Example #1
0
/* Evaluate fx = rel entropy - etarget, which we want to be = 0,
* for effective sequence number <x>.
*/
static int
eweight_target_f(double Neff, void *params, double *ret_fx)
{
    struct ew_param_s *p = (struct ew_param_s *) params;

    p7_hmm_CopyParameters(p->hmm, p->h2);
    p7_hmm_Scale(p->h2, Neff / (double) p->h2->nseq);
    p7_ParameterEstimation(p->h2, p->pri);
    *ret_fx = p7_MeanMatchRelativeEntropy(p->h2, p->bg) - p->etarget;
    return eslOK;
}
Example #2
0
/* set_effective_seqnumber()
 *
 * <hmm> comes in with weighted observed counts. It goes out with
 * those observed counts rescaled to sum to the "effective sequence
 * number". 
 *
 * <msa> is needed because we may need to see the sequences in order 
 * to determine effective seq #. (for --eclust)
 *
 * <prior> is needed because we may need to parameterize test models
 * looking for the right relative entropy. (for --eent, the default)
 */
static int
effective_seqnumber(P7_BUILDER *bld, const ESL_MSA *msa, P7_HMM *hmm, const P7_BG *bg)
{
  int    status;

  if      (bld->effn_strategy == p7_EFFN_NONE)    hmm->eff_nseq = msa->nseq;
  else if (bld->effn_strategy == p7_EFFN_SET)     hmm->eff_nseq = bld->eset;
  else if (bld->effn_strategy == p7_EFFN_CLUST)
    {
      int nclust;

      status = esl_msacluster_SingleLinkage(msa, bld->eid, NULL, NULL, &nclust);
      if      (status == eslEMEM) ESL_XFAIL(status, bld->errbuf, "memory allocation failed");
      else if (status != eslOK)   ESL_XFAIL(status, bld->errbuf, "single linkage clustering algorithm (at %d%% id) failed", (int)(100 * bld->eid));

      hmm->eff_nseq = (double) nclust;
    }

  else if (bld->effn_strategy == p7_EFFN_ENTROPY)
    {
      double etarget; 
      double eff_nseq;

      etarget = (bld->esigma - eslCONST_LOG2R * log( 2.0 / ((double) hmm->M * (double) (hmm->M+1)))) / (double) hmm->M; /* xref J5/36. */
      etarget = ESL_MAX(bld->re_target, etarget);

      status = p7_EntropyWeight(hmm, bg, bld->prior, etarget, &eff_nseq);
      if      (status == eslEMEM) ESL_XFAIL(status, bld->errbuf, "memory allocation failed");
      else if (status != eslOK)   ESL_XFAIL(status, bld->errbuf, "internal failure in entropy weighting algorithm");
      hmm->eff_nseq = eff_nseq;
    }
    
  p7_hmm_Scale(hmm, hmm->eff_nseq / (double) hmm->nseq);
  return eslOK;

 ERROR:
  return status;
}