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Merged
GenevieveKrause merged 1 commit into from
Sep 17, 2026
Merged

Skip unused distributions in entropy-weighting bisection #14

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4 changes: 2 additions & 2 deletions src/eweight.c
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ eweight_target_f(double Neff, void *params, double *ret_fx)

p7_hmm_CopyParameters(p->hmm, p->h2);
p7_hmm_Scale(p->h2, Neff / (double) p->h2->nseq);
p7_ParameterEstimation(p->h2, p->pri);
p7_ParameterEstimation_MatchOnly(p->h2, p->pri);
*ret_fx = p7_MeanMatchRelativeEntropy(p->h2, p->bg) - p->etarget;
return eslOK;
}
Expand Down Expand Up @@ -107,7 +107,7 @@ eweight_target_exp_f(double exp, void *params, double *ret_fx)

p7_hmm_CopyParameters(p->hmm, p->h2);
p7_hmm_ScaleExponential(p->h2, exp);
p7_ParameterEstimation(p->h2, p->pri);
p7_ParameterEstimation_MatchOnly(p->h2, p->pri);
*ret_fx = p7_MeanMatchRelativeEntropy(p->h2, p->bg) - p->etarget;
return eslOK;
}
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1 change: 1 addition & 0 deletions src/hmmer.h
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Expand Up @@ -1588,6 +1588,7 @@ extern P7_PRIOR *p7_prior_CreateLaplace(const ESL_ALPHABET *abc);
extern void p7_prior_Destroy(P7_PRIOR *pri);

extern int p7_ParameterEstimation(P7_HMM *hmm, const P7_PRIOR *pri);
extern int p7_ParameterEstimation_MatchOnly(P7_HMM *hmm, const P7_PRIOR *pri);

/* p7_profile.c */
extern P7_PROFILE *p7_profile_Create(int M, const ESL_ALPHABET *abc);
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24 changes: 24 additions & 0 deletions src/p7_prior.c
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Expand Up @@ -277,6 +277,30 @@ p7_prior_Destroy(P7_PRIOR *pri)



/* Function: p7_ParameterEstimation_MatchOnly()
* Purpose: Like p7_ParameterEstimation(), but only the match emissions.
* For callers (entropy weighting) that only read hmm->mat.
*/
int
p7_ParameterEstimation_MatchOnly(P7_HMM *hmm, const P7_PRIOR *pri)
{
int k;
double c[p7_MAXABET];
double p[p7_MAXABET];

if (pri==NULL) return p7_hmm_Renormalize(hmm);

for (k = 1; k <= hmm->M; k++) {
esl_vec_F2D(hmm->mat[k], hmm->abc->K, c);
esl_mixdchlet_MPParameters(pri->em, c, p);
esl_vec_D2F(p, hmm->abc->K, hmm->mat[k]);
}
esl_vec_FSet(hmm->mat[0], hmm->abc->K, 0.);
hmm->mat[0][0] = 1.0;
return eslOK;
}


/* Function: p7_ParameterEstimation()
* Incept: SRE, Sat Mar 24 10:15:37 2007 [Janelia]
*
Expand Down