/* gcc --std=gnu99 -g -Wall -pthread -o esl_workqueue_example -I. -DeslWORKQUEUE_EXAMPLE esl_workqueue.c easel.c */
static void
worker_thread(void *data)
{
ESL_THREADS *thr = (ESL_THREADS *) data;
WORK_INFO *info = NULL;
int idx;
int *obj;
esl_threads_Started(thr, &idx);
info = (WORK_INFO *) esl_threads_GetData(thr, idx);
printf("THREAD %c: ready\n", info->id);
esl_workqueue_WorkerUpdate(info->queue, NULL, (void *) &obj);
while (*obj > 0)
{
printf("THREAD %c: processing %d\n", info->id, *obj);
esl_workqueue_WorkerUpdate(info->queue, obj, (void *) &obj);
}
printf("THREAD %c: done\n", info->id);
esl_threads_Finished(thr, idx);
return;
}
static void
pipeline_thread(void *arg)
{
int workeridx;
int status;
WORK_ITEM *item;
void *newItem;
WORKER_INFO *info;
ESL_THREADS *obj;
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
status = esl_workqueue_WorkerUpdate(info->queue, NULL, &newItem);
if (status != eslOK) esl_fatal("Work queue worker failed");
/* loop until all blocks have been processed */
item = (WORK_ITEM *) newItem;
while (item->msa != NULL)
{
status = p7_Builder(info->bld, item->msa, info->bg, &item->hmm, NULL, NULL, NULL, &item->postmsa);
if (status != eslOK) p7_Fail("build failed: %s", info->bld->errbuf);
item->entropy = p7_MeanMatchRelativeEntropy(item->hmm, info->bg);
item->processed = TRUE;
status = esl_workqueue_WorkerUpdate(info->queue, item, &newItem);
if (status != eslOK) esl_fatal("Work queue worker failed");
item = (WORK_ITEM *) newItem;
}
status = esl_workqueue_WorkerUpdate(info->queue, item, NULL);
if (status != eslOK) esl_fatal("Work queue worker failed");
esl_threads_Finished(obj, workeridx);
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;
}
