/* Function: CP9Logoddsify()
*
* Purpose: Take an HMM with valid probabilities, and
* fill in the integer log-odds score section of the model.
*
* Notes on log-odds scores (simplified from plan7.c):
* type of parameter probability score
* ----------------- ----------- ------
* any emission p_x log_2 p_x/null_x
* any transition t_x log_2 t_x
*
* Args: hmm - the hmm to calculate scores in.
*
* Return: (void)
* hmm scores are filled in.
*/
void
CP9Logoddsify(CP9_t *hmm)
{
/*printf("in CP9Logoddsify()\n");*/
int k; /* counter for model position */
int x; /* counter for symbols */
int *sc;
int status;
if (hmm->flags & CPLAN9_HASBITS) return;
ESL_ALLOC(sc, hmm->abc->Kp * sizeof(int));
/* Symbol emission scores
*/
sc[hmm->abc->K] = -INFTY; /* gap character */
sc[hmm->abc->Kp-1] = -INFTY; /* missing data character */
sc[hmm->abc->Kp-2] = -INFTY; /* non-residue data character */
/* Insert emission scores, relies on sc[K, Kp-1] initialization to -inf above */
for (k = 0; k <= hmm->M; k++) {
for (x = 0; x < hmm->abc->K; x++)
sc[x] = Prob2Score(hmm->ins[k][x], hmm->null[x]);
esl_abc_IExpectScVec(hmm->abc, sc, hmm->null);
for (x = 0; x < hmm->abc->Kp; x++) {
hmm->isc[x][k] = sc[x];
}
}
/* Match emission scores, relies on sc[K, Kp-1] initialization to -inf above */
for (k = 1; k <= hmm->M; k++) {
for (x = 0; x < hmm->abc->K; x++)
sc[x] = Prob2Score(hmm->mat[k][x], hmm->null[x]);
esl_abc_IExpectScVec(hmm->abc, sc, hmm->null);
for (x = 0; x < hmm->abc->Kp; x++) {
hmm->msc[x][k] = sc[x];
}
}
for (k = 0; k <= hmm->M; k++)
{
hmm->tsc[CTMM][k] = Prob2Score(hmm->t[k][CTMM], 1.0);
hmm->tsc[CTMI][k] = Prob2Score(hmm->t[k][CTMI], 1.0);
hmm->tsc[CTMD][k] = Prob2Score(hmm->t[k][CTMD], 1.0);
hmm->tsc[CTMEL][k] = Prob2Score(hmm->t[k][CTMEL], 1.0);
hmm->tsc[CTIM][k] = Prob2Score(hmm->t[k][CTIM], 1.0);
hmm->tsc[CTII][k] = Prob2Score(hmm->t[k][CTII], 1.0);
hmm->tsc[CTID][k] = Prob2Score(hmm->t[k][CTID], 1.0);
if(k != 0)
{
hmm->tsc[CTDM][k] = Prob2Score(hmm->t[k][CTDM], 1.0);
hmm->tsc[CTDI][k] = Prob2Score(hmm->t[k][CTDI], 1.0);
hmm->tsc[CTDD][k] = Prob2Score(hmm->t[k][CTDD], 1.0);
}
else
{
hmm->tsc[CTDM][k] = -INFTY;
hmm->tsc[CTDD][k] = -INFTY; /*D_0 doesn't exist*/
hmm->tsc[CTDI][k] = -INFTY;
}
if(k != 0)
{
hmm->bsc[k] = Prob2Score(hmm->begin[k], 1.0);
hmm->esc[k] = Prob2Score(hmm->end[k], 1.0);
}
}
hmm->el_selfsc = Prob2Score(hmm->el_self, 1.0);
/* Finally, fill the efficiently reordered transition scores for this HMM. */
for (k = 0 ; k <= hmm->M; k++) {
int *otsc_k = hmm->otsc + k*cp9O_NTRANS;
otsc_k[cp9O_MM] = hmm->tsc[CTMM][k];
otsc_k[cp9O_MI] = hmm->tsc[CTMI][k];
otsc_k[cp9O_MD] = hmm->tsc[CTMD][k];
otsc_k[cp9O_IM] = hmm->tsc[CTIM][k];
otsc_k[cp9O_II] = hmm->tsc[CTII][k];
otsc_k[cp9O_DM] = hmm->tsc[CTDM][k];
otsc_k[cp9O_DD] = hmm->tsc[CTDD][k];
otsc_k[cp9O_ID] = hmm->tsc[CTID][k];
otsc_k[cp9O_DI] = hmm->tsc[CTDI][k];
otsc_k[cp9O_BM] = hmm->bsc[k];
otsc_k[cp9O_MEL]= hmm->tsc[CTMEL][k];
otsc_k[cp9O_ME] = hmm->esc[k];
}
hmm->flags |= CPLAN9_HASBITS; /* raise the log-odds ready flag */
free(sc);
return;
ERROR:
cm_Fail("Memory allocation error.\n");
return; /* never reached */
}
/* Function: CP9Logoddsify()
*
* Purpose: Take an HMM with valid probabilities, and
* fill in the integer log-odds score section of the model.
*
* Notes on log-odds scores (simplified from plan7.c):
* type of parameter probability score
* ----------------- ----------- ------
* any emission p_x log_2 p_x/null_x
* any transition t_x log_2 t_x
*
* Args: hmm - the hmm to calculate scores in.
*
* Return: (void)
* hmm scores are filled in.
*/
void
CP9Logoddsify(CP9_t *hmm)
{
int k; /* counter for model position */
int x; /* counter for symbols */
int sc[MAXDEGEN]; /* 17, NEED TO INCREASE FOR BIGGER ALPHABETS! */
if (hmm->flags & CPLAN9_HASBITS) return;
/* Symbol emission scores
*/
sc[hmm->abc->K] = -INFTY; /* gap character */
sc[hmm->abc->Kp-1] = -INFTY; /* missing data character */
/* Insert emission scores, relies on sc[K, Kp-1] initialization to -inf above */
for (k = 0; k <= hmm->M; k++) {
for (x = 0; x < hmm->abc->K; x++)
sc[x] = Prob2Score(hmm->ins[k][x], hmm->null[x]);
esl_abc_IExpectScVec(hmm->abc, sc, hmm->null);
for (x = 0; x < hmm->abc->Kp; x++) {
hmm->isc[x][k] = sc[x];
}
}
/* Match emission scores, relies on sc[K, Kp-1] initialization to -inf above */
for (k = 1; k <= hmm->M; k++) {
for (x = 0; x < hmm->abc->K; x++)
sc[x] = Prob2Score(hmm->mat[k][x], hmm->null[x]);
esl_abc_IExpectScVec(hmm->abc, sc, hmm->null);
for (x = 0; x < hmm->abc->Kp; x++) {
hmm->msc[x][k] = sc[x];
}
}
for (k = 0; k <= hmm->M; k++)
{
hmm->tsc[CTMM][k] = Prob2Score(hmm->t[k][CTMM], 1.0);
hmm->tsc[CTMI][k] = Prob2Score(hmm->t[k][CTMI], 1.0);
hmm->tsc[CTMD][k] = Prob2Score(hmm->t[k][CTMD], 1.0);
hmm->tsc[CTMEL][k] = Prob2Score(hmm->t[k][CTMEL], 1.0);
hmm->tsc[CTIM][k] = Prob2Score(hmm->t[k][CTIM], 1.0);
hmm->tsc[CTII][k] = Prob2Score(hmm->t[k][CTII], 1.0);
hmm->tsc[CTID][k] = Prob2Score(hmm->t[k][CTID], 1.0);
if(k != 0)
{
hmm->tsc[CTDM][k] = Prob2Score(hmm->t[k][CTDM], 1.0);
hmm->tsc[CTDI][k] = Prob2Score(hmm->t[k][CTDI], 1.0);
hmm->tsc[CTDD][k] = Prob2Score(hmm->t[k][CTDD], 1.0);
}
else
{
hmm->tsc[CTDM][k] = -INFTY;
hmm->tsc[CTDD][k] = -INFTY; /*D_0 doesn't exist*/
hmm->tsc[CTDI][k] = -INFTY;
}
if(k != 0)
{
hmm->bsc[k] = Prob2Score(hmm->begin[k], 1.0);
//if(hmm->flags & CPLAN9_LOCAL_END) hmm->esc[k] = 0;
//else hmm->esc[k] = -INFTY;
hmm->esc[k] = Prob2Score(hmm->end[k], 1.0);
}
}
hmm->el_selfsc = Prob2Score(hmm->el_self, 1.0);
/* Finally, fill the efficiently reordered transition scores for this HMM. */
for (k = 0 ; k <= hmm->M; k++) {
int *otsc_k = hmm->otsc + k*cp9O_NTRANS;
otsc_k[cp9O_MM] = hmm->tsc[CTMM][k];
otsc_k[cp9O_MI] = hmm->tsc[CTMI][k];
otsc_k[cp9O_MD] = hmm->tsc[CTMD][k];
otsc_k[cp9O_IM] = hmm->tsc[CTIM][k];
otsc_k[cp9O_II] = hmm->tsc[CTII][k];
otsc_k[cp9O_DM] = hmm->tsc[CTDM][k];
otsc_k[cp9O_DD] = hmm->tsc[CTDD][k];
otsc_k[cp9O_ID] = hmm->tsc[CTID][k];
otsc_k[cp9O_DI] = hmm->tsc[CTDI][k];
otsc_k[cp9O_BM] = hmm->bsc[k];
otsc_k[cp9O_MEL]= hmm->tsc[CTMEL][k];
otsc_k[cp9O_ME] = hmm->esc[k];
}
hmm->flags |= CPLAN9_HASBITS; /* raise the log-odds ready flag */
}