/* Function: p7_GOATrace()
* Synopsis: Optimal accuracy decoding: traceback.
* Incept: SRE, Fri Feb 29 12:59:11 2008 [Janelia]
*
* Purpose: The traceback stage of the optimal accuracy decoding algorithm
* \citep{Kall05}.
*
* Caller provides the OA DP matrix <gx> that was just
* calculated by <p7_GOptimalAccuracy()>, as well as the
* posterior decoding matrix <pp>, which was calculated by
* Forward/Backward on a target sequence of length <L>
* using the query model <gm>.
*
* Caller provides an empty traceback structure <tr> to
* hold the result, allocated to hold optional posterior
* probability annotation on residues (with
* <p7_trace_CreateWithPP()>, generally). This will be
* internally reallocated as needed for larger traces.
*
* Args: gm - query profile
* pp - posterior decoding matrix created by <p7_PosteriorDecoding()>
* gx - OA DP matrix calculated by <p7_OptimalAccuracyDP()>
* tr - RESULT: OA traceback, allocated with posterior probs
*
* Returns: <eslOK> on success, and <tr> contains the OA traceback.
*
* Throws: <eslEMEM> on allocation error.
*/
int
p7_GOATrace(const P7_PROFILE *gm, const P7_GMX *pp, const P7_GMX *gx, P7_TRACE *tr)
{
int i = gx->L; /* position in seq (1..L) */
int k = 0; /* position in model (1..M) */
float postprob;
int sprv, scur;
int status;
#ifdef p7_DEBUGGING
if (tr->N != 0) ESL_EXCEPTION(eslEINVAL, "trace isn't empty: forgot to Reuse()?");
#endif
if ((status = p7_trace_AppendWithPP(tr, p7T_T, k, i, 0.0)) != eslOK) return status;
if ((status = p7_trace_AppendWithPP(tr, p7T_C, k, i, 0.0)) != eslOK) return status;
sprv = p7T_C;
while (sprv != p7T_S)
{
switch (sprv) {
case p7T_M: scur = select_m(gm, gx, i, k); k--; i--; break;
case p7T_D: scur = select_d(gm, gx, i, k); k--; break;
case p7T_I: scur = select_i(gm, gx, i, k); i--; break;
case p7T_N: scur = select_n(i); break;
case p7T_C: scur = select_c(gm, pp, gx, i); break;
case p7T_J: scur = select_j(gm, pp, gx, i); break;
case p7T_E: scur = select_e(gm, gx, i, &k); break;
case p7T_B: scur = select_b(gm, gx, i); break;
default: ESL_EXCEPTION(eslEINVAL, "bogus state in traceback");
}
if (scur == -1) ESL_EXCEPTION(eslEINVAL, "OA traceback choice failed");
postprob = get_postprob(pp, scur, sprv, k, i);
if ((status = p7_trace_AppendWithPP(tr, scur, k, i, postprob)) != eslOK) return status;
/* For NCJ, we had to defer i decrement. */
if ( (scur == p7T_N || scur == p7T_J || scur == p7T_C) && scur == sprv) i--;
sprv = scur;
}
tr->M = gm->M;
tr->L = gx->L;
return p7_trace_Reverse(tr);
}
/* Function: p7_StochasticTrace()
* Synopsis: Sample a traceback from a Forward matrix
* Incept: SRE, Fri Aug 8 17:40:18 2008 [UA217, IAD-SFO]
*
* Purpose: Perform a stochastic traceback from Forward matrix <ox>,
* using random number generator <r>, in order to sample an
* alignment of model <om> to digital sequence <dsq> of
* length <L>.
*
* The sampled traceback is returned in <tr>, which the
* caller provides with at least an initial allocation;
* the <tr> allocation will be grown as needed here.
*
* Args: r - source of random numbers
* dsq - digital sequence being aligned, 1..L
* L - length of dsq
* om - profile
* ox - Forward matrix to trace, LxM
* tr - storage for the recovered traceback
*
* Returns: <eslOK> on success
*
* Throws: <eslEMEM> on allocation error.
* <eslEINVAL> on several types of problems, including:
* the trace isn't empty (wasn't Reuse()'d);
*/
int
p7_StochasticTrace(ESL_RANDOMNESS *rng, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *ox,
P7_TRACE *tr)
{
int i; /* position in sequence 1..L */
int k; /* position in model 1..M */
int s0, s1; /* choice of a state */
int status;
if (tr->N != 0) ESL_EXCEPTION(eslEINVAL, "trace not empty; needs to be Reuse()'d?");
i = L;
k = 0;
if ((status = p7_trace_Append(tr, p7T_T, k, i)) != eslOK) return status;
if ((status = p7_trace_Append(tr, p7T_C, k, i)) != eslOK) return status;
s0 = tr->st[tr->N-1];
while (s0 != p7T_S)
{
switch (s0) {
case p7T_M: s1 = select_m(rng, om, ox, i, k); k--; i--; break;
case p7T_D: s1 = select_d(rng, om, ox, i, k); k--; break;
case p7T_I: s1 = select_i(rng, om, ox, i, k); i--; break;
case p7T_N: s1 = select_n(i); break;
case p7T_C: s1 = select_c(rng, om, ox, i); break;
case p7T_J: s1 = select_j(rng, om, ox, i); break;
case p7T_E: s1 = select_e(rng, om, ox, i, &k); break;
case p7T_B: s1 = select_b(rng, om, ox, i); break;
default: ESL_EXCEPTION(eslEINVAL, "bogus state in traceback");
}
if (s1 == -1) ESL_EXCEPTION(eslEINVAL, "Stochastic traceback choice failed");
if ((status = p7_trace_Append(tr, s1, k, i)) != eslOK) return status;
if ( (s1 == p7T_N || s1 == p7T_J || s1 == p7T_C) && s1 == s0) i--;
s0 = s1;
} /* end traceback, at S state */
tr->M = om->M;
tr->L = L;
return p7_trace_Reverse(tr);
}
/* Function: p7_OATrace()
* Synopsis: Optimal accuracy decoding: traceback.
* Incept: SRE, Mon Aug 18 13:53:33 2008 [Janelia]
*
* Purpose: The traceback stage of the optimal accuracy decoding algorithm
* \citep{Kall05}.
*
* Caller provides the OA DP matrix <ox> that was just
* calculated by <p7_OptimalAccuracyDP()>, as well as the
* posterior decoding matrix <pp>, which was calculated by
* Forward/Backward on a target sequence using the query
* model <gm>. Because the calculation depends only on
* <pp>, the target sequence itself need not be provided.
*
* The resulting optimal accuracy decoding traceback is put
* in a caller-provided traceback structure <tr>, which the
* caller has allocated for optional posterior probability
* annotation on residues (with <p7_trace_CreateWithPP()>,
* generally). This structure will be reallocated
* internally if necessary.
*
* Args: om - profile
* pp - posterior probability matrix
* ox - OA matrix to trace, LxM
* tr - storage for the recovered traceback
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation error.
* <eslEINVAL> if the trace <tr> isn't empty (needs to be Reuse()'d).
*/
int
p7_OATrace(const P7_OPROFILE *om, const P7_OMX *pp, const P7_OMX *ox, P7_TRACE *tr)
{
int i = ox->L; /* position in sequence 1..L */
int k = 0; /* position in model 1..M */
int s0, s1; /* choice of a state */
float postprob;
int status;
if (tr->N != 0) ESL_EXCEPTION(eslEINVAL, "trace not empty; needs to be Reuse()'d?");
if ((status = p7_trace_AppendWithPP(tr, p7T_T, k, i, 0.0)) != eslOK) return status;
if ((status = p7_trace_AppendWithPP(tr, p7T_C, k, i, 0.0)) != eslOK) return status;
s0 = tr->st[tr->N-1];
while (s0 != p7T_S)
{
switch (s0) {
case p7T_M: s1 = select_m(om, ox, i, k); k--; i--; break;
case p7T_D: s1 = select_d(om, ox, i, k); k--; break;
case p7T_I: s1 = select_i(om, ox, i, k); i--; break;
case p7T_N: s1 = select_n(i); break;
case p7T_C: s1 = select_c(om, pp, ox, i); break;
case p7T_J: s1 = select_j(om, pp, ox, i); break;
case p7T_E: s1 = select_e(om, ox, i, &k); break;
case p7T_B: s1 = select_b(om, ox, i); break;
default: ESL_EXCEPTION(eslEINVAL, "bogus state in traceback");
}
if (s1 == -1) ESL_EXCEPTION(eslEINVAL, "OA traceback choice failed");
postprob = get_postprob(pp, s1, s0, k, i);
if ((status = p7_trace_AppendWithPP(tr, s1, k, i, postprob)) != eslOK) return status;
if ( (s1 == p7T_N || s1 == p7T_J || s1 == p7T_C) && s1 == s0) i--;
s0 = s1;
} /* end traceback, at S state */
tr->M = om->M;
tr->L = ox->L;
return p7_trace_Reverse(tr);
}
/* Basic select() implementation on top of poll() */
int select (int nfds,
fd_set * readfds,
fd_set * writefds,
fd_set * exceptfds,
struct timeval * timeout)
{
int timeout_ms, error, i;
int poll_fd_idx = 0;
int num_fds = 0;
struct pollfd *req = NULL;
size_t max_size = sizeof(struct pollfd) * nfds;
select_d("select(nfds=%d, readfds=0x%lx, writefds=0x%lx, exceptfds=0x%lx, timeout=0x%lx)",
nfds, readfds, writefds, exceptfds, timeout);
if ((nfds < 0) || (nfds > FD_SETSIZE+1)) {
select_d("select() failed 1");
errno = EINVAL;
return -1;
}
/* Some programs call select() with nfds=0 in order to sleep */
if (nfds == 0) {
struct timespec ts = {};
if (timeout == NULL) {
errno = EINVAL;
return -1;
}
ts.tv_sec = timeout->tv_sec;
ts.tv_nsec = timeout->tv_usec * 1000;
nanosleep(&ts, 0);
return 0;
}
req = malloc(max_size);
if (req == NULL) {
select_d("select() failed no memory");
errno = ENOMEM;
return -1;
}
/* prepare poll request */
for (i=0; i < nfds; i++) {
short int events = 0;
if (readfds) {
/* read_fds */
if (FD_ISSET(i, readfds))
events = POLLIN;
}
if (writefds) {
/* write_fds */
if (FD_ISSET(i, writefds))
events |= POLLOUT;
}
if (events) {
req[poll_fd_idx].fd = i;
req[poll_fd_idx].events = events;
req[poll_fd_idx].revents = 0;
poll_fd_idx++;
}
}
if (timeout) {
/* FIXME: we use a ms granularity while select uses timeval (microsec) */
timeout_ms = timeout->tv_sec * 1000 + timeout->tv_usec/1000;
} else {
timeout_ms = -1;
}
select_d("select() timeout_ms=%d", timeout_ms);
/* call poll() */
error = poll(req, poll_fd_idx, timeout_ms);
if (error < 0) {
select_d("select() poll() failed");
free(req);
return -1;
}
/* handle result */
if (readfds)
FD_ZERO(readfds);
if (writefds)
FD_ZERO(writefds);
if (exceptfds)
FD_ZERO(exceptfds);
for (i=0; i < poll_fd_idx; i++) {
if (req[i].revents == 0)
continue;
if (req[i].revents & POLLNVAL) {
errno = EBADF;
error = -1;
break;
}
bool event = false;
if (readfds) {
if (req[i].revents & (POLLIN | POLLHUP | POLLERR)) {
FD_SET(req[i].fd, readfds);
event = true;
}
}
if (writefds) {
if (req[i].revents & (POLLOUT | POLLRDHUP | POLLERR)) {
FD_SET(req[i].fd, writefds);
event = true;
}
}
if (exceptfds) {
if (req[i].revents & POLLPRI) {
FD_SET(req[i].fd, exceptfds);
event = true;
}
}
if (event) {
num_fds++;
}
}
free(req);
if (error == -1)
return -1;
select_d("select() return: %d", num_fds);
return num_fds;
}