/* Function: p7_hmm_ScoreDataCreate() * Synopsis: Create a <P7_SCOREDATA> model object, based on MSV-filter * part of profile * * Purpose: Allocate a <P7_SCOREDATA> object, then populate * it with data based on the given optimized matrix. * * Once a hit passes the MSV filter, and the prefix/suffix * values of P7_SCOREDATA are required, p7_hmm_ScoreDataComputeRest() * must be called. * * Args: om - P7_OPROFILE containing scores used to produce SCOREDATA contents * do_opt_ext - boolean, TRUE if optimal-extension scores are required (for FM-MSV) * * Returns: a pointer to the new <P7_SCOREDATA> object. * * Throws: <NULL> on allocation failure. */ P7_SCOREDATA * p7_hmm_ScoreDataCreate(P7_OPROFILE *om, P7_PROFILE *gm ) { P7_SCOREDATA *data = NULL; int status; ESL_ALLOC(data, sizeof(P7_SCOREDATA)); data->ssv_scores = NULL; data->ssv_scores_f = NULL; data->opt_ext_fwd = NULL; data->opt_ext_rev = NULL; data->prefix_lengths = NULL; data->suffix_lengths = NULL; data->fwd_scores = NULL; data->fwd_transitions = NULL; scoredata_GetSSVScoreArrays(om, gm, data); return data; ERROR: p7_hmm_ScoreDataDestroy(data); return NULL; }
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 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; }