kevinmoran1988 · Oct 1, 2026 · Oct 4, 2026 · Oct 4, 2026 · Oct 4, 2026 · Oct 4, 2026
diff --git a/src/bathsearch.c b/src/bathsearch.c
@@ -830,7 +830,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
       info[i].hw = p7_hmmwindow_CreateList();
       info[i].gcode = gcode;
       info[i].wrk = esl_gencode_WorkstateCreate(go, gcode);
-      info[i].wrk->orf_block = esl_sq_CreateDigitalBlock(BLOCK_SIZE, abcAA);
+      info[i].wrk->orf_block = esl_gencode_OrfBlockCreate(BLOCK_SIZE);
       info[i].th     = p7_tophits_Create();
       info[i].om     = p7_oprofile_Clone(om);
       info[i].gm     = p7_profile_Clone(gm);
@@ -923,7 +923,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
       p7_hmmwindow_DestroyList(info[i].hw);
       if(info[i].wrk->orf_block != NULL)
       {
-        esl_sq_DestroyBlock(info[i].wrk->orf_block);
+        esl_gencode_OrfBlockDestroy(info[i].wrk->orf_block);
         info[i].wrk->orf_block = NULL;
         esl_gencode_WorkstateDestroy(info[i].wrk);
       }
@@ -1098,7 +1098,7 @@ serial_loop(WORKER_INFO *info, ID_LENGTH_LIST *id_length_list, ESL_SQFILE *dbfp,
       p7_Pipeline_BATH(info->pli, info->om, info->gm, info->om_fs3, info->om_fs5, info->gm_fs5, info->scoredata, info->bg, info->th, info->pli->nseqs, dbsq_dna, info->wrk->orf_block, info->gcode, info->hw, p7_NOCOMPLEMENT);
       p7_pipeline_Reuse_BATH(info->pli); // prepare for next search
 
-      esl_sq_ReuseBlock(info->wrk->orf_block);    
+      esl_gencode_OrfBlockReuse(info->wrk->orf_block);
     } 
 
     if (info->pli->strands != p7_STRAND_TOPONLY) 
@@ -1112,7 +1112,7 @@ serial_loop(WORKER_INFO *info, ID_LENGTH_LIST *id_length_list, ESL_SQFILE *dbfp,
       p7_Pipeline_BATH(info->pli, info->om, info->gm, info->om_fs3, info->om_fs5, info->gm_fs5, info->scoredata, info->bg, info->th, info->pli->nseqs, dbsq_dna, info->wrk->orf_block, info->gcode, info->hw, p7_COMPLEMENT); 
       p7_pipeline_Reuse_BATH(info->pli); // prepare for next search
 
-      esl_sq_ReuseBlock(info->wrk->orf_block);
+      esl_gencode_OrfBlockReuse(info->wrk->orf_block);
 
       /* Reverse sequence back to original */
       esl_sq_ReverseComplement(dbsq_dna);
@@ -1283,7 +1283,7 @@ pipeline_thread(void *arg)
         p7_Pipeline_BATH(info->pli, info->om, info->gm, info->om_fs3, info->om_fs5, info->gm_fs5, info->scoredata, info->bg, info->th, block->first_seqidx + i, dnaSeq, info->wrk->orf_block, info->gcode, info->hw, p7_NOCOMPLEMENT);
         p7_pipeline_Reuse_BATH(info->pli); // prepare for next search
 
-        esl_sq_ReuseBlock(info->wrk->orf_block);
+        esl_gencode_OrfBlockReuse(info->wrk->orf_block);
       } 
 
       if (info->pli->strands != p7_STRAND_TOPONLY) {
@@ -1294,7 +1294,7 @@ pipeline_thread(void *arg)
         p7_Pipeline_BATH(info->pli, info->om, info->gm, info->om_fs3, info->om_fs5, info->gm_fs5, info->scoredata, info->bg, info->th, block->first_seqidx + i, dnaSeq, info->wrk->orf_block, info->gcode, info->hw, p7_COMPLEMENT);
         p7_pipeline_Reuse_BATH(info->pli); // prepare for next search
 
-	    esl_sq_ReuseBlock(info->wrk->orf_block);
+	    esl_gencode_OrfBlockReuse(info->wrk->orf_block);
         esl_sq_ReverseComplement(dnaSeq);
       }
     }  

diff --git a/src/hmmer.h b/src/hmmer.h
@@ -1130,6 +1130,7 @@ typedef struct p7_pipeline_s {
   enum p7_pipemodes_e mode;      /* p7_SCAN_MODELS | p7_SEARCH_SEQS          */
   int           spliced;         /* TRUE if user uses --splice slaf to enable spliced alignments */
   int           fs_pipe;         /* TRUE if bathsearch is allowed to use the frameshift aware pipeline branch (use --fs flag) */
+  uint16_t     *ssv_cut;         /* ssv_cut[L]: lowest SSV maximum at which an ORF of length L is not rejected by SSV alone; 0 if not yet known */
   int           std_pipe;        /* TRUE if bathsearch is allowed to use the standard translation pipeline (do not use --fsonly flag)  */
   int           strands;         /*  p7_STRAND_TOPONLY  | p7_STRAND_BOTTOMONLY |  p7_STRAND_BOTH */
   int           W;               /* window length for nhmmer scan - essentially maximum length of model that we expect to find*/
@@ -1393,7 +1394,7 @@ extern int p7_tracealign_getMSAandStats(P7_HMM *hmm, ESL_SQ  **sq, int N, ESL_MS
 /* p7_alidisplay.c */
 extern P7_ALIDISPLAY *p7_alidisplay_Create(const P7_TRACE *tr, int which, const P7_OPROFILE *om, const ESL_SQ *sq, const ESL_SQ *ntsq);
 extern P7_ALIDISPLAY *p7_alidisplay_fs_Create(const P7_TRACE *tr, int which, const P7_FS_PROFILE *gm_fs5, const ESL_SQ *sq, int show_cigar);
-extern P7_ALIDISPLAY *p7_alidisplay_nonfs_Create(const P7_TRACE *tr, int which, const P7_OPROFILE *om, const ESL_SQ *sq, const ESL_SQ *orfsq, int orf_pos, int show_cigar); 
+extern P7_ALIDISPLAY *p7_alidisplay_nonfs_Create(const P7_TRACE *tr, int which, const P7_OPROFILE *om, const ESL_SQ *sq, const ESL_ORF *orfsq, int orf_pos, int show_cigar);
 extern P7_ALIDISPLAY *p7_alidisplay_splice_Create(const P7_TRACE *tr, int which, const P7_OPROFILE *om, const ESL_SQ *target_seq, const ESL_SQ *amino_sq, int amino_pos, int splice_cnt, int show_cigar);
 extern P7_ALIDISPLAY *p7_alidisplay_splice_fs_Create(const P7_TRACE *tr, int which, const P7_FS_PROFILE *gm_fs, const ESL_SQ *sq, ESL_DSQ *nuc_dsq, int64_t *nuc_index, int nuc_pos, int splice_cnt, int show_cigar);
 extern P7_ALIDISPLAY *p7_alidisplay_Create_empty();
@@ -1459,7 +1460,7 @@ extern int           p7_domaindef_DumpPosteriors(FILE *ofp, P7_DOMAINDEF *ddef);
 extern void          p7_domaindef_Destroy_BATH(P7_DOMAINDEF *ddef);
 
 extern int p7_domaindef_ByPosteriorHeuristics_Frameshift_BATH(P7_PIPELINE *pli, ESL_SQ *windowsq, P7_FS_OPROFILE *om_fs5, P7_FS_PROFILE *gm_fs5, P7_BG *bg, const ESL_GENCODE *gcode);
-extern int p7_domaindef_ByPosteriorHeuristics_BATH(const ESL_SQ *orfsq, const ESL_SQ *sq, const int64_t ntsqlen, P7_OPROFILE *om, P7_PROFILE *gm, P7_OMX *oxf, P7_OMX *oxb, P7_OMX *fwd, P7_OMX *bck, P7_DOMAINDEF *ddef);
+extern int p7_domaindef_ByPosteriorHeuristics_BATH(const ESL_ORF *orfsq, const ESL_SQ *sq, const int64_t ntsqlen, P7_OPROFILE *om, P7_PROFILE *gm, P7_OMX *oxf, P7_OMX *oxb, P7_OMX *fwd, P7_OMX *bck, P7_DOMAINDEF *ddef);
 
 /* p7_gmx.c */
 extern P7_GMX *p7_gmx_Create (int allocM, int allocL, int allocLx, int nscells);
@@ -1576,9 +1577,9 @@ extern int p7_pli_DomainIncludable  (P7_PIPELINE *pli, float dom_score, double l
 extern int p7_pli_NewModel          (P7_PIPELINE *pli, const P7_OPROFILE *om, P7_BG *bg);
 extern int p7_pli_NewModelThresholds(P7_PIPELINE *pli, const P7_OPROFILE *om);
 extern int p7_pli_NewSeq            (P7_PIPELINE *pli, const ESL_SQ *sq);
-extern int p7_pli_computeAliScores_BATH(P7_DOMAIN *dom, P7_TRACE *tr, const ESL_SQ *orfsq, const P7_PROFILE *gm);
+extern int p7_pli_computeAliScores_BATH(P7_DOMAIN *dom, P7_TRACE *tr, const ESL_ORF *orfsq, const P7_PROFILE *gm);
 extern int p7_pli_computeAliScores_Frameshift_BATH(P7_DOMAIN *dom, P7_TRACE *tr, const ESL_SQ *seq, const P7_FS_PROFILE *gm_fs);
-extern int p7_Pipeline_BATH   (P7_PIPELINE *pli, P7_OPROFILE *om, P7_PROFILE *gm, P7_FS_OPROFILE *om_fs3, P7_FS_OPROFILE *om_fs5, P7_FS_PROFILE *gm_fs5, P7_SCOREDATA *data, P7_BG *bg, P7_TOPHITS *hitlist, int64_t seqidx, ESL_SQ *dnasq, ESL_SQ_BLOCK *orf_block, ESL_GENCODE *gcode, P7_HMM_WINDOWLIST *splcing_windows, int complementarity);
+extern int p7_Pipeline_BATH   (P7_PIPELINE *pli, P7_OPROFILE *om, P7_PROFILE *gm, P7_FS_OPROFILE *om_fs3, P7_FS_OPROFILE *om_fs5, P7_FS_PROFILE *gm_fs5, P7_SCOREDATA *data, P7_BG *bg, P7_TOPHITS *hitlist, int64_t seqidx, ESL_SQ *dnasq, ESL_ORF_BLOCK *orf_block, ESL_GENCODE *gcode, P7_HMM_WINDOWLIST *splcing_windows, int complementarity);
 
 extern int p7_pli_Statistics(FILE *ofp, P7_PIPELINE *pli, ESL_STOPWATCH *w);
 

diff --git a/src/impl_avx/impl_avx.h b/src/impl_avx/impl_avx.h
@@ -15,6 +15,7 @@
 #include "esl_alphabet.h"
 #include "esl_random.h"
 #include "esl_cpu.h"
+#include "esl_gencode.h"  /* ESL_ORF                 */
 
 #ifdef eslENABLE_SSE
 #include <xmmintrin.h>   /* SSE  */
@@ -784,11 +785,18 @@ extern int (*p7_SSVFilter)(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, flo
 /* ssvfilter_sse.c — SSE implementation */
 #ifdef eslENABLE_SSE
 extern int p7_SSVFilter_sse(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float *ret_sc);
+extern void p7_SSVFilter_OrfBlock_sse(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE);
 #endif
 /* ssvfilter_avx.c — AVX2 implementation */
 #ifdef eslENABLE_AVX
 extern int p7_SSVFilter_avx(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float *ret_sc);
+extern void p7_SSVFilter_OrfBlock_avx(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE);
 #endif
+/* SSV over a block of ORFs: the pipeline can take each ORF's SSV maximum from
+ * one call, and turn it into the SSV filter's status and score itself */
+#define p7_SSV_ORFBLOCK 1
+extern int p7_SSVFilter_OrfBlock(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE);
+extern int p7_SSVFilter_FromXE(int xE, const P7_OPROFILE *om, float *ret_sc);
 
 /* stotrace.c — self-patching dispatcher */
 extern int (*p7_StochasticTrace)(ESL_RANDOMNESS *rng, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *ox, P7_TRACE *tr);

diff --git a/src/impl_avx/ssvfilter.c b/src/impl_avx/ssvfilter.c
@@ -42,3 +42,82 @@ p7_SSVFilter_Dispatcher(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float
   return eslENORESULT;
 #endif
 }
+
+
+/* Function:  p7_SSVFilter_FromXE()
+ * Synopsis:  The SSV filter's result, from the SSV matrix's highest cell.
+ *
+ * Purpose:   <xE> is the highest cell of the SSV matrix of a sequence against
+ *            <om>, as p7_SSVFilter_OrfBlock() gives it. Return what
+ *            p7_SSVFilter() returns for that sequence, and its score in
+ *            <*ret_sc>; <om> must be configured for the sequence's length.
+ *
+ * Returns:   <eslOK>, <eslENORESULT> or <eslERANGE>, as p7_SSVFilter().
+ */
+int
+p7_SSVFilter_FromXE(int xE_in, const P7_OPROFILE *om, float *ret_sc)
+{
+  uint16_t xE = (uint16_t) xE_in;
+  uint16_t xJ;
+
+  if (om->tjb_b + om->tbm_b + om->tec_b + om->bias_b >= 127)
+    return eslENORESULT;
+
+  /* Saturation floors every diagonal at the begin score (128), so a
+   * max of 128 means no diagonal scored above it and the true best
+   * may be lower; let the full MSV filter compute it. */
+  if (xE <= 128) return eslENORESULT;
+
+  if (xE >= 255 - om->bias_b) {
+    *ret_sc = eslINFINITY;
+
+    if (om->base_b - om->tjb_b - om->tbm_b < 128)
+      return eslENORESULT;
+
+    return eslERANGE;
+  }
+
+  xE += om->base_b - om->tjb_b - om->tbm_b;
+  xE -= 128;
+
+  if (xE >= 255 - om->bias_b) {
+    *ret_sc = eslINFINITY;
+    return eslERANGE;
+  }
+
+  xJ = xE - om->tec_b;
+
+  if (xJ > om->base_b) return eslENORESULT;
+
+  *ret_sc  = ((float)(xJ - om->tjb_b) - (float) om->base_b);
+  *ret_sc /= om->scale_b;
+  *ret_sc -= 3.0f;
+
+  return eslOK;
+}
+
+
+/* Function:  p7_SSVFilter_OrfBlock()
+ * Synopsis:  SSV maximum of every ORF in a block.
+ *
+ * Purpose:   For each of the <n> ORFs in <orf>, store in <xE[i]> the highest
+ *            cell of its SSV matrix against <om>. It does not depend on the
+ *            length <om> is configured for; p7_SSVFilter_FromXE() makes the
+ *            filter's status and score from it.
+ *
+ * Returns:   <eslOK> on success; <eslENORESULT> if there is no SIMD
+ *            implementation, and <xE> is unset.
+ */
+int
+p7_SSVFilter_OrfBlock(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE)
+{
+#ifdef eslENABLE_AVX
+  if (esl_cpu_has_avx()) { p7_SSVFilter_OrfBlock_avx(om, orf, n, xE); return eslOK; }
+#endif
+#ifdef eslENABLE_SSE
+  p7_SSVFilter_OrfBlock_sse(om, orf, n, xE);
+  return eslOK;
+#else
+  return eslENORESULT;
+#endif
+}
diff --git a/src/impl_avx/ssvfilter_avx.c b/src/impl_avx/ssvfilter_avx.c
@@ -436,6 +436,18 @@ calc_band_18(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m256i be
  * 2. p7_SSVFilter_avx()
  *****************************************************************/
 
+/* the band function for each band width */
+static __m256i (* const fs[MAX_BANDS + 1])(const ESL_DSQ *, int, const P7_OPROFILE *, int, register __m256i, __m256i)
+  = { NULL
+    , calc_band_1,  calc_band_2,  calc_band_3,  calc_band_4,  calc_band_5,  calc_band_6
+#if MAX_BANDS > 6
+    , calc_band_7,  calc_band_8,  calc_band_9,  calc_band_10, calc_band_11, calc_band_12, calc_band_13, calc_band_14
+#endif
+#if MAX_BANDS > 14
+    , calc_band_15, calc_band_16, calc_band_17, calc_band_18
+#endif
+  };
+
 static uint8_t
 get_xE_avx(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om)
 {
@@ -448,17 +460,6 @@ get_xE_avx(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om)
   int last_q = 0;
   int i;
 
-  __m256i (*fs[MAX_BANDS + 1])(const ESL_DSQ *, int, const P7_OPROFILE *, int, register __m256i, __m256i)
-    = { NULL
-      , calc_band_1,  calc_band_2,  calc_band_3,  calc_band_4,  calc_band_5,  calc_band_6
-#if MAX_BANDS > 6
-      , calc_band_7,  calc_band_8,  calc_band_9,  calc_band_10, calc_band_11, calc_band_12, calc_band_13, calc_band_14
-#endif
-#if MAX_BANDS > 14
-      , calc_band_15, calc_band_16, calc_band_17, calc_band_18
-#endif
-    };
-
   beginv = _mm256_set1_epi8(-128);
   xEv    = beginv;
 
@@ -497,45 +498,51 @@ get_xE_avx(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om)
 int
 p7_SSVFilter_avx(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float *ret_sc)
 {
-  uint16_t xE;
-  uint16_t xJ;
-
   if (om->tjb_b + om->tbm_b + om->tec_b + om->bias_b >= 127)
     return eslENORESULT;
 
-  xE = get_xE_avx(dsq, L, om);
-
-  /* Saturation floors every diagonal at the begin score (128), so a
-   * max of 128 means no diagonal scored above it and the true best
-   * may be lower; let the full MSV filter compute it. */
-  if (xE <= 128) return eslENORESULT;
-
-  if (xE >= 255 - om->bias_b) {
-    *ret_sc = eslINFINITY;
+  return p7_SSVFilter_FromXE(get_xE_avx(dsq, L, om), om, ret_sc);
+}
 
-    if (om->base_b - om->tjb_b - om->tbm_b < 128)
-      return eslENORESULT;
 
-    return eslERANGE;
+/* Function:  p7_SSVFilter_OrfBlock_avx()
+ * Synopsis:  SSV maximum of every ORF in a block, AVX2 path.
+ *
+ * Purpose:   See p7_SSVFilter_OrfBlock(). <xE[i]> is what get_xE_avx() gives
+ *            for ORF <i>. The bands depend only on the model, so they are laid
+ *            out once for the block.
+ */
+#define SSV_BLOCK_BANDS 64   /* bands laid out up front; enough for a model of 28,672 positions */
+void
+p7_SSVFilter_OrfBlock_avx(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE)
+{
+  __m256i beginv = _mm256_set1_epi8(-128);
+  __m256i xEv;
+  int     Q      = p7O_NQB_AVX(om->M);
+  int     bands  = (Q + MAX_BANDS - 1) / MAX_BANDS;
+  int     q0[SSV_BLOCK_BANDS];    /* first vector of each band */
+  int     w[SSV_BLOCK_BANDS];     /* its width                 */
+  int     last_q = 0;
+  int     q, b, i;
+
+  if (bands > SSV_BLOCK_BANDS) {
+    for (i = 0; i < n; i++) xE[i] = get_xE_avx(orf[i].dsq, (int) orf[i].n, om);
+    return;
   }
 
-  xE += om->base_b - om->tjb_b - om->tbm_b;
-  xE -= 128;
-
-  if (xE >= 255 - om->bias_b) {
-    *ret_sc = eslINFINITY;
-    return eslERANGE;
+  for (b = 0; b < bands; b++) {
+    q      = (Q * (b + 1)) / bands;
+    q0[b]  = last_q;
+    w[b]   = q - last_q;
+    last_q = q;
   }
 
-  xJ = xE - om->tec_b;
-
-  if (xJ > om->base_b) return eslENORESULT;
-
-  *ret_sc  = ((float)(xJ - om->tjb_b) - (float) om->base_b);
-  *ret_sc /= om->scale_b;
-  *ret_sc -= 3.0f;
-
-  return eslOK;
+  for (i = 0; i < n; i++) {
+    xEv = beginv;
+    for (b = 0; b < bands; b++)
+      xEv = fs[w[b]](orf[i].dsq, (int) orf[i].n, om, q0[b], beginv, xEv);
+    xE[i] = esl_avx_hmax_epu8(xEv);
+  }
 }
 
 #endif /* eslENABLE_AVX */
diff --git a/src/impl_avx/ssvfilter_sse.c b/src/impl_avx/ssvfilter_sse.c
@@ -500,45 +500,25 @@ get_xE_sse(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om)
 int
 p7_SSVFilter_sse(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float *ret_sc)
 {
-  uint16_t xE;
-  uint16_t xJ;
-
   if (om->tjb_b + om->tbm_b + om->tec_b + om->bias_b >= 127)
     return eslENORESULT;
 
-  xE = get_xE_sse(dsq, L, om);
-
-  /* Saturation floors every diagonal at the begin score (128), so a
-   * max of 128 means no diagonal scored above it and the true best
-   * may be lower; let the full MSV filter compute it. */
-  if (xE <= 128) return eslENORESULT;
-
-  if (xE >= 255 - om->bias_b) {
-    *ret_sc = eslINFINITY;
-
-    if (om->base_b - om->tjb_b - om->tbm_b < 128)
-      return eslENORESULT;
-
-    return eslERANGE;
-  }
-
-  xE += om->base_b - om->tjb_b - om->tbm_b;
-  xE -= 128;
-
-  if (xE >= 255 - om->bias_b) {
-    *ret_sc = eslINFINITY;
-    return eslERANGE;
-  }
-
-  xJ = xE - om->tec_b;
+  return p7_SSVFilter_FromXE(get_xE_sse(dsq, L, om), om, ret_sc);
+}
 
-  if (xJ > om->base_b) return eslENORESULT;
 
-  *ret_sc  = ((float)(xJ - om->tjb_b) - (float) om->base_b);
-  *ret_sc /= om->scale_b;
-  *ret_sc -= 3.0f;
+/* Function:  p7_SSVFilter_OrfBlock_sse()
+ * Synopsis:  SSV maximum of every ORF in a block, SSE path.
+ *
+ * Purpose:   See p7_SSVFilter_OrfBlock(). <xE[i]> is what get_xE_sse() gives
+ *            for ORF <i>.
+ */
+void
+p7_SSVFilter_OrfBlock_sse(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE)
+{
+  int i;
 
-  return eslOK;
+  for (i = 0; i < n; i++) xE[i] = get_xE_sse(orf[i].dsq, (int) orf[i].n, om);
 }
 
 #endif /* eslENABLE_SSE */
diff --git a/src/impl_sse/impl_sse.h b/src/impl_sse/impl_sse.h
@@ -502,6 +502,11 @@ extern void p7_oprofile_DestroyBlock(P7_OM_BLOCK *block);
 
 /* ssvfilter.c */
 extern int p7_SSVFilter    (const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, float *ret_sc);
+/* SSV over a block of ORFs: the pipeline can take each ORF's SSV maximum from
+ * one call, and turn it into the SSV filter's status and score itself */
+#define p7_SSV_ORFBLOCK 1
+extern int p7_SSVFilter_OrfBlock(const P7_OPROFILE *om, const ESL_ORF *orf, int n, uint8_t *xE);
+extern int p7_SSVFilter_FromXE(int xE, const P7_OPROFILE *om, float *ret_sc);
 
 /* msvfilter.c */
 extern int p7_MSVFilter           (const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *ret_sc);