/* Function: PAMPrior()
*
* Purpose: Produces an ad hoc "Dirichlet mixture" prior for
* match emissions, using a PAM matrix.
*
* Side effect notice: PAMPrior() replaces the match
* emission section of an existing Dirichlet prior,
* which is /expected/ to be a simple one-component
* kind of prior. The insert emissions /must/ be a
* one-component prior (because of details in how
* PriorifyEmissionVector() is done). However,
* the transitions /could/ be a mixture Dirichlet prior
* without causing problems. In other words, the
* -p and -P options of hmmb can coexist, but there
* may be conflicts. PAMPrior() checks for these,
* so there's no serious problem, except that the
* error message from PAMPrior() might be confusing to
* a user.
*/
void
PAMPrior(char *pamfile, struct p7prior_s *pri, float wt)
{
FILE *fp;
char *blastpamfile; /* BLAST looks in aa/ subdirectory of BLASTMAT */
int **pam;
float scale;
int xi, xj;
int idx1, idx2;
if (Alphabet_type != hmmAMINO)
Die("PAM prior is only valid for protein sequences");
if (pri->strategy != PRI_DCHLET)
Die("PAM prior may only be applied over an existing Dirichlet prior");
if (pri->inum != 1)
Die("PAM prior requires that the insert emissions be a single Dirichlet");
if (MAXDCHLET < 20)
Die("Whoa, code is misconfigured; MAXDCHLET must be >= 20 for PAM prior");
blastpamfile = FileConcat("aa", pamfile);
if ((fp = fopen(pamfile, "r")) == NULL &&
(fp = EnvFileOpen(pamfile, "BLASTMAT", NULL)) == NULL &&
(fp = EnvFileOpen(blastpamfile, "BLASTMAT", NULL)) == NULL)
Die("Failed to open PAM scoring matrix file %s", pamfile);
if (! ParsePAMFile(fp, &pam, &scale))
Die("Failed to parse PAM scoring matrix file %s", pamfile);
fclose(fp);
free(blastpamfile);
pri->strategy = PRI_PAM;
pri->mnum = 20;
/* Convert PAM entries back to conditional prob's P(xj | xi),
* which we'll use as "pseudocounts" weighted by wt.
*/
for (xi = 0; xi < Alphabet_size; xi++)
for (xj = 0; xj < Alphabet_size; xj++)
{
idx1 = Alphabet[xi] - 'A';
idx2 = Alphabet[xj] - 'A';
pri->m[xi][xj] = aafq[xj] * exp((float) pam[idx1][idx2] * scale);
}
/* Normalize so that rows add up to wt.
* i.e. Sum(xj) mat[xi][xj] = wt for every row xi
*/
for (xi = 0; xi < Alphabet_size; xi++)
{
pri->mq[xi] = 1. / Alphabet_size;
FNorm(pri->m[xi], Alphabet_size);
FScale(pri->m[xi], Alphabet_size, wt);
}
Free2DArray((void **)pam,27);
}
/* Function: Plan7RenormalizeExits()
* Date: SRE, Fri Aug 14 11:22:19 1998 [St. Louis]
*
* Purpose: Renormalize just the match state transitions;
* for instance, after a Config() function has
* modified the exit distribution.
*
* Args: hmm - hmm to renormalize
*
* Returns: void
*/
void
Plan7RenormalizeExits(struct plan7_s *hmm)
{
int k;
float d;
for (k = 1; k < hmm->M; k++)
{
d = FSum(hmm->t[k], 3);
FScale(hmm->t[k], 3, 1./(d + d*hmm->end[k]));
}
}
/* Function: Plan7Renormalize()
*
* Purpose: Take an HMM in counts form, and renormalize
* all of its probability vectors. Also enforces
* Plan7 restrictions on nonexistent transitions.
*
* Args: hmm - the model to renormalize.
*
* Return: (void)
* hmm is changed.
*/
void
Plan7Renormalize(struct plan7_s *hmm)
{
int k; /* counter for model position */
int st; /* counter for special states */
float d; /* denominator */
/* match emissions */
for (k = 1; k <= hmm->M; k++)
FNorm(hmm->mat[k], Alphabet_size);
/* insert emissions */
for (k = 1; k < hmm->M; k++)
FNorm(hmm->ins[k], Alphabet_size);
/* begin transitions */
d = FSum(hmm->begin+1, hmm->M) + hmm->tbd1;
FScale(hmm->begin+1, hmm->M, 1./d);
hmm->tbd1 /= d;
/* main model transitions */
for (k = 1; k < hmm->M; k++)
{
d = FSum(hmm->t[k], 3) + hmm->end[k];
FScale(hmm->t[k], 3, 1./d);
hmm->end[k] /= d;
FNorm(hmm->t[k]+3, 2); /* insert */
FNorm(hmm->t[k]+5, 2); /* delete */
}
/* null model emissions */
FNorm(hmm->null, Alphabet_size);
/* special transitions */
for (st = 0; st < 4; st++)
FNorm(hmm->xt[st], 2);
/* enforce nonexistent transitions */
/* (is this necessary?) */
hmm->t[0][TDM] = hmm->t[0][TDD] = 0.0;
hmm->flags &= ~PLAN7_HASBITS; /* clear the log-odds ready flag */
hmm->flags |= PLAN7_HASPROB; /* set the probabilities OK flag */
}
