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_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)
{
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_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;
}
