/* Function: P7PriorifyHMM()
*
* Purpose: Add pseudocounts to an HMM using Dirichlet priors,
* and renormalize the HMM.
*
* Args: hmm -- the HMM to add counts to (counts form)
* pri -- the Dirichlet prior to use
*
* Return: (void)
* HMM returns in probability form.
*/
void
P7PriorifyHMM(struct plan7_s *hmm, struct p7prior_s *pri)
{
int k; /* counter for model position */
float d; /* a denominator */
/* Model-dependent transitions are handled simply; Laplace.
*/
FSet(hmm->begin+2, hmm->M-1, 0.); /* wipe internal BM entries */
FSet(hmm->end+1, hmm->M-1, 0.); /* wipe internal ME exits */
d = hmm->tbd1 + hmm->begin[1] + 2.;
hmm->tbd1 = (hmm->tbd1 + 1.)/ d;
hmm->begin[1] = (hmm->begin[1] + 1.)/ d;
hmm->end[hmm->M] = 1.0;
/* Main model transitions and emissions
*/
for (k = 1; k < hmm->M; k++)
{
P7PriorifyTransitionVector(hmm->t[k], pri);
P7PriorifyEmissionVector(hmm->mat[k], pri, pri->mnum, pri->mq, pri->m, NULL);
P7PriorifyEmissionVector(hmm->ins[k], pri, pri->inum, pri->iq, pri->i, NULL);
}
P7PriorifyEmissionVector(hmm->mat[hmm->M], pri, pri->mnum, pri->mq, pri->m, NULL);
Plan7Renormalize(hmm);
}
/* Function: P7PriorifyHMM()
*
* Purpose: Add pseudocounts to an HMM using Dirichlet priors,
* and renormalize the HMM.
*
* Args: hmm -- the HMM to add counts to (counts form)
* pri -- the Dirichlet prior to use
*
* Return: (void)
* HMM returns in probability form.
*/
void
P7PriorifyHMM(struct plan7_s *hmm, struct p7prior_s *pri)
{
int k; /* counter for model position */
float d; /* a denominator */
float tq[MAXDCHLET]; /* prior distribution over mixtures */
float mq[MAXDCHLET]; /* prior distribution over mixtures */
float iq[MAXDCHLET]; /* prior distribution over mixtures */
/* Model-dependent transitions are handled simply; Laplace.
*/
FSet(hmm->begin+2, hmm->M-1, 0.); /* wipe internal BM entries */
FSet(hmm->end+1, hmm->M-1, 0.); /* wipe internal ME exits */
d = hmm->tbd1 + hmm->begin[1] + 2.;
hmm->tbd1 = (hmm->tbd1 + 1.)/ d;
hmm->begin[1] = (hmm->begin[1] + 1.)/ d;
hmm->end[hmm->M] = 1.0;
/* Main model transitions and emissions
*/
for (k = 1; k < hmm->M; k++)
{
/* The following code chunk is experimental.
* Collaboration with Michael Asman, Erik Sonnhammer, CGR Stockholm.
* Only activated if X-PR* annotation has been used, in which
* priors are overridden and a single Dirichlet component is
* specified for each column (using structural annotation).
* If X-PR* annotation is not used, which is usually the case,
* the following code has no effect (observe how the real prior
* distributions are copied into tq, mq, iq).
*/
if (hmm->tpri != NULL && hmm->tpri[k] >= 0)
{
if (hmm->tpri[k] >= pri->tnum) Die("X-PRT annotation out of range");
FSet(tq, pri->tnum, 0.0);
tq[hmm->tpri[k]] = 1.0;
}
else
FCopy(tq, pri->tq, pri->tnum);
if (hmm->mpri != NULL && hmm->mpri[k] >= 0)
{
if (hmm->mpri[k] >= pri->mnum) Die("X-PRM annotation out of range");
FSet(mq, pri->mnum, 0.0);
mq[hmm->mpri[k]] = 1.0;
}
else
FCopy(mq, pri->mq, pri->mnum);
if (hmm->ipri != NULL && hmm->ipri[k] >= 0)
{
if (hmm->ipri[k] >= pri->inum) Die("X-PRI annotation out of range");
FSet(iq, pri->inum, 0.0);
iq[hmm->ipri[k]] = 1.0;
}
else
FCopy(iq, pri->iq, pri->inum);
/* This is the main line of the code:
*/
P7PriorifyTransitionVector(hmm->t[k], pri, tq);
P7PriorifyEmissionVector(hmm->mat[k], pri, pri->mnum, mq, pri->m, NULL);
P7PriorifyEmissionVector(hmm->ins[k], pri, pri->inum, iq, pri->i, NULL);
}
/* We repeat the above steps just for the final match state, M.
*/
if (hmm->mpri != NULL && hmm->mpri[hmm->M] >= 0)
{
if (hmm->mpri[hmm->M] >= pri->mnum) Die("X-PRM annotation out of range");
FSet(mq, pri->mnum, 0.0);
mq[hmm->mpri[hmm->M]] = 1.0;
}
else
FCopy(mq, pri->mq, pri->mnum);
P7PriorifyEmissionVector(hmm->mat[hmm->M], pri, pri->mnum, mq, pri->m, NULL);
/* Now we're done. Convert the counts-based HMM to probabilities.
*/
Plan7Renormalize(hmm);
}
