Add m-esr52 at 52.6.0

1 files changed, 825 insertions, 0 deletions

diff --git a/media/pocketsphinx/src/hmm.c b/media/pocketsphinx/src/hmm.c
new file mode 100644
index 000000000..73b2c98cc
--- /dev/null
+++ b/media/pocketsphinx/src/hmm.c
@@ -0,0 +1,825 @@
+/* -*- c-basic-offset: 4; indent-tabs-mode: nil -*- */
+/* ====================================================================
+ * Copyright (c) 1999-2004 Carnegie Mellon University.  All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer. 
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This work was supported in part by funding from the Defense Advanced 
+ * Research Projects Agency and the National Science Foundation of the 
+ * United States of America, and the CMU Sphinx Speech Consortium.
+ *
+ * THIS SOFTWARE IS PROVIDED BY CARNEGIE MELLON UNIVERSITY ``AS IS'' AND 
+ * ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+ * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL CARNEGIE MELLON UNIVERSITY
+ * NOR ITS EMPLOYEES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * ====================================================================
+ *
+ */
+
+/**
+ * @file hmm.h Implementation of HMM base structure.
+ */
+
+/* System headers. */
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+/* SphinxBase headers. */
+#include <sphinxbase/ckd_alloc.h>
+#include <sphinxbase/err.h>
+
+/* Local headers. */
+#include "hmm.h"
+
+hmm_context_t *
+hmm_context_init(int32 n_emit_state,
+		 uint8 ** const *tp,
+		 int16 const *senscore,
+		 uint16 * const *sseq)
+{
+    hmm_context_t *ctx;
+
+    assert(n_emit_state > 0);
+    if (n_emit_state > HMM_MAX_NSTATE) {
+        E_ERROR("Number of emitting states must be <= %d\n", HMM_MAX_NSTATE);
+        return NULL;
+    }
+
+    ctx = ckd_calloc(1, sizeof(*ctx));
+    ctx->n_emit_state = n_emit_state;
+    ctx->tp = tp;
+    ctx->senscore = senscore;
+    ctx->sseq = sseq;
+    ctx->st_sen_scr = ckd_calloc(n_emit_state, sizeof(*ctx->st_sen_scr));
+
+    return ctx;
+}
+
+void
+hmm_context_free(hmm_context_t *ctx)
+{
+    if (ctx == NULL)
+        return;
+    ckd_free(ctx->st_sen_scr);
+    ckd_free(ctx);
+}
+
+void
+hmm_init(hmm_context_t *ctx, hmm_t *hmm, int mpx, int ssid, int tmatid)
+{
+    hmm->ctx = ctx;
+    hmm->mpx = mpx;
+    hmm->n_emit_state = ctx->n_emit_state;
+    if (mpx) {
+        int i;
+        hmm->ssid = BAD_SSID;
+        hmm->senid[0] = ssid;
+        for (i = 1; i < hmm_n_emit_state(hmm); ++i) {
+            hmm->senid[i] = BAD_SSID;
+        }
+    }
+    else {
+        hmm->ssid = ssid;
+        memcpy(hmm->senid, ctx->sseq[ssid], hmm->n_emit_state * sizeof(*hmm->senid));
+    }
+    hmm->tmatid = tmatid;
+    hmm_clear(hmm);
+}
+
+void
+hmm_deinit(hmm_t *hmm)
+{
+}
+
+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_scores(hmm_t * h)
+{
+    int32 i;
+
+    hmm_in_score(h) = WORST_SCORE;
+    for (i = 1; i < hmm_n_emit_state(h); i++)
+        hmm_score(h, i) = WORST_SCORE;
+    hmm_out_score(h) = WORST_SCORE;
+
+    h->bestscore = WORST_SCORE;
+}
+
+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;
+}
+
+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_normalize(hmm_t *h, int32 bestscr)
+{
+    int32 i;
+
+    for (i = 0; i < hmm_n_emit_state(h); i++) {
+        if (hmm_score(h, i) BETTER_THAN WORST_SCORE)
+            hmm_score(h, i) -= bestscr;
+    }
+    if (hmm_out_score(h) BETTER_THAN WORST_SCORE)
+        hmm_out_score(h) -= bestscr;
+}
+
+#define hmm_tprob_5st(i, j) (-tp[(i)*6+(j)])
+#define nonmpx_senscr(i) (-senscore[sseq[i]])
+
+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;
+}
+
+#define mpx_senid(st) sseq[ssid[st]][st]
+#define mpx_senscr(st) (-senscore[mpx_senid(st)])
+
+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;
+}
+
+#define hmm_tprob_3st(i, j) (-tp[(i)*4+(j)])
+
+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_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_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;
+}
+
+int32
+hmm_vit_eval(hmm_t * hmm)
+{
+    if (hmm_is_mpx(hmm)) {
+        if (hmm_n_emit_state(hmm) == 5)
+            return hmm_vit_eval_5st_lr_mpx(hmm);
+        else if (hmm_n_emit_state(hmm) == 3)
+            return hmm_vit_eval_3st_lr_mpx(hmm);
+        else
+            return hmm_vit_eval_anytopo(hmm);
+    }
+    else {
+        if (hmm_n_emit_state(hmm) == 5)
+            return hmm_vit_eval_5st_lr(hmm);
+        else if (hmm_n_emit_state(hmm) == 3)
+            return hmm_vit_eval_3st_lr(hmm);
+        else
+            return hmm_vit_eval_anytopo(hmm);
+    }
+}
+
+int32
+hmm_dump_vit_eval(hmm_t * hmm, FILE * fp)
+{
+    int32 bs = 0;
+
+    if (fp) {
+        fprintf(fp, "BEFORE:\n");
+        hmm_dump(hmm, fp);
+    }
+    bs = hmm_vit_eval(hmm);
+    if (fp) {
+        fprintf(fp, "AFTER:\n");
+        hmm_dump(hmm, fp);
+    }
+
+    return bs;
+}