void
hmm_enter(hmm_t *h, int32 score, int32 histid, int frame)
{
hmm_in_score(h) = score;
hmm_in_history(h) = histid;
hmm_frame(h) = frame;
}
void
hmm_dump(hmm_t * hmm,
FILE * fp)
{
int32 i;
if (hmm_is_mpx(hmm)) {
fprintf(fp, "MPX ");
for (i = 0; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, " %11d", hmm_senid(hmm, i));
fprintf(fp, " ( ");
for (i = 0; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, "%d ", hmm_ssid(hmm, i));
fprintf(fp, ")\n");
}
else {
fprintf(fp, "SSID ");
for (i = 0; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, " %11d", hmm_senid(hmm, i));
fprintf(fp, " (%d)\n", hmm_ssid(hmm, 0));
}
if (hmm->ctx->senscore) {
fprintf(fp, "SENSCR");
for (i = 0; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, " %11d", hmm_senscr(hmm, i));
fprintf(fp, "\n");
}
fprintf(fp, "SCORES %11d", hmm_in_score(hmm));
for (i = 1; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, " %11d", hmm_score(hmm, i));
fprintf(fp, " %11d", hmm_out_score(hmm));
fprintf(fp, "\n");
fprintf(fp, "HISTID %11d", hmm_in_history(hmm));
for (i = 1; i < hmm_n_emit_state(hmm); i++)
fprintf(fp, " %11d", hmm_history(hmm, i));
fprintf(fp, " %11d", hmm_out_history(hmm));
fprintf(fp, "\n");
if (hmm_in_score(hmm) > 0)
fprintf(fp,
"ALERT!! The input score %d is large than 0. Probably wrap around.\n",
hmm_in_score(hmm));
if (hmm_out_score(hmm) > 0)
fprintf(fp,
"ALERT!! The output score %d is large than 0. Probably wrap around\n.",
hmm_out_score(hmm));
fflush(fp);
}
void
hmm_clear(hmm_t * h)
{
int32 i;
hmm_in_score(h) = WORST_SCORE;
hmm_in_history(h) = -1;
for (i = 1; i < hmm_n_emit_state(h); i++) {
hmm_score(h, i) = WORST_SCORE;
hmm_history(h, i) = -1;
}
hmm_out_score(h) = WORST_SCORE;
hmm_out_history(h) = -1;
h->bestscore = WORST_SCORE;
h->frame = -1;
}
static int32
hmm_vit_eval_anytopo(hmm_t * hmm)
{
hmm_context_t *ctx = hmm->ctx;
int32 to, from, bestfrom;
int32 newscr, scr, bestscr;
int final_state;
/* Compute previous state-score + observation output prob for each emitting state */
ctx->st_sen_scr[0] = hmm_in_score(hmm) + hmm_senscr(hmm, 0);
for (from = 1; from < hmm_n_emit_state(hmm); ++from) {
if ((ctx->st_sen_scr[from] =
hmm_score(hmm, from) + hmm_senscr(hmm, from)) WORSE_THAN WORST_SCORE)
ctx->st_sen_scr[from] = WORST_SCORE;
}
/* FIXME/TODO: Use the BLAS for all this. */
/* Evaluate final-state first, which does not have a self-transition */
final_state = hmm_n_emit_state(hmm);
to = final_state;
scr = WORST_SCORE;
bestfrom = -1;
for (from = to - 1; from >= 0; --from) {
if ((hmm_tprob(hmm, from, to) BETTER_THAN TMAT_WORST_SCORE) &&
((newscr = ctx->st_sen_scr[from]
+ hmm_tprob(hmm, from, to)) BETTER_THAN scr)) {
scr = newscr;
bestfrom = from;
}
}
hmm_out_score(hmm) = scr;
if (bestfrom >= 0)
hmm_out_history(hmm) = hmm_history(hmm, bestfrom);
bestscr = scr;
/* Evaluate all other states, which might have self-transitions */
for (to = final_state - 1; to >= 0; --to) {
/* Score from self-transition, if any */
scr =
(hmm_tprob(hmm, to, to) BETTER_THAN TMAT_WORST_SCORE)
? ctx->st_sen_scr[to] + hmm_tprob(hmm, to, to)
: WORST_SCORE;
/* Scores from transitions from other states */
bestfrom = -1;
for (from = to - 1; from >= 0; --from) {
if ((hmm_tprob(hmm, from, to) BETTER_THAN TMAT_WORST_SCORE) &&
((newscr = ctx->st_sen_scr[from]
+ hmm_tprob(hmm, from, to)) BETTER_THAN scr)) {
scr = newscr;
bestfrom = from;
}
}
/* Update new result for state to */
if (to == 0) {
hmm_in_score(hmm) = scr;
if (bestfrom >= 0)
hmm_in_history(hmm) = hmm_history(hmm, bestfrom);
}
else {
hmm_score(hmm, to) = scr;
if (bestfrom >= 0)
hmm_history(hmm, to) = hmm_history(hmm, bestfrom);
}
/* Propagate ssid for multiplex HMMs */
if (bestfrom >= 0 && hmm_is_mpx(hmm))
hmm->senid[to] = hmm->senid[bestfrom];
if (bestscr WORSE_THAN scr)
bestscr = scr;
}
hmm_bestscore(hmm) = bestscr;
return bestscr;
}
static int32
hmm_vit_eval_3st_lr_mpx(hmm_t * hmm)
{
uint8 const *tp = hmm->ctx->tp[hmm->tmatid][0];
int16 const *senscore = hmm->ctx->senscore;
uint16 * const *sseq = hmm->ctx->sseq;
uint16 *ssid = hmm->senid;
int32 bestScore;
int32 s3, s2, s1, s0, t2, t1, t0;
/* Don't propagate WORST_SCORE */
t2 = INT_MIN; /* Not used unless skipstate is true */
if (ssid[2] == BAD_SSID)
s2 = t1 = WORST_SCORE;
else {
s2 = hmm_score(hmm, 2) + mpx_senscr(2);
t1 = s2 + hmm_tprob_3st(2, 3);
}
if (ssid[1] == BAD_SSID)
s1 = t2 = WORST_SCORE;
else {
s1 = hmm_score(hmm, 1) + mpx_senscr(1);
if (hmm_tprob_3st(1,3) BETTER_THAN TMAT_WORST_SCORE)
t2 = s1 + hmm_tprob_3st(1, 3);
}
if (t1 BETTER_THAN t2) {
s3 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 2);
}
else {
s3 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 1);
}
if (s3 WORSE_THAN WORST_SCORE) s3 = WORST_SCORE;
hmm_out_score(hmm) = s3;
bestScore = s3;
/* State 0 is always active */
s0 = hmm_in_score(hmm) + mpx_senscr(0);
/* Don't propagate WORST_SCORE */
t0 = t1 = WORST_SCORE;
if (s2 != WORST_SCORE)
t0 = s2 + hmm_tprob_3st(2, 2);
if (s1 != WORST_SCORE)
t1 = s1 + hmm_tprob_3st(1, 2);
if (hmm_tprob_3st(0,2) BETTER_THAN TMAT_WORST_SCORE)
t2 = s0 + hmm_tprob_3st(0, 2);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else
s2 = t0;
}
else {
if (t2 BETTER_THAN t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
ssid[2] = ssid[1];
}
}
if (s2 WORSE_THAN WORST_SCORE) s2 = WORST_SCORE;
if (s2 BETTER_THAN bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* Don't propagate WORST_SCORE */
t0 = WORST_SCORE;
if (s1 != WORST_SCORE)
t0 = s1 + hmm_tprob_3st(1, 1);
t1 = s0 + hmm_tprob_3st(0, 1);
if (t0 BETTER_THAN t1) {
s1 = t0;
}
else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
ssid[1] = ssid[0];
}
if (s1 WORSE_THAN WORST_SCORE) s1 = WORST_SCORE;
if (s1 BETTER_THAN bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* State 0 is always active */
s0 += hmm_tprob_3st(0, 0);
if (s0 WORSE_THAN WORST_SCORE) s0 = WORST_SCORE;
if (s0 BETTER_THAN bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_3st_lr(hmm_t * hmm)
{
int16 const *senscore = hmm->ctx->senscore;
uint8 const *tp = hmm->ctx->tp[hmm->tmatid][0];
uint16 const *sseq = hmm->senid;
int32 s3, s2, s1, s0, t2, t1, t0, bestScore;
s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);
s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);
s0 = hmm_in_score(hmm) + nonmpx_senscr(0);
/* It was the best of scores, it was the worst of scores. */
bestScore = WORST_SCORE;
t2 = INT_MIN; /* Not used unless skipstate is true */
/* Transitions into non-emitting state 3 */
if (s1 BETTER_THAN WORST_SCORE) {
t1 = s2 + hmm_tprob_3st(2, 3);
if (hmm_tprob_3st(1,3) BETTER_THAN TMAT_WORST_SCORE)
t2 = s1 + hmm_tprob_3st(1, 3);
if (t1 BETTER_THAN t2) {
s3 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 2);
} else {
s3 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 1);
}
if (s3 WORSE_THAN WORST_SCORE) s3 = WORST_SCORE;
hmm_out_score(hmm) = s3;
bestScore = s3;
}
/* All transitions into state 2 (state 0 is always active) */
t0 = s2 + hmm_tprob_3st(2, 2);
t1 = s1 + hmm_tprob_3st(1, 2);
if (hmm_tprob_3st(0, 2) BETTER_THAN TMAT_WORST_SCORE)
t2 = s0 + hmm_tprob_3st(0, 2);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else
s2 = t0;
} else {
if (t2 BETTER_THAN t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
}
}
if (s2 WORSE_THAN WORST_SCORE) s2 = WORST_SCORE;
if (s2 BETTER_THAN bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* All transitions into state 1 */
t0 = s1 + hmm_tprob_3st(1, 1);
t1 = s0 + hmm_tprob_3st(0, 1);
if (t0 BETTER_THAN t1) {
s1 = t0;
} else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
}
if (s1 WORSE_THAN WORST_SCORE) s1 = WORST_SCORE;
if (s1 BETTER_THAN bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* All transitions into state 0 */
s0 = s0 + hmm_tprob_3st(0, 0);
if (s0 WORSE_THAN WORST_SCORE) s0 = WORST_SCORE;
if (s0 BETTER_THAN bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_5st_lr_mpx(hmm_t * hmm)
{
uint8 const *tp = hmm->ctx->tp[hmm->tmatid][0];
int16 const *senscore = hmm->ctx->senscore;
uint16 * const *sseq = hmm->ctx->sseq;
uint16 *ssid = hmm->senid;
int32 bestScore;
int32 s5, s4, s3, s2, s1, s0, t2, t1, t0;
/* Don't propagate WORST_SCORE */
if (ssid[4] == BAD_SSID)
s4 = t1 = WORST_SCORE;
else {
s4 = hmm_score(hmm, 4) + mpx_senscr(4);
t1 = s4 + hmm_tprob_5st(4, 5);
}
if (ssid[3] == BAD_SSID)
s3 = t2 = WORST_SCORE;
else {
s3 = hmm_score(hmm, 3) + mpx_senscr(3);
t2 = s3 + hmm_tprob_5st(3, 5);
}
if (t1 BETTER_THAN t2) {
s5 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 4);
}
else {
s5 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 3);
}
if (s5 WORSE_THAN WORST_SCORE) s5 = WORST_SCORE;
hmm_out_score(hmm) = s5;
bestScore = s5;
/* Don't propagate WORST_SCORE */
if (ssid[2] == BAD_SSID)
s2 = t2 = WORST_SCORE;
else {
s2 = hmm_score(hmm, 2) + mpx_senscr(2);
t2 = s2 + hmm_tprob_5st(2, 4);
}
t0 = t1 = WORST_SCORE;
if (s4 != WORST_SCORE)
t0 = s4 + hmm_tprob_5st(4, 4);
if (s3 != WORST_SCORE)
t1 = s3 + hmm_tprob_5st(3, 4);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
ssid[4] = ssid[2];
}
else
s4 = t0;
}
else {
if (t2 BETTER_THAN t1) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
ssid[4] = ssid[2];
}
else {
s4 = t1;
hmm_history(hmm, 4) = hmm_history(hmm, 3);
ssid[4] = ssid[3];
}
}
if (s4 WORSE_THAN WORST_SCORE) s4 = WORST_SCORE;
if (s4 BETTER_THAN bestScore)
bestScore = s4;
hmm_score(hmm, 4) = s4;
/* Don't propagate WORST_SCORE */
if (ssid[1] == BAD_SSID)
s1 = t2 = WORST_SCORE;
else {
s1 = hmm_score(hmm, 1) + mpx_senscr(1);
t2 = s1 + hmm_tprob_5st(1, 3);
}
t0 = t1 = WORST_SCORE;
if (s3 != WORST_SCORE)
t0 = s3 + hmm_tprob_5st(3, 3);
if (s2 != WORST_SCORE)
t1 = s2 + hmm_tprob_5st(2, 3);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
ssid[3] = ssid[1];
}
else
s3 = t0;
}
else {
if (t2 BETTER_THAN t1) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
ssid[3] = ssid[1];
}
else {
s3 = t1;
hmm_history(hmm, 3) = hmm_history(hmm, 2);
ssid[3] = ssid[2];
}
}
if (s3 WORSE_THAN WORST_SCORE) s3 = WORST_SCORE;
if (s3 BETTER_THAN bestScore) bestScore = s3;
hmm_score(hmm, 3) = s3;
/* State 0 is always active */
s0 = hmm_in_score(hmm) + mpx_senscr(0);
/* Don't propagate WORST_SCORE */
t0 = t1 = WORST_SCORE;
if (s2 != WORST_SCORE)
t0 = s2 + hmm_tprob_5st(2, 2);
if (s1 != WORST_SCORE)
t1 = s1 + hmm_tprob_5st(1, 2);
t2 = s0 + hmm_tprob_5st(0, 2);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else
s2 = t0;
}
else {
if (t2 BETTER_THAN t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
ssid[2] = ssid[1];
}
}
if (s2 WORSE_THAN WORST_SCORE) s2 = WORST_SCORE;
if (s2 BETTER_THAN bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* Don't propagate WORST_SCORE */
t0 = WORST_SCORE;
if (s1 != WORST_SCORE)
t0 = s1 + hmm_tprob_5st(1, 1);
t1 = s0 + hmm_tprob_5st(0, 1);
if (t0 BETTER_THAN t1) {
s1 = t0;
}
else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
ssid[1] = ssid[0];
}
if (s1 WORSE_THAN WORST_SCORE) s1 = WORST_SCORE;
if (s1 BETTER_THAN bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
s0 += hmm_tprob_5st(0, 0);
if (s0 WORSE_THAN WORST_SCORE) s0 = WORST_SCORE;
if (s0 BETTER_THAN bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_5st_lr(hmm_t * hmm)
{
int16 const *senscore = hmm->ctx->senscore;
uint8 const *tp = hmm->ctx->tp[hmm->tmatid][0];
uint16 const *sseq = hmm->senid;
int32 s5, s4, s3, s2, s1, s0, t2, t1, t0, bestScore;
/* It was the best of scores, it was the worst of scores. */
bestScore = WORST_SCORE;
/* Cache problem here! */
s4 = hmm_score(hmm, 4) + nonmpx_senscr(4);
s3 = hmm_score(hmm, 3) + nonmpx_senscr(3);
/* Transitions into non-emitting state 5 */
if (s3 BETTER_THAN WORST_SCORE) {
t1 = s4 + hmm_tprob_5st(4, 5);
t2 = s3 + hmm_tprob_5st(3, 5);
if (t1 BETTER_THAN t2) {
s5 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 4);
} else {
s5 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 3);
}
if (s5 WORSE_THAN WORST_SCORE) s5 = WORST_SCORE;
hmm_out_score(hmm) = s5;
bestScore = s5;
}
s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);
/* All transitions into state 4 */
if (s2 BETTER_THAN WORST_SCORE) {
t0 = s4 + hmm_tprob_5st(4, 4);
t1 = s3 + hmm_tprob_5st(3, 4);
t2 = s2 + hmm_tprob_5st(2, 4);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
} else
s4 = t0;
} else {
if (t2 BETTER_THAN t1) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
} else {
s4 = t1;
hmm_history(hmm, 4) = hmm_history(hmm, 3);
}
}
if (s4 WORSE_THAN WORST_SCORE) s4 = WORST_SCORE;
if (s4 BETTER_THAN bestScore) bestScore = s4;
hmm_score(hmm, 4) = s4;
}
s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);
/* All transitions into state 3 */
if (s1 BETTER_THAN WORST_SCORE) {
t0 = s3 + hmm_tprob_5st(3, 3);
t1 = s2 + hmm_tprob_5st(2, 3);
t2 = s1 + hmm_tprob_5st(1, 3);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
} else
s3 = t0;
} else {
if (t2 BETTER_THAN t1) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
} else {
s3 = t1;
hmm_history(hmm, 3) = hmm_history(hmm, 2);
}
}
if (s3 WORSE_THAN WORST_SCORE) s3 = WORST_SCORE;
if (s3 BETTER_THAN bestScore) bestScore = s3;
hmm_score(hmm, 3) = s3;
}
s0 = hmm_in_score(hmm) + nonmpx_senscr(0);
/* All transitions into state 2 (state 0 is always active) */
t0 = s2 + hmm_tprob_5st(2, 2);
t1 = s1 + hmm_tprob_5st(1, 2);
t2 = s0 + hmm_tprob_5st(0, 2);
if (t0 BETTER_THAN t1) {
if (t2 BETTER_THAN t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else
s2 = t0;
} else {
if (t2 BETTER_THAN t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
}
}
if (s2 WORSE_THAN WORST_SCORE) s2 = WORST_SCORE;
if (s2 BETTER_THAN bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* All transitions into state 1 */
t0 = s1 + hmm_tprob_5st(1, 1);
t1 = s0 + hmm_tprob_5st(0, 1);
if (t0 BETTER_THAN t1) {
s1 = t0;
} else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
}
if (s1 WORSE_THAN WORST_SCORE) s1 = WORST_SCORE;
if (s1 BETTER_THAN bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* All transitions into state 0 */
s0 = s0 + hmm_tprob_5st(0, 0);
if (s0 WORSE_THAN WORST_SCORE) s0 = WORST_SCORE;
if (s0 BETTER_THAN bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_3st_lr_mpx(hmm_t * hmm)
{
const int32 *tp = hmm->ctx->tp[hmm->tmatid][0];
const int32 *senscore = hmm->ctx->senscore;
const s3senid_t **sseq = hmm->ctx->sseq;
int32 *ssid = hmm->s.mpx_ssid;
int32 bestScore;
int32 s3, s2, s1, s0, t2, t1, t0;
/* Don't propagate WORST_SCORE */
t2 = INT_MIN; /* Not used unless skipstate is true */
if (ssid[2] == -1)
s2 = t1 = WORST_SCORE;
else {
s2 = hmm_score(hmm, 2) + mpx_senscr(2);
if (s2 < WORST_SCORE) s2 = WORST_SCORE;
t1 = s2 + hmm_tprob_3st(2, 3);
}
if (ssid[1] == -1)
s1 = WORST_SCORE;
else {
s1 = hmm_score(hmm, 1) + mpx_senscr(1);
if (s1 < WORST_SCORE) s1 = WORST_SCORE;
t2 = s1 + hmm_tprob_3st(1, 3);
}
if (t1 > t2) {
s3 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 2);
}
else {
s3 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 1);
}
if (s3 < WORST_SCORE) s3 = WORST_SCORE;
hmm_out_score(hmm) = s3;
bestScore = s3;
/* State 0 is always active */
s0 = hmm_in_score(hmm) + mpx_senscr(0);
if (s0 < WORST_SCORE) s0 = WORST_SCORE;
/* Don't propagate WORST_SCORE */
t0 = t1 = WORST_SCORE;
if (s2 != WORST_SCORE)
t0 = s2 + hmm_tprob_3st(2, 2);
if (s1 != WORST_SCORE)
t1 = s1 + hmm_tprob_3st(1, 2);
if (hmm_tprob_3st(0,2) > WORST_SCORE)
t2 = s0 + hmm_tprob_3st(0, 2);
if (t0 > t1) {
if (t2 > t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else
s2 = t0;
}
else {
if (t2 > t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
ssid[2] = ssid[1];
}
}
if (s2 < WORST_SCORE) s2 = WORST_SCORE;
if (s2 > bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* Don't propagate WORST_SCORE */
t0 = WORST_SCORE;
if (s1 != WORST_SCORE)
t0 = s1 + hmm_tprob_3st(1, 1);
t1 = s0 + hmm_tprob_3st(0, 1);
if (t0 > t1) {
s1 = t0;
}
else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
ssid[1] = ssid[0];
}
if (s1 < WORST_SCORE) s1 = WORST_SCORE;
if (s1 > bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* State 0 is always active */
s0 += hmm_tprob_3st(0, 0);
if (s0 < WORST_SCORE) s0 = WORST_SCORE;
if (s0 > bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_3st_lr(hmm_t * hmm)
{
const int32 *senscore = hmm->ctx->senscore;
const int32 *tp = hmm->ctx->tp[hmm->tmatid][0];
const s3senid_t *sseq = hmm->ctx->sseq[hmm_ssid(hmm, 0)];
int32 s3, s2, s1, s0, t2, t1, t0, bestScore;
s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);
s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);
s0 = hmm_in_score(hmm) + nonmpx_senscr(0);
/* It was the best of scores, it was the worst of scores. */
t0 = t1 = bestScore = WORST_SCORE;
t2 = INT_MIN; /* Not used unless skipstate is true */
/* Transitions into non-emitting state 3 */
if (s2 > WORST_SCORE) {
t1 = s2 + hmm_tprob_3st(2, 3);
t0 = s2 + hmm_tprob_3st(2, 2);
}
if (s1 > WORST_SCORE && hmm_tprob_3st(1,3) > WORST_SCORE)
t2 = s1 + hmm_tprob_3st(1, 3);
if (t1 > t2) {
s3 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 2);
} else {
s3 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 1);
}
if (s3 < WORST_SCORE) s3 = WORST_SCORE;
hmm_out_score(hmm) = s3;
bestScore = s3;
/* All transitions into state 2 (state 0 is always active) */
t1 = t2 = WORST_SCORE;
if (s1 > WORST_SCORE)
t1 = s1 + hmm_tprob_3st(1, 2);
if (hmm_tprob_3st(0, 2) > WORST_SCORE)
t2 = s0 + hmm_tprob_3st(0, 2);
if (t0 > t1) {
if (t2 > t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else
s2 = t0;
} else {
if (t2 > t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
}
}
if (s2 < WORST_SCORE) s2 = WORST_SCORE;
if (s2 > bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* All transitions into state 1 */
t0 = t1 = WORST_SCORE;
if (s1 > WORST_SCORE)
t0 = s1 + hmm_tprob_3st(1, 1);
if (s0 > WORST_SCORE)
t1 = s0 + hmm_tprob_3st(0, 1);
if (t0 > t1) {
s1 = t0;
} else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
}
if (s1 < WORST_SCORE) s1 = WORST_SCORE;
if (s1 > bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* All transitions into state 0 */
s0 = s0 + hmm_tprob_3st(0, 0);
if (s0 < WORST_SCORE) s0 = WORST_SCORE;
if (s0 > bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_5st_lr_mpx(hmm_t * hmm)
{
const int32 *tp = hmm->ctx->tp[hmm->tmatid][0];
const int32 *senscore = hmm->ctx->senscore;
const s3senid_t **sseq = hmm->ctx->sseq;
int32 *ssid = hmm->s.mpx_ssid;
int32 bestScore;
int32 s5, s4, s3, s2, s1, s0, t2, t1, t0;
/* Don't propagate WORST_SCORE */
if (ssid[4] == -1)
s4 = t1 = WORST_SCORE;
else {
s4 = hmm_score(hmm, 4) + mpx_senscr(4);
t1 = s4 + hmm_tprob_5st(4, 5);
}
if (ssid[3] == -1)
s3 = t2 = WORST_SCORE;
else {
s3 = hmm_score(hmm, 3) + mpx_senscr(3);
t2 = s3 + hmm_tprob_5st(3, 5);
}
if (t1 > t2) {
s5 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 4);
}
else {
s5 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 3);
}
if (s5 < WORST_SCORE) s5 = WORST_SCORE;
hmm_out_score(hmm) = s5;
bestScore = s5;
/* Don't propagate WORST_SCORE */
if (ssid[2] == -1)
s2 = t2 = WORST_SCORE;
else {
s2 = hmm_score(hmm, 2) + mpx_senscr(2);
t2 = s2 + hmm_tprob_5st(2, 4);
}
t0 = t1 = WORST_SCORE;
if (s4 != WORST_SCORE)
t0 = s4 + hmm_tprob_5st(4, 4);
if (s3 != WORST_SCORE)
t1 = s3 + hmm_tprob_5st(3, 4);
if (t0 > t1) {
if (t2 > t0) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
ssid[4] = ssid[2];
}
else
s4 = t0;
}
else {
if (t2 > t1) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
ssid[4] = ssid[2];
}
else {
s4 = t1;
hmm_history(hmm, 4) = hmm_history(hmm, 3);
ssid[4] = ssid[3];
}
}
if (s4 < WORST_SCORE) s4 = WORST_SCORE;
if (s4 > bestScore)
bestScore = s4;
hmm_score(hmm, 4) = s4;
/* Don't propagate WORST_SCORE */
if (ssid[1] == -1)
s1 = t2 = WORST_SCORE;
else {
s1 = hmm_score(hmm, 1) + mpx_senscr(1);
t2 = s1 + hmm_tprob_5st(1, 3);
}
t0 = t1 = WORST_SCORE;
if (s3 != WORST_SCORE)
t0 = s3 + hmm_tprob_5st(3, 3);
if (s2 != WORST_SCORE)
t1 = s2 + hmm_tprob_5st(2, 3);
if (t0 > t1) {
if (t2 > t0) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
ssid[3] = ssid[1];
}
else
s3 = t0;
}
else {
if (t2 > t1) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
ssid[3] = ssid[1];
}
else {
s3 = t1;
hmm_history(hmm, 3) = hmm_history(hmm, 2);
ssid[3] = ssid[2];
}
}
if (s3 < WORST_SCORE) s3 = WORST_SCORE;
if (s3 > bestScore) bestScore = s3;
hmm_score(hmm, 3) = s3;
/* State 0 is always active */
s0 = hmm_in_score(hmm) + mpx_senscr(0);
/* Don't propagate WORST_SCORE */
t0 = t1 = WORST_SCORE;
if (s2 != WORST_SCORE)
t0 = s2 + hmm_tprob_5st(2, 2);
if (s1 != WORST_SCORE)
t1 = s1 + hmm_tprob_5st(1, 2);
t2 = s0 + hmm_tprob_5st(0, 2);
if (t0 > t1) {
if (t2 > t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else
s2 = t0;
}
else {
if (t2 > t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
ssid[2] = ssid[0];
}
else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
ssid[2] = ssid[1];
}
}
if (s2 < WORST_SCORE) s2 = WORST_SCORE;
if (s2 > bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* Don't propagate WORST_SCORE */
t0 = WORST_SCORE;
if (s1 != WORST_SCORE)
t0 = s1 + hmm_tprob_5st(1, 1);
t1 = s0 + hmm_tprob_5st(0, 1);
if (t0 > t1) {
s1 = t0;
}
else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
ssid[1] = ssid[0];
}
if (s1 < WORST_SCORE) s1 = WORST_SCORE;
if (s1 > bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
s0 += hmm_tprob_5st(0, 0);
if (s0 < WORST_SCORE) s0 = WORST_SCORE;
if (s0 > bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
static int32
hmm_vit_eval_5st_lr(hmm_t * hmm)
{
const int32 *senscore = hmm->ctx->senscore;
const int32 *tp = hmm->ctx->tp[hmm->tmatid][0];
const s3senid_t *sseq = hmm->ctx->sseq[hmm_ssid(hmm, 0)];
int32 s5, s4, s3, s2, s1, s0, t2, t1, t0, bestScore;
/* It was the best of scores, it was the worst of scores. */
bestScore = WORST_SCORE;
s4 = hmm_score(hmm, 4) + nonmpx_senscr(4);
s3 = hmm_score(hmm, 3) + nonmpx_senscr(3);
/* Transitions into non-emitting state 5 */
if (s3 > WORST_SCORE) {
t1 = s4 + hmm_tprob_5st(4, 5);
t2 = s3 + hmm_tprob_5st(3, 5);
if (t1 > t2) {
s5 = t1;
hmm_out_history(hmm) = hmm_history(hmm, 4);
} else {
s5 = t2;
hmm_out_history(hmm) = hmm_history(hmm, 3);
}
if (s5 < WORST_SCORE) s5 = WORST_SCORE;
hmm_out_score(hmm) = s5;
bestScore = s5;
}
s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);
/* All transitions into state 4 */
if (s2 > WORST_SCORE) {
t0 = s4 + hmm_tprob_5st(4, 4);
t1 = s3 + hmm_tprob_5st(3, 4);
t2 = s2 + hmm_tprob_5st(2, 4);
if (t0 > t1) {
if (t2 > t0) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
} else
s4 = t0;
} else {
if (t2 > t1) {
s4 = t2;
hmm_history(hmm, 4) = hmm_history(hmm, 2);
} else {
s4 = t1;
hmm_history(hmm, 4) = hmm_history(hmm, 3);
}
}
if (s4 < WORST_SCORE) s4 = WORST_SCORE;
if (s4 > bestScore) bestScore = s4;
hmm_score(hmm, 4) = s4;
}
s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);
/* All transitions into state 3 */
if (s1 > WORST_SCORE) {
t0 = s3 + hmm_tprob_5st(3, 3);
t1 = s2 + hmm_tprob_5st(2, 3);
t2 = s1 + hmm_tprob_5st(1, 3);
if (t0 > t1) {
if (t2 > t0) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
} else
s3 = t0;
} else {
if (t2 > t1) {
s3 = t2;
hmm_history(hmm, 3) = hmm_history(hmm, 1);
} else {
s3 = t1;
hmm_history(hmm, 3) = hmm_history(hmm, 2);
}
}
if (s3 < WORST_SCORE) s3 = WORST_SCORE;
if (s3 > bestScore) bestScore = s3;
hmm_score(hmm, 3) = s3;
}
s0 = hmm_in_score(hmm) + nonmpx_senscr(0);
/* All transitions into state 2 (state 0 is always active) */
t0 = s2 + hmm_tprob_5st(2, 2);
t1 = s1 + hmm_tprob_5st(1, 2);
t2 = s0 + hmm_tprob_5st(0, 2);
if (t0 > t1) {
if (t2 > t0) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else
s2 = t0;
} else {
if (t2 > t1) {
s2 = t2;
hmm_history(hmm, 2) = hmm_in_history(hmm);
} else {
s2 = t1;
hmm_history(hmm, 2) = hmm_history(hmm, 1);
}
}
if (s2 < WORST_SCORE) s2 = WORST_SCORE;
if (s2 > bestScore) bestScore = s2;
hmm_score(hmm, 2) = s2;
/* All transitions into state 1 */
t0 = s1 + hmm_tprob_5st(1, 1);
t1 = s0 + hmm_tprob_5st(0, 1);
if (t0 > t1) {
s1 = t0;
} else {
s1 = t1;
hmm_history(hmm, 1) = hmm_in_history(hmm);
}
if (s1 < WORST_SCORE) s1 = WORST_SCORE;
if (s1 > bestScore) bestScore = s1;
hmm_score(hmm, 1) = s1;
/* All transitions into state 0 */
s0 = s0 + hmm_tprob_5st(0, 0);
if (s0 < WORST_SCORE) s0 = WORST_SCORE;
if (s0 > bestScore) bestScore = s0;
hmm_in_score(hmm) = s0;
hmm_bestscore(hmm) = bestScore;
return bestScore;
}
