
}
/* make available the pipeline objects to the main thread */
info->th = th;
info->pli = pli;
/* clean up */
p7_bg_Destroy(bg);
esl_stopwatch_Stop(w);
info->elapsed = w->elapsed;
esl_stopwatch_Destroy(w);
esl_threads_Finished(obj, workeridx);
pthread_exit(NULL);
return;
}
static void
pipeline_thread(void *arg)
{
int i, j;
int status;
int workeridx;
WORKER_INFO *info;
ESL_THREADS *obj;
P7_OM_BLOCK *block;
void *newBlock;
P7_OPROFILE *om = NULL;
P7_SCOREDATA *scoredata = NULL; /* hmm-specific data used by nhmmer */
P7_DOMAIN *dcl;
int seq_len = 0;
int prev_hit_cnt = 0;
#ifdef eslAUGMENT_ALPHABET
ESL_SQ *sq_revcmp = NULL;
#endif /*eslAUGMENT_ALPHABET*/
impl_ThreadInit();
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
status = esl_workqueue_WorkerUpdate(info->queue, NULL, &newBlock);
if (status != eslOK) esl_fatal("Work queue worker failed");
#ifdef eslAUGMENT_ALPHABET
//reverse complement
if (info->pli->strand != p7_STRAND_TOPONLY && info->qsq->abc->complement != NULL ) {
sq_revcmp = esl_sq_CreateDigital(info->qsq->abc);
esl_sq_Copy(info->qsq,sq_revcmp);
esl_sq_ReverseComplement(sq_revcmp);
info->pli->nres += info->qsq->n;
}
#endif /*eslAUGMENT_ALPHABET*/
/* loop until all blocks have been processed */
block = (P7_OM_BLOCK *) newBlock;
while (block->count > 0)
{
/* Main loop: */
for (i = 0; i < block->count; ++i)
{
om = block->list[i];
seq_len = 0;
p7_pli_NewModel(info->pli, om, info->bg);
p7_bg_SetLength(info->bg, info->qsq->n);
p7_oprofile_ReconfigLength(om, info->qsq->n);
scoredata = p7_hmm_ScoreDataCreate(om, FALSE);
#ifdef eslAUGMENT_ALPHABET
//reverse complement
if (info->pli->strand != p7_STRAND_TOPONLY && info->qsq->abc->complement != NULL )
{
p7_Pipeline_LongTarget(info->pli, om, scoredata, info->bg, sq_revcmp, info->th, 0);
p7_pipeline_Reuse(info->pli); // prepare for next search
seq_len = info->qsq->n;
for (j = prev_hit_cnt; j < info->th->N ; j++)
{
dcl = info->th->unsrt[j].dcl;
// modify hit positions to account for the position of the window in the full sequence
dcl->ienv = seq_len - dcl->ienv + 1;
dcl->jenv = seq_len - dcl->jenv + 1;
dcl->iali = seq_len - dcl->iali + 1;
dcl->jali = seq_len - dcl->jali + 1;
dcl->ad->sqfrom = seq_len - dcl->ad->sqfrom + 1;
dcl->ad->sqto = seq_len - dcl->ad->sqto + 1;
}
}
#endif
if (info->pli->strand != p7_STRAND_BOTTOMONLY) {
p7_Pipeline_LongTarget(info->pli, om, scoredata, info->bg, info->qsq, info->th, 0);
p7_pipeline_Reuse(info->pli);
seq_len += info->qsq->n;
}
for (j = prev_hit_cnt; j < info->th->N ; j++)
{
info->th->unsrt[j].lnP += log((float)seq_len / (float)om->max_length);
info->th->unsrt[j].dcl[0].lnP = info->th->unsrt[j].lnP;
info->th->unsrt[j].sortkey = -1.0 * info->th->unsrt[j].lnP;
info->th->unsrt[j].dcl[0].ad->L = om->M;
}
prev_hit_cnt = info->th->N;
p7_hmm_ScoreDataDestroy(scoredata);
p7_oprofile_Destroy(om);
block->list[i] = NULL;
}
status = esl_workqueue_WorkerUpdate(info->queue, block, &newBlock);
if (status != eslOK) esl_fatal("Work queue worker failed");
block = (P7_OM_BLOCK *) newBlock;
}
#ifdef eslAUGMENT_ALPHABET
esl_sq_Destroy(sq_revcmp);
#endif
status = esl_workqueue_WorkerUpdate(info->queue, block, NULL);
if (status != eslOK) esl_fatal("Work queue worker failed");
esl_threads_Finished(obj, workeridx);
return;
}
static void
search_thread(void *arg)
{
int i;
int count;
int seed;
int status;
int workeridx;
WORKER_INFO *info;
ESL_THREADS *obj;
ESL_SQ dbsq;
ESL_STOPWATCH *w = NULL; /* timing stopwatch */
P7_BUILDER *bld = NULL; /* HMM construction configuration */
P7_BG *bg = NULL; /* null model */
P7_PIPELINE *pli = NULL; /* work pipeline */
P7_TOPHITS *th = NULL; /* top hit results */
P7_PROFILE *gm = NULL; /* generic model */
P7_OPROFILE *om = NULL; /* optimized query profile */
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
w = esl_stopwatch_Create();
bg = p7_bg_Create(info->abc);
esl_stopwatch_Start(w);
/* set up the dummy description and accession fields */
dbsq.desc = "";
dbsq.acc = "";
/* process a query sequence or hmm */
if (info->seq != NULL) {
bld = p7_builder_Create(NULL, info->abc);
if ((seed = esl_opt_GetInteger(info->opts, "--seed")) > 0) {
esl_randomness_Init(bld->r, seed);
bld->do_reseeding = TRUE;
}
bld->EmL = esl_opt_GetInteger(info->opts, "--EmL");
bld->EmN = esl_opt_GetInteger(info->opts, "--EmN");
bld->EvL = esl_opt_GetInteger(info->opts, "--EvL");
bld->EvN = esl_opt_GetInteger(info->opts, "--EvN");
bld->EfL = esl_opt_GetInteger(info->opts, "--EfL");
bld->EfN = esl_opt_GetInteger(info->opts, "--EfN");
bld->Eft = esl_opt_GetReal (info->opts, "--Eft");
if (esl_opt_IsOn(info->opts, "--mxfile")) status = p7_builder_SetScoreSystem (bld, esl_opt_GetString(info->opts, "--mxfile"), NULL, esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
else status = p7_builder_LoadScoreSystem(bld, esl_opt_GetString(info->opts, "--mx"), esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
if (status != eslOK) {
//client_error(info->sock, status, "hmmgpmd: failed to set single query sequence score system: %s", bld->errbuf);
fprintf(stderr, "hmmpgmd: failed to set single query sequence score system: %s", bld->errbuf);
pthread_exit(NULL);
return;
}
p7_SingleBuilder(bld, info->seq, bg, NULL, NULL, NULL, &om); /* bypass HMM - only need model */
p7_builder_Destroy(bld);
} else {
gm = p7_profile_Create (info->hmm->M, info->abc);
om = p7_oprofile_Create(info->hmm->M, info->abc);
p7_ProfileConfig(info->hmm, bg, gm, 100, p7_LOCAL);
p7_oprofile_Convert(gm, om);
}
/* Create processing pipeline and hit list */
th = p7_tophits_Create();
pli = p7_pipeline_Create(info->opts, om->M, 100, FALSE, p7_SEARCH_SEQS);
p7_pli_NewModel(pli, om, bg);
if (pli->Z_setby == p7_ZSETBY_NTARGETS) pli->Z = info->db_Z;
/* loop until all sequences have been processed */
count = 1;
while (count > 0) {
int inx;
int blksz;
HMMER_SEQ **sq;
/* grab the next block of sequences */
if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
inx = *info->inx;
blksz = *info->blk_size;
if (inx > *info->limit) {
blksz /= 5;
if (blksz < 1000) {
*info->limit = info->sq_cnt * 2;
} else {
*info->limit = inx + (info->sq_cnt - inx) * 2 / 3;
}
}
*info->blk_size = blksz;
*info->inx += blksz;
if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");
sq = info->sq_list + inx;
count = info->sq_cnt - inx;
if (count > blksz) count = blksz;
/* Main loop: */
for (i = 0; i < count; ++i, ++sq) {
if ( !(info->range_list) || hmmpgmd_IsWithinRanges ((*sq)->idx, info->range_list)) {
dbsq.name = (*sq)->name;
dbsq.dsq = (*sq)->dsq;
dbsq.n = (*sq)->n;
dbsq.idx = (*sq)->idx;
if((*sq)->desc != NULL) dbsq.desc = (*sq)->desc;
p7_bg_SetLength(bg, dbsq.n);
p7_oprofile_ReconfigLength(om, dbsq.n);
p7_Pipeline(pli, om, bg, &dbsq, th);
p7_pipeline_Reuse(pli);
}
}
}
/* make available the pipeline objects to the main thread */
info->th = th;
info->pli = pli;
/* clean up */
p7_bg_Destroy(bg);
p7_oprofile_Destroy(om);
if (gm != NULL) p7_profile_Destroy(gm);
esl_stopwatch_Stop(w);
info->elapsed = w->elapsed;
esl_stopwatch_Destroy(w);
esl_threads_Finished(obj, workeridx);
pthread_exit(NULL);
return;
}
static int
serial_loop(WORKER_INFO *info, P7_HMMFILE *hfp)
{
int status;
int i;
int seq_len = 0;
int prev_hit_cnt = 0;
P7_OPROFILE *om = NULL;
P7_SCOREDATA *scoredata = NULL; /* hmm-specific data used by nhmmer */
ESL_ALPHABET *abc = NULL;
P7_DOMAIN *dcl;
#ifdef eslAUGMENT_ALPHABET
ESL_SQ *sq_revcmp = NULL;
if (info->pli->strand != p7_STRAND_TOPONLY && info->qsq->abc->complement != NULL ) {
sq_revcmp = esl_sq_CreateDigital(info->qsq->abc);
esl_sq_Copy(info->qsq,sq_revcmp);
esl_sq_ReverseComplement(sq_revcmp);
info->pli->nres += info->qsq->n;
}
#endif /*eslAUGMENT_ALPHABET*/
/* Main loop: */
while ((status = p7_oprofile_ReadMSV(hfp, &abc, &om)) == eslOK)
{
seq_len = 0;
p7_pli_NewModel(info->pli, om, info->bg);
p7_bg_SetLength(info->bg, info->qsq->n);
p7_oprofile_ReconfigLength(om, info->qsq->n);
scoredata = p7_hmm_ScoreDataCreate(om, FALSE);
#ifdef eslAUGMENT_ALPHABET
//reverse complement
if (info->pli->strand != p7_STRAND_TOPONLY && info->qsq->abc->complement != NULL )
{
p7_Pipeline_LongTarget(info->pli, om, scoredata, info->bg, sq_revcmp, info->th, 0);
p7_pipeline_Reuse(info->pli); // prepare for next search
seq_len = info->qsq->n;
for (i = prev_hit_cnt; i < info->th->N ; i++)
{
dcl = info->th->unsrt[i].dcl;
// modify hit positions to account for the position of the window in the full sequence
dcl->ienv = seq_len - dcl->ienv + 1;
dcl->jenv = seq_len - dcl->jenv + 1;
dcl->iali = seq_len - dcl->iali + 1;
dcl->jali = seq_len - dcl->jali + 1;
dcl->ad->sqfrom = seq_len - dcl->ad->sqfrom + 1;
dcl->ad->sqto = seq_len - dcl->ad->sqto + 1;
}
}
#endif
if (info->pli->strand != p7_STRAND_BOTTOMONLY) {
p7_Pipeline_LongTarget(info->pli, om, scoredata, info->bg, info->qsq, info->th, 0);
p7_pipeline_Reuse(info->pli);
seq_len += info->qsq->n;
}
for (i = prev_hit_cnt; i < info->th->N ; i++)
{
info->th->unsrt[i].lnP += log((float)seq_len / (float)om->max_length);
info->th->unsrt[i].dcl[0].lnP = info->th->unsrt[i].lnP;
info->th->unsrt[i].sortkey = -1.0 * info->th->unsrt[i].lnP;
info->th->unsrt[i].dcl[0].ad->L = om->M;
}
prev_hit_cnt = info->th->N;
p7_oprofile_Destroy(om);
p7_hmm_ScoreDataDestroy(scoredata);
}
esl_alphabet_Destroy(abc);
#ifdef eslAUGMENT_ALPHABET
esl_sq_Destroy(sq_revcmp);
#endif
return status;
}
