/* Function: p7_GNull2_ByTrace()
* Synopsis: Assign null2 scores to an envelope by the sampling method.
* Incept: SRE, Thu May 1 10:00:43 2008 [Janelia]
*
* Purpose: Given a traceback <tr> for an alignment of model <gm> to
* some target sequence; calculate null2 odds ratios $\frac{f'{x}}{f{x}}$
* as the state-usage-weighted emission probabilities,
* with state usages calculated by counting emissions used
* at positions <zstart..zend> in the trace.
*
* Because we only need to collect state usages from the
* trace <tr>, the target sequence is irrelevant. Because
* we are only averaging emission odds ratios from model
* <gm>, the configuration of <gm> is irrelevant (uni
* vs. multihit, or length config).
*
* Args: gm - model, in any configuration; only emission odds are used
* tr - traceback for any region (or all) of a target sequence
* zstart - first elem in <tr> to collect from; use 0 for complete
* zend - last elem in <tr> to collect from; use tr->N-1 for complete
* wrk - DP matrix w/ at least one row, for workspace
* null2 - RESULT: odds ratios f'(x)/f(x) for all Kp residues
*
* Returns: <eslOK> on success, and the <ddef->n2sc> scores are set
* for region <i..j>.
*
* Throws: <eslEMEM> on allocation error.
*/
int
p7_GNull2_ByTrace(const P7_PROFILE *gm, const P7_TRACE *tr, int zstart, int zend, P7_GMX *wrk, float *null2)
{
float **dp = wrk->dp; /* so that {MDI}MX() macros work */
float *xmx = wrk->xmx; /* so that XMX() macro works */
int Ld = 0;
int M = gm->M;
int k; /* index over model position */
int x; /* index over residues */
int z; /* index over trace position */
float xfactor;
/* We'll use the i=0 row in wrk for working space: dp[0][] and xmx[0..4]. */
esl_vec_FSet(wrk->dp[0], (M+1)*p7G_NSCELLS, 0.0);
esl_vec_FSet(wrk->xmx, p7G_NXCELLS, 0.0);
/* Calculate emitting state usage in this particular trace segment: */
for (z = zstart; z <= zend; z++)
{
switch (tr->st[z]) {
case p7T_M: Ld++; MMX(0,tr->k[z]) += 1.0; break;
case p7T_I: Ld++; IMX(0,tr->k[z]) += 1.0; break;
case p7T_N: if (tr->st[z-1] == p7T_N) { Ld++; XMX(0,p7G_N) += 1.0; } break;
case p7T_C: if (tr->st[z-1] == p7T_C) { Ld++; XMX(0,p7G_C) += 1.0; } break;
case p7T_J: if (tr->st[z-1] == p7T_J) { Ld++; XMX(0,p7G_J) += 1.0; } break;
}
}
esl_vec_FScale(wrk->dp[0], (M+1)*p7G_NSCELLS, (1.0 / (float) Ld));
esl_vec_FScale(wrk->xmx, p7G_NXCELLS, (1.0 / (float) Ld));
/* Calculate null2's odds ratio emission probabilities, by taking
* posterior weighted sum over all emission vectors used in paths
* explaining the domain.
*/
esl_vec_FSet(null2, gm->abc->K, 0.0);
xfactor = XMX(0,p7G_N) + XMX(0,p7G_C) + XMX(0,p7G_J);
for (x = 0; x < gm->abc->K; x++)
{
for (k = 1; k < M; k++)
{
null2[x] += MMX(0,k) * expf(p7P_MSC(gm, k, x));
null2[x] += IMX(0,k) * expf(p7P_ISC(gm, k, x));
}
null2[x] += MMX(0,M) * expf(p7P_MSC(gm, M, x));
null2[x] += xfactor;
}
/* now null2[x] = \frac{f_d(x)}{f_0(x)} odds ratios for all x in alphabet,
* 0..K-1, where f_d(x) are the ad hoc "null2" residue frequencies
* for this envelope.
*/
/* make valid scores for all degeneracies, by averaging the odds ratios. */
esl_abc_FAvgScVec(gm->abc, null2);
null2[gm->abc->K] = 1.0; /* gap character */
null2[gm->abc->Kp-2] = 1.0; /* nonresidue "*" */
null2[gm->abc->Kp-1] = 1.0; /* missing data "~" */
return eslOK;
}
/* Function: p7_Null2_ByExpectation()
* Synopsis: Calculate null2 model from posterior probabilities.
* Incept: SRE, Mon Aug 18 08:32:55 2008 [Janelia]
*
* Purpose: Identical to <p7_GNull2_ByExpectation()> except that
* <om>, <pp> are SSE optimized versions of the profile
* and the residue posterior probability matrix. See
* <p7_GNull2_ByExpectation()> documentation.
*
* Args: om - profile, in any mode, target length model set to <L>
* pp - posterior prob matrix, for <om> against domain envelope <dsq+i-1> (offset)
* null2 - RETURN: null2 log odds scores per residue; <0..Kp-1>; caller allocated space
*/
int
p7_Null2_ByExpectation(const P7_OPROFILE *om, const P7_OMX *pp, float *null2)
{
int M = om->M;
int Ld = pp->L;
int Q = p7O_NQF(M);
float *xmx = pp->xmx; /* enables use of XMXo(i,s) macro */
float norm;
__m128 *rp;
__m128 sv;
float xfactor;
int i,q,x;
/* Calculate expected # of times that each emitting state was used
* in generating the Ld residues in this domain.
* The 0 row in <wrk> is used to hold these numbers.
*/
memcpy(pp->dpf[0], pp->dpf[1], sizeof(__m128) * 3 * Q);
XMXo(0,p7X_N) = XMXo(1,p7X_N);
XMXo(0,p7X_C) = XMXo(1,p7X_C); /* 0.0 */
XMXo(0,p7X_J) = XMXo(1,p7X_J); /* 0.0 */
for (i = 2; i <= Ld; i++)
{
for (q = 0; q < Q; q++)
{
pp->dpf[0][q*3 + p7X_M] = _mm_add_ps(pp->dpf[i][q*3 + p7X_M], pp->dpf[0][q*3 + p7X_M]);
pp->dpf[0][q*3 + p7X_I] = _mm_add_ps(pp->dpf[i][q*3 + p7X_I], pp->dpf[0][q*3 + p7X_I]);
}
XMXo(0,p7X_N) += XMXo(i,p7X_N);
XMXo(0,p7X_C) += XMXo(i,p7X_C);
XMXo(0,p7X_J) += XMXo(i,p7X_J);
}
/* Convert those expected #'s to frequencies, to use as posterior weights. */
norm = 1.0 / (float) Ld;
sv = _mm_set1_ps(norm);
for (q = 0; q < Q; q++)
{
pp->dpf[0][q*3 + p7X_M] = _mm_mul_ps(pp->dpf[0][q*3 + p7X_M], sv);
pp->dpf[0][q*3 + p7X_I] = _mm_mul_ps(pp->dpf[0][q*3 + p7X_I], sv);
}
XMXo(0,p7X_N) *= norm;
XMXo(0,p7X_C) *= norm;
XMXo(0,p7X_J) *= norm;
/* Calculate null2's emission odds, by taking posterior weighted sum
* over all emission vectors used in paths explaining the domain.
*/
xfactor = XMXo(0, p7X_N) + XMXo(0, p7X_C) + XMXo(0, p7X_J);
for (x = 0; x < om->abc->K; x++)
{
sv = _mm_setzero_ps();
rp = om->rfv[x];
for (q = 0; q < Q; q++)
{
sv = _mm_add_ps(sv, _mm_mul_ps(pp->dpf[0][q*3 + p7X_M], *rp)); rp++;
sv = _mm_add_ps(sv, pp->dpf[0][q*3 + p7X_I]); /* insert odds implicitly 1.0 */
// sv = _mm_add_ps(sv, _mm_mul_ps(pp->dpf[0][q*3 + p7X_I], *rp)); rp++;
}
esl_sse_hsum_ps(sv, &(null2[x]));
null2[x] += xfactor;
}
/* now null2[x] = \frac{f_d(x)}{f_0(x)} for all x in alphabet,
* 0..K-1, where f_d(x) are the ad hoc "null2" residue frequencies
* for this envelope.
*/
/* make valid scores for all degeneracies, by averaging the odds ratios. */
esl_abc_FAvgScVec(om->abc, null2);
null2[om->abc->K] = 1.0; /* gap character */
null2[om->abc->Kp-2] = 1.0; /* nonresidue "*" */
null2[om->abc->Kp-1] = 1.0; /* missing data "~" */
return eslOK;
}
/* Function: p7_Null2_ByTrace()
* Synopsis: Assign null2 scores to an envelope by the sampling method.
* Incept: SRE, Mon Aug 18 10:22:49 2008 [Janelia]
*
* Purpose: Identical to <p7_GNull2_ByTrace()> except that
* <om>, <wrk> are SSE optimized versions of the profile
* and the residue posterior probability matrix. See
* <p7_GNull2_ByTrace()> documentation.
*/
int
p7_Null2_ByTrace(const P7_OPROFILE *om, const P7_TRACE *tr, int zstart, int zend, P7_OMX *wrk, float *null2)
{
union { __m128 v; float p[4]; } u;
int Q = p7O_NQF(om->M);
int Ld = 0;
float *xmx = wrk->xmx; /* enables use of XMXo macro */
float norm;
float xfactor;
__m128 sv;
__m128 *rp;
int q, r, s;
int x;
int z;
/* We'll use the i=0 row in wrk for working space: dp[0][] and xmx[][0]. */
for (q = 0; q < Q; q++)
{
wrk->dpf[0][q*3 + p7X_M] = _mm_setzero_ps();
wrk->dpf[0][q*3 + p7X_I] = _mm_setzero_ps();
}
XMXo(0,p7X_N) = 0.0;
XMXo(0,p7X_C) = 0.0;
XMXo(0,p7X_J) = 0.0;
/* Calculate emitting state usage in this particular trace segment */
for (z = zstart; z <= zend; z++)
{
if (tr->i[z] == 0) continue; /* quick test for whether this trace elem emitted or not */
Ld++;
if (tr->k[z] > 0) /* must be an M or I */
{ /* surely there's an easier way? but our workspace is striped, interleaved quads... */
s = ( (tr->st[z] == p7T_M) ? p7X_M : p7X_I);
q = p7X_NSCELLS * ( (tr->k[z] - 1) % Q) + p7X_M;
r = (tr->k[z] - 1) / Q;
u.v = wrk->dpf[0][q];
u.p[r] += 1.0; /* all this to increment a count by one! */
wrk->dpf[0][q] = u.v;
}
else /* emitted an x_i with no k; must be an N,C,J */
{
switch (tr->st[z]) {
case p7T_N: XMXo(0,p7X_N) += 1.0; break;
case p7T_C: XMXo(0,p7X_C) += 1.0; break;
case p7T_J: XMXo(0,p7X_J) += 1.0; break;
}
}
}
norm = 1.0 / (float) Ld;
sv = _mm_set1_ps(norm);
for (q = 0; q < Q; q++)
{
wrk->dpf[0][q*3 + p7X_M] = _mm_mul_ps(wrk->dpf[0][q*3 + p7X_M], sv);
wrk->dpf[0][q*3 + p7X_I] = _mm_mul_ps(wrk->dpf[0][q*3 + p7X_I], sv);
}
XMXo(0,p7X_N) *= norm;
XMXo(0,p7X_C) *= norm;
XMXo(0,p7X_J) *= norm;
/* Calculate null2's emission odds, by taking posterior weighted sum
* over all emission vectors used in paths explaining the domain.
*/
xfactor = XMXo(0,p7X_N) + XMXo(0,p7X_C) + XMXo(0,p7X_J);
for (x = 0; x < om->abc->K; x++)
{
sv = _mm_setzero_ps();
rp = om->rfv[x];
for (q = 0; q < Q; q++)
{
sv = _mm_add_ps(sv, _mm_mul_ps(wrk->dpf[0][q*3 + p7X_M], *rp)); rp++;
sv = _mm_add_ps(sv, wrk->dpf[0][q*3 + p7X_I]); /* insert emission odds implicitly 1.0 */
// sv = _mm_add_ps(sv, _mm_mul_ps(wrk->dpf[0][q*3 + p7X_I], *rp)); rp++;
}
esl_sse_hsum_ps(sv, &(null2[x]));
null2[x] += xfactor;
}
/* now null2[x] = \frac{f_d(x)}{f_0(x)} for all x in alphabet,
* 0..K-1, where f_d(x) are the ad hoc "null2" residue frequencies
* for this envelope.
*/
/* make valid scores for all degeneracies, by averaging the odds ratios. */
esl_abc_FAvgScVec(om->abc, null2);
null2[om->abc->K] = 1.0; /* gap character */
null2[om->abc->Kp-2] = 1.0; /* nonresidue "*" */
null2[om->abc->Kp-1] = 1.0; /* missing data "~" */
return eslOK;
}
/* Function: p7_GNull2_ByExpectation()
* Synopsis: Calculate null2 model from posterior probabilities.
* Incept: SRE, Thu Feb 28 09:52:28 2008 [Janelia]
*
* Purpose: Calculate the "null2" model for the envelope encompassed
* by a posterior probability calculation <pp> for model
* <gm>. Return the null2 odds emission probabilities
* $\frac{f'{x}}{f{x}}$ in <null2>, which caller
* provides as space for at least <alphabet->Kp> residues.
*
* The expectation method is applied to envelopes in
* simple, well resolved regions (regions containing just a
* single envelope, where no stochastic traceback
* clustering was required).
*
* Make sure that the posterior probability matrix <pp> has
* been calculated by the caller for only the envelope; thus
* its rows are numbered <1..Ld>, for envelope <ienv..jenv>
* of length <Ld=jenv-ienv+1>.
*
* Args: gm - profile, in any mode, target length model set to <L>
* pp - posterior prob matrix, for <gm> against domain envelope <dsq+i-1> (offset)
* null2 - RETURN: null2 odds ratios per residue; <0..Kp-1>; caller allocated space
*
* Returns: <eslOK> on success; <null2> contains the null2 scores. The 0
* row of <pp> has been used as temp space, and happens to contain
* the expected frequency that each M,I,N,C,J state is used in this
* <pp> matrix to generate residues.
*
* Throws: (no abnormal error conditions)
*/
int
p7_GNull2_ByExpectation(const P7_PROFILE *gm, P7_GMX *pp, float *null2)
{
int M = gm->M;
int Ld = pp->L;
float **dp = pp->dp;
float *xmx = pp->xmx;
float xfactor;
int x; /* over symbols 0..K-1 */
int i; /* over offset envelope dsq positions 1..Ld */
int k; /* over model M states 1..M, I states 1..M-1 */
/* Calculate expected # of times that each emitting state was used
* in generating the Ld residues in this domain.
* The 0 row in <wrk> is used to hold these numbers.
*/
esl_vec_FCopy(pp->dp[1], (M+1)*p7G_NSCELLS, pp->dp[0]);
esl_vec_FCopy(pp->xmx+p7G_NXCELLS, p7G_NXCELLS, pp->xmx);
for (i = 2; i <= Ld; i++)
{
esl_vec_FAdd(pp->dp[0], pp->dp[i], (M+1)*p7G_NSCELLS);
esl_vec_FAdd(pp->xmx, pp->xmx+i*p7G_NXCELLS, p7G_NXCELLS);
}
/* Convert those expected #'s to log frequencies; these we'll use as
* the log posterior weights.
*/
esl_vec_FLog(pp->dp[0], (M+1)*p7G_NSCELLS);
esl_vec_FLog(pp->xmx, p7G_NXCELLS);
esl_vec_FIncrement(pp->dp[0], (M+1)*p7G_NSCELLS, -log((float)Ld));
esl_vec_FIncrement(pp->xmx, p7G_NXCELLS, -log((float)Ld));
/* Calculate null2's log odds emission probabilities, by taking
* posterior weighted sum over all emission vectors used in paths
* explaining the domain.
* This is dog-slow; a point for future optimization.
*/
xfactor = XMX(0,p7G_N);
xfactor = p7_FLogsum(xfactor, XMX(0,p7G_C));
xfactor = p7_FLogsum(xfactor, XMX(0,p7G_J));
esl_vec_FSet(null2, gm->abc->K, -eslINFINITY);
for (x = 0; x < gm->abc->K; x++)
{
for (k = 1; k < M; k++)
{
null2[x] = p7_FLogsum(null2[x], MMX(0,k) + p7P_MSC(gm, k, x));
null2[x] = p7_FLogsum(null2[x], IMX(0,k) + p7P_ISC(gm, k, x));
}
null2[x] = p7_FLogsum(null2[x], MMX(0,M) + p7P_MSC(gm, k, x));
null2[x] = p7_FLogsum(null2[x], xfactor);
}
esl_vec_FExp (null2, gm->abc->K);
/* now null2[x] = \frac{f_d(x)}{f_0(x)} for all x in alphabet,
* 0..K-1, where f_d(x) are the ad hoc "null2" residue frequencies
* for this envelope.
*/
/* make valid scores for all degeneracies, by averaging the odds ratios. */
esl_abc_FAvgScVec(gm->abc, null2); /* does not set gap, nonres, missing */
null2[gm->abc->K] = 1.0; /* gap character */
null2[gm->abc->Kp-2] = 1.0; /* nonresidue "*" */
null2[gm->abc->Kp-1] = 1.0; /* missing data "~" */
return eslOK;
}