/* M(i,k) is reached from B(i-1), M(i-1,k-1), D(i-1,k-1), or I(i-1,k-1). */
static inline int
select_m(const P7_OPROFILE *om, const P7_OMX *ox, int i, int k)
{
int Q = p7O_NQF(ox->M);
int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */
int r = (k-1) / Q;
vector float *tp = om->tfv + 7*q; /* *tp now at start of transitions to cur cell M(i,k) */
vector float xBv;
vector float zerov;
vector float mpv, dpv, ipv;
union { vector float v; float p[4]; } u, tv;
float path[4];
int state[4] = { p7T_M, p7T_I, p7T_D, p7T_B };
xBv = esl_vmx_set_float(ox->xmx[(i-1)*p7X_NXCELLS+p7X_B]);
zerov = (vector float) vec_splat_u32(0);
if (q > 0) {
mpv = ox->dpf[i-1][(q-1)*3 + p7X_M];
dpv = ox->dpf[i-1][(q-1)*3 + p7X_D];
ipv = ox->dpf[i-1][(q-1)*3 + p7X_I];
} else {
mpv = vec_sld(zerov, ox->dpf[i-1][(Q-1)*3 + p7X_M], 12);
dpv = vec_sld(zerov, ox->dpf[i-1][(Q-1)*3 + p7X_D], 12);
ipv = vec_sld(zerov, ox->dpf[i-1][(Q-1)*3 + p7X_I], 12);
}
/* paths are numbered so that most desirable choice in case of tie is first. */
u.v = xBv; tv.v = *tp; path[3] = ((tv.p[r] == 0.0) ? -eslINFINITY : u.p[r]); tp++;
u.v = mpv; tv.v = *tp; path[0] = ((tv.p[r] == 0.0) ? -eslINFINITY : u.p[r]); tp++;
u.v = ipv; tv.v = *tp; path[1] = ((tv.p[r] == 0.0) ? -eslINFINITY : u.p[r]); tp++;
u.v = dpv; tv.v = *tp; path[2] = ((tv.p[r] == 0.0) ? -eslINFINITY : u.p[r]);
return state[esl_vec_FArgMax(path, 4)];
}
/* Function: p7_emit_FancyConsensus()
* Synopsis: Emit a fancier consensus with upper/lower case and N/X's.
* Incept: SRE, Fri May 14 09:33:10 2010 [Janelia]
*
* Purpose: Generate a consensus sequence for model <hmm>, consisting
* of the maximum probability residue in each match state;
* store this sequence in text-mode <sq> provided by the caller.
*
* If the probability of the consensus residue is less than
* <min_lower>, show an ``any'' residue (N or X) instead.
* If the probability of the consensus residue is $\geq$
* <min_lower> and less than <min_upper>, show the residue
* as lower case; if it is $\geq$ <min_upper>, show it as
* upper case.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if the <sq> isn't in text mode.
*
* Xref: SRE:J6/59.
*/
int
p7_emit_FancyConsensus(const P7_HMM *hmm, float min_lower, float min_upper, ESL_SQ *sq)
{
int k, x;
float p;
char c;
int status;
if (! esl_sq_IsText(sq)) ESL_EXCEPTION(eslEINVAL, "p7_emit_FancyConsensus() expects a text-mode <sq>");
if ((status = esl_sq_GrowTo(sq, hmm->M)) != eslOK) return status;
for (k = 1; k <= hmm->M; k++)
{
if (hmm->mm && hmm->mm[k] == 'm') { //masked position, spit out the degenerate code
if ((status = esl_sq_CAddResidue(sq, tolower(esl_abc_CGetUnknown(hmm->abc))) ) != eslOK) return status;
} else {
p = esl_vec_FMax( hmm->mat[k], hmm->abc->K);
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
if (p < min_lower) c = tolower(esl_abc_CGetUnknown(hmm->abc));
else if (p >= min_upper) c = toupper(hmm->abc->sym[x]);
else c = tolower(hmm->abc->sym[x]);
if ((status = esl_sq_CAddResidue(sq, c)) != eslOK) return status;
}
}
if ((status = esl_sq_CAddResidue(sq, '\0')) != eslOK) return status;
return eslOK;
}
static inline int
select_m(const P7_PROFILE *gm, const P7_GMX *gx, int i, int k)
{
float **dp = gx->dp; /* so {MDI}MX() macros work */
float *xmx = gx->xmx; /* so XMX() macro works */
float const *tsc = gm->tsc; /* so TSCDELTA() macro works */
float path[4];
int state[4] = { p7T_M, p7T_I, p7T_D, p7T_B };
path[0] = TSCDELTA(p7P_MM, k-1) * MMX(i-1,k-1);
path[1] = TSCDELTA(p7P_IM, k-1) * IMX(i-1,k-1);
path[2] = TSCDELTA(p7P_DM, k-1) * DMX(i-1,k-1);
path[3] = TSCDELTA(p7P_BM, k-1) * XMX(i-1,p7G_B);
return state[esl_vec_FArgMax(path, 4)];
}
/* Function: p7_emit_SimpleConsensus()
* Synopsis: Generate simple consensus: ML residue in each match state
* Incept: SRE, Mon Sep 1 09:10:47 2008 [Janelia]
*
* Purpose: Generate a simple consensus sequence for model <hmm>
* consisting of the maximum probability residue in each
* match state; store this consensus in digital <sq>.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if the <sq> isn't in digital mode.
*/
int
p7_emit_SimpleConsensus(const P7_HMM *hmm, ESL_SQ *sq)
{
int k;
int x;
int status;
if (! esl_sq_IsDigital(sq)) ESL_EXCEPTION(eslEINVAL, "p7_emit_SimpleConsensus() expects a digital-mode <sq>");
if ((status = esl_sq_GrowTo(sq, hmm->M)) != eslOK) return status;
for (k = 1; k <= hmm->M; k++)
{
if (hmm->mm && hmm->mm[k] == 'm') { //masked position, spit out the degenerate code
if ((status = esl_sq_XAddResidue(sq, hmm->abc->Kp-3)) != eslOK) return status;
} else {
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
if ((status = esl_sq_XAddResidue(sq, x)) != eslOK) return status;
}
}
if ((status = esl_sq_XAddResidue(sq, eslDSQ_SENTINEL)) != eslOK) return status;
return eslOK;
}
/* Function: p7_ProfileConfig()
* Synopsis: Configure a search profile.
* Incept: SRE, Sun Sep 25 12:21:25 2005 [St. Louis]
*
* Purpose: Given a model <hmm> with core probabilities, the null1
* model <bg>, a desired search <mode> (one of <p7_LOCAL>,
* <p7_GLOCAL>, <p7_UNILOCAL>, or <p7_UNIGLOCAL>), and an
* expected target sequence length <L>; configure the
* search model in <gm> with lod scores relative to the
* background frequencies in <bg>.
*
* Returns: <eslOK> on success; the profile <gm> now contains
* scores and is ready for searching target sequences.
*
* Throws: <eslEMEM> on allocation error.
*/
int
p7_ProfileConfig(const P7_HMM *hmm, const P7_BG *bg, P7_PROFILE *gm, int L, int mode)
{
int k, x, z; /* counters over states, residues, annotation */
int status;
float *occ = NULL;
float *tp, *rp;
float sc[p7_MAXCODE];
float mthresh;
float Z;
/* Contract checks */
if (gm->abc->type != hmm->abc->type) ESL_XEXCEPTION(eslEINVAL, "HMM and profile alphabet don't match");
if (hmm->M > gm->allocM) ESL_XEXCEPTION(eslEINVAL, "profile too small to hold HMM");
/* Copy some pointer references and other info across from HMM */
gm->M = hmm->M;
gm->mode = mode;
gm->roff = -1;
gm->eoff = -1;
gm->offs[p7_MOFFSET] = -1;
gm->offs[p7_FOFFSET] = -1;
gm->offs[p7_POFFSET] = -1;
if (gm->name != NULL) free(gm->name);
if (gm->acc != NULL) free(gm->acc);
if (gm->desc != NULL) free(gm->desc);
if ((status = esl_strdup(hmm->name, -1, &(gm->name))) != eslOK) goto ERROR;
if ((status = esl_strdup(hmm->acc, -1, &(gm->acc))) != eslOK) goto ERROR;
if ((status = esl_strdup(hmm->desc, -1, &(gm->desc))) != eslOK) goto ERROR;
if (hmm->flags & p7H_RF) strcpy(gm->rf, hmm->rf);
if (hmm->flags & p7H_CS) strcpy(gm->cs, hmm->cs);
for (z = 0; z < p7_NEVPARAM; z++) gm->evparam[z] = hmm->evparam[z];
for (z = 0; z < p7_NCUTOFFS; z++) gm->cutoff[z] = hmm->cutoff[z];
for (z = 0; z < p7_MAXABET; z++) gm->compo[z] = hmm->compo[z];
/* Determine the "consensus" residue for each match position.
* This is only used for alignment displays, not in any calculations.
*/
if (hmm->abc->type == eslAMINO) mthresh = 0.5;
else if (hmm->abc->type == eslDNA) mthresh = 0.9;
else if (hmm->abc->type == eslRNA) mthresh = 0.9;
else mthresh = 0.5;
gm->consensus[0] = ' ';
for (k = 1; k <= hmm->M; k++) {
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
gm->consensus[k] = ((hmm->mat[k][x] > mthresh) ? toupper(hmm->abc->sym[x]) : tolower(hmm->abc->sym[x]));
}
gm->consensus[hmm->M+1] = '\0';
/* Entry scores. */
if (p7_profile_IsLocal(gm))
{
/* Local mode entry: occ[k] /( \sum_i occ[i] * (M-i+1))
* (Reduces to uniform 2/(M(M+1)) for occupancies of 1.0) */
Z = 0.;
ESL_ALLOC(occ, sizeof(float) * (hmm->M+1));
if ((status = p7_hmm_CalculateOccupancy(hmm, occ, NULL)) != eslOK) goto ERROR;
for (k = 1; k <= hmm->M; k++)
Z += occ[k] * (float) (hmm->M-k+1);
for (k = 1; k <= hmm->M; k++)
p7P_TSC(gm, k-1, p7P_BM) = log(occ[k] / Z); /* note off-by-one: entry at Mk stored as [k-1][BM] */
free(occ);
}
else /* glocal modes: left wing retraction; must be in log space for precision */
{
Z = log(hmm->t[0][p7H_MD]);
p7P_TSC(gm, 0, p7P_BM) = log(1.0 - hmm->t[0][p7H_MD]);
for (k = 1; k < hmm->M; k++)
{
p7P_TSC(gm, k, p7P_BM) = Z + log(hmm->t[k][p7H_DM]);
Z += log(hmm->t[k][p7H_DD]);
}
}
/* E state loop/move probabilities: nonzero for MOVE allows loops/multihits
* N,C,J transitions are set later by length config
*/
if (p7_profile_IsMultihit(gm)) {
gm->xsc[p7P_E][p7P_MOVE] = -eslCONST_LOG2;
gm->xsc[p7P_E][p7P_LOOP] = -eslCONST_LOG2;
gm->nj = 1.0f;
} else {
gm->xsc[p7P_E][p7P_MOVE] = 0.0f;
gm->xsc[p7P_E][p7P_LOOP] = -eslINFINITY;
gm->nj = 0.0f;
}
/* Transition scores. */
for (k = 1; k < gm->M; k++) {
tp = gm->tsc + k * p7P_NTRANS;
tp[p7P_MM] = log(hmm->t[k][p7H_MM]);
tp[p7P_MI] = log(hmm->t[k][p7H_MI]);
tp[p7P_MD] = log(hmm->t[k][p7H_MD]);
tp[p7P_IM] = log(hmm->t[k][p7H_IM]);
tp[p7P_II] = log(hmm->t[k][p7H_II]);
tp[p7P_DM] = log(hmm->t[k][p7H_DM]);
tp[p7P_DD] = log(hmm->t[k][p7H_DD]);
}
/* Match emission scores. */
sc[hmm->abc->K] = -eslINFINITY; /* gap character */
sc[hmm->abc->Kp-2] = -eslINFINITY; /* nonresidue character */
sc[hmm->abc->Kp-1] = -eslINFINITY; /* missing data character */
for (k = 1; k <= hmm->M; k++) {
for (x = 0; x < hmm->abc->K; x++)
sc[x] = log(hmm->mat[k][x] / bg->f[x]);
esl_abc_FExpectScVec(hmm->abc, sc, bg->f);
for (x = 0; x < hmm->abc->Kp; x++) {
rp = gm->rsc[x] + k * p7P_NR;
rp[p7P_MSC] = sc[x];
}
}
/* Insert emission scores */
/* SRE, Fri Dec 5 08:41:08 2008: We currently hardwire insert scores
* to 0, i.e. corresponding to the insertion emission probabilities
* being equal to the background probabilities. Benchmarking shows
* that setting inserts to informative emission distributions causes
* more problems than it's worth: polar biased composition hits
* driven by stretches of "insertion" occur, and are difficult to
* correct for.
*/
for (x = 0; x < gm->abc->Kp; x++)
{
for (k = 1; k < hmm->M; k++) p7P_ISC(gm, k, x) = 0.0f;
p7P_ISC(gm, hmm->M, x) = -eslINFINITY; /* init I_M to impossible. */
}
for (k = 1; k <= hmm->M; k++) p7P_ISC(gm, k, gm->abc->K) = -eslINFINITY; /* gap symbol */
for (k = 1; k <= hmm->M; k++) p7P_ISC(gm, k, gm->abc->Kp-2) = -eslINFINITY; /* nonresidue symbol */
for (k = 1; k <= hmm->M; k++) p7P_ISC(gm, k, gm->abc->Kp-1) = -eslINFINITY; /* missing data symbol */
#if 0
/* original (informative) insert setting: 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] = log(hmm->ins[k][x] / bg->f[x]);
esl_abc_FExpectScVec(hmm->abc, sc, bg->f);
for (x = 0; x < hmm->abc->Kp; x++) {
rp = gm->rsc[x] + k*p7P_NR;
rp[p7P_ISC] = sc[x];
}
}
for (x = 0; x < hmm->abc->Kp; x++)
p7P_ISC(gm, hmm->M, x) = -eslINFINITY; /* init I_M to impossible. */
#endif
/* Remaining specials, [NCJ][MOVE | LOOP] are set by ReconfigLength()
*/
gm->L = 0; /* force ReconfigLength to reconfig */
if ((status = p7_ReconfigLength(gm, L)) != eslOK) goto ERROR;
return eslOK;
ERROR:
if (occ != NULL) free(occ);
return status;
}
/* Function: p7_ProfileConfig()
* Synopsis: Configure a search profile.
* Incept: SRE, Sun Sep 25 12:21:25 2005 [St. Louis]
*
* Purpose: Given a model <hmm> with core probabilities, the null1
* model <bg>, a desired search <mode> (one of <p7_LOCAL>,
* <p7_GLOCAL>, <p7_UNILOCAL>, or <p7_UNIGLOCAL>), and an
* expected target sequence length <L>; configure the
* search model in <gm> with lod scores relative to the
* background frequencies in <bg>.
*
* Returns: <eslOK> on success; the profile <gm> now contains
* scores and is ready for searching target sequences.
*
* Throws: <eslEMEM> on allocation error.
*/
int
p7_ProfileConfig(const P7_HMM *hmm, const P7_BG *bg, P7_PROFILE *gm, int L, int mode)
{
int k, x, z; /* counters over states, residues, annotation */
int status;
float *occ = NULL;
float *tp, *rp;
float sc[p7_MAXCODE];
float mthresh;
float Z;
/* Contract checks */
if (gm->abc->type != hmm->abc->type) ESL_XEXCEPTION(eslEINVAL, "HMM and profile alphabet don't match");
if (hmm->M > gm->allocM) ESL_XEXCEPTION(eslEINVAL, "profile too small to hold HMM");
/* Copy some pointer references and other info across from HMM */
gm->M = hmm->M;
gm->mode = mode;
gm->roff = -1;
gm->eoff = -1;
gm->offs[p7_MOFFSET] = -1;
gm->offs[p7_FOFFSET] = -1;
gm->offs[p7_POFFSET] = -1;
if (gm->name != NULL) free(gm->name);
if (gm->acc != NULL) free(gm->acc);
if (gm->desc != NULL) free(gm->desc);
if ((status = esl_strdup(hmm->name, -1, &(gm->name))) != eslOK) goto ERROR;
if ((status = esl_strdup(hmm->acc, -1, &(gm->acc))) != eslOK) goto ERROR;
if ((status = esl_strdup(hmm->desc, -1, &(gm->desc))) != eslOK) goto ERROR;
if (hmm->flags & p7H_RF) strcpy(gm->rf, hmm->rf);
if (hmm->flags & p7H_CS) strcpy(gm->cs, hmm->cs);
for (z = 0; z < p7_NEVPARAM; z++) gm->evparam[z] = hmm->evparam[z];
for (z = 0; z < p7_NCUTOFFS; z++) gm->cutoff[z] = hmm->cutoff[z];
for (z = 0; z < p7_MAXABET; z++) gm->compo[z] = hmm->compo[z];
/* Determine the "consensus" residue for each match position.
* This is only used for alignment displays, not in any calculations.
*/
if (hmm->abc->type == eslAMINO) mthresh = 0.5;
else if (hmm->abc->type == eslDNA) mthresh = 0.9;
else if (hmm->abc->type == eslRNA) mthresh = 0.9;
else mthresh = 0.5;
gm->consensus[0] = ' ';
for (k = 1; k <= hmm->M; k++) {
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
gm->consensus[k] = ((hmm->mat[k][x] > mthresh) ? toupper(hmm->abc->sym[x]) : tolower(hmm->abc->sym[x]));
}
gm->consensus[hmm->M+1] = '\0';
/* Entry scores. */
if (p7_profile_IsLocal(gm))
{
/* Local mode entry: occ[k] /( \sum_i occ[i] * (M-i+1))
* (Reduces to uniform 2/(M(M+1)) for occupancies of 1.0) */
Z = 0.;
ESL_ALLOC_WITH_TYPE(occ, float*, sizeof(float) * (hmm->M+1));
if ((status = p7_hmm_CalculateOccupancy(hmm, occ, NULL)) != eslOK) goto ERROR;
for (k = 1; k <= hmm->M; k++)
Z += occ[k] * (float) (hmm->M-k+1);
for (k = 1; k <= hmm->M; k++)
p7P_TSC(gm, k-1, p7P_BM) = log((double)(occ[k] / Z)); /* note off-by-one: entry at Mk stored as [k-1][BM] */
free(occ);
}
else /* glocal modes: left wing retraction; must be in log space for precision */
{
