Ejemplos de esl_workqueue_Complete en C++ (Cpp)

Ejemplo n.º 1

Archivo: nhmmscan.c Proyecto: ElofssonLab/TOPCONS2

static int
thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, P7_HMMFILE *hfp)
{
  int  status   = eslOK;
  int  sstatus  = eslOK;
  int  eofCount = 0;
  P7_OM_BLOCK   *block;
  ESL_ALPHABET  *abc = NULL;
  void          *newBlock;

  esl_workqueue_Reset(queue);
  esl_threads_WaitForStart(obj);

  status = esl_workqueue_ReaderUpdate(queue, NULL, &newBlock);
  if (status != eslOK) esl_fatal("Work queue reader failed");
      
  /* Main loop: */
  while (sstatus == eslOK)
  {
      block = (P7_OM_BLOCK *) newBlock;
      sstatus = p7_oprofile_ReadBlockMSV(hfp, &abc, block);

      if (sstatus == eslEOF)
      {
        if (eofCount < esl_threads_GetWorkerCount(obj)) sstatus = eslOK;
        ++eofCount;
      }
	  
      if (sstatus == eslOK)
      {
        status = esl_workqueue_ReaderUpdate(queue, block, &newBlock);
        if (status != eslOK) esl_fatal("Work queue reader failed");
      }
  }

  status = esl_workqueue_ReaderUpdate(queue, block, NULL);
  if (status != eslOK) esl_fatal("Work queue reader failed");

  if (sstatus == eslEOF)
  {
      /* wait for all the threads to complete */
      esl_threads_WaitForFinish(obj);
      esl_workqueue_Complete(queue);  
  }
  
  esl_alphabet_Destroy(abc);
  return sstatus;
}

Ejemplo n.º 2

Archivo: hmmbuild.c Proyecto: TuftsBCB/SMURFBuild

static int
thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, struct cfg_s *cfg)
{
  int          status    = eslOK;
  int          sstatus   = eslOK;
  int          processed = 0;
  WORK_ITEM   *item;
  void        *newItem;

  int           next     = 1;
  PENDING_ITEM *top      = NULL;
  PENDING_ITEM *empty    = NULL;
  PENDING_ITEM *tmp      = NULL;

  char        errmsg[eslERRBUFSIZE];

  esl_workqueue_Reset(queue);
  esl_threads_WaitForStart(obj);

  status = esl_workqueue_ReaderUpdate(queue, NULL, &newItem);
  if (status != eslOK) esl_fatal("Work queue reader failed");
      
  /* Main loop: */
  item = (WORK_ITEM *) newItem;
  while (sstatus == eslOK) {
    sstatus = esl_msa_Read(cfg->afp, &item->msa);
    if (sstatus == eslOK) {
      item->nali = ++cfg->nali;
      if (set_msa_name(cfg, errmsg, item->msa) != eslOK) p7_Fail("%s\n", errmsg);
    }
    if (sstatus == eslEOF && processed < cfg->nali) sstatus = eslOK;
	  
    if (sstatus == eslOK) {
      status = esl_workqueue_ReaderUpdate(queue, item, &newItem);
      if (status != eslOK) esl_fatal("Work queue reader failed");

      /* process any results */
      item = (WORK_ITEM *) newItem;
      if (item->processed == TRUE) {
	++processed;

	/* try to keep the input output order the same */
	if (item->nali == next) {
	  sstatus = output_result(cfg, errmsg, item->nali, item->msa, item->hmm, item->postmsa, item->entropy);
	  if (sstatus != eslOK) p7_Fail(errmsg);

	  p7_hmm_Destroy(item->hmm);
	  esl_msa_Destroy(item->msa);
	  esl_msa_Destroy(item->postmsa);

	  ++next;

	  /* output any pending msa as long as the order
	   * remains the same as read in.
	   */
	  while (top != NULL && top->nali == next) {
	    sstatus = output_result(cfg, errmsg, top->nali, top->msa, top->hmm, top->postmsa, top->entropy);
	    if (sstatus != eslOK) p7_Fail(errmsg);

	    p7_hmm_Destroy(top->hmm);
	    esl_msa_Destroy(top->msa);
	    esl_msa_Destroy(top->postmsa);

	    tmp = top;
	    top = tmp->next;

	    tmp->next = empty;
	    empty     = tmp;
	    
	    ++next;
	  }
	} else {
	  /* queue up the msa so the sequence order is the same in
	   * the .sto and .hmm
	   */
	  if (empty != NULL) {
	    tmp   = empty;
	    empty = tmp->next;
	  } else {
	    ESL_ALLOC(tmp, sizeof(PENDING_ITEM));
	  }

	  tmp->nali     = item->nali;
	  tmp->hmm      = item->hmm;
	  tmp->msa      = item->msa;
	  tmp->postmsa  = item->postmsa;
	  tmp->entropy  = item->entropy;

	  /* add the msa to the pending list */
	  if (top == NULL || tmp->nali < top->nali) {
	    tmp->next = top;
	    top       = tmp;
	  } else {
	    PENDING_ITEM *ptr = top;
	    while (ptr->next != NULL && tmp->nali > ptr->next->nali) {
	      ptr = ptr->next;
	    }
	    tmp->next = ptr->next;
	    ptr->next = tmp;
	  }
	}

	item->nali      = 0;
	item->processed = FALSE;
	item->hmm       = NULL;
	item->msa       = NULL;
	item->postmsa   = NULL;
	item->entropy   = 0.0;
      }
    }
  }

  if (top != NULL) esl_fatal("Top is not empty\n");

  while (empty != NULL) {
    tmp   = empty;
    empty = tmp->next;
    free(tmp);
  }

  status = esl_workqueue_ReaderUpdate(queue, item, NULL);
  if (status != eslOK) esl_fatal("Work queue reader failed");

  if (sstatus == eslEOF)
    {
      /* wait for all the threads to complete */
      esl_threads_WaitForFinish(obj);
      esl_workqueue_Complete(queue);  
    }

  return sstatus;

 ERROR:
  return eslEMEM;
}