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/* p7 model configuration for defining envelopes for truncated hits:
*
* Contents:
* 1. Routines in the exposed API.
*
* EPN, Mon Nov 21 10:02:03 2011
*/
#include "esl_config.h"
#include "p7_config.h"
#include "config.h"
#include <math.h>
#include <float.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#include "esl_vectorops.h"
#include "hmmer.h"
#include "infernal.h"
/*****************************************************************
* 1. Routines in the exposed API.
*****************************************************************/
/* Function: p7_ProfileConfig5PrimeTrunc()
*/
int
p7_ProfileConfig5PrimeTrunc(P7_PROFILE *gm, int L)
{
int status;
int k;
/* we should be in glocal mode */
assert(! p7_IsLocal(gm->mode));
/* Local mode entry, uniform: 1/M */
for (k = 1; k <= gm->M; k++)
p7P_TSC(gm, k-1, p7P_BM) = log(1. / gm->M); /* note off-by-one: entry at Mk stored as [k-1][BM] */
/* set profile's mode to UNIGLOCAL, even though we're really a hybrid of local/glocal
* We do this so p7_GForward, p7_GBackward set end scores to -eslINFINITY
* forcing us to only exit from last node of the model
*/
gm->mode = p7_UNIGLOCAL;
/* borrowed and modified from p7_ReconfigUnihit(),
* make J unreachable (unihit) and N->N transitions impossible (special to this func)
*/
gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_E][p7P_MOVE] = 0.0f;
gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_E][p7P_LOOP] = -eslINFINITY;
/* Remaining specials, [C][MOVE | LOOP] are set by ReconfigLength5PrimeTrunc()
*/
gm->L = 0; /* force ReconfigLength to reconfig */
if ((status = p7_ReconfigLength5PrimeTrunc(gm, L)) != eslOK) return status;
return eslOK;
}
/* Function: p7_ProfileConfig3PrimeTrunc()
*/
int
p7_ProfileConfig3PrimeTrunc(const P7_HMM *hmm, P7_PROFILE *gm, int L)
{
int status;
int k;
float Z;
/* we should be in glocal mode */
assert(! p7_IsLocal(gm->mode));
/* glocal mode entry: left wing retraction, must be in log space for precision
* (copied from HMMER's modelconfig.c:p7_ProfileConfig()) */
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]);
}
/* set profile's mode to UNILOCAL, even though we're really a hybrid of local/glocal
* We do this so p7_GForward, p7_GBackward do NOT set end scores to -eslINFINITY
* this allows us to exit from any model node (like local ends in a CP9)
*/
gm->mode = p7_UNILOCAL;
/* borrowed and modified from p7_ReconfigUnihit(),
* make J unreachable (unihit) and C->C transitions impossible (special to this func)
*/
gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_E][p7P_MOVE] = 0.0f;
gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_E][p7P_LOOP] = -eslINFINITY;
/* Remaining specials, [N][MOVE | LOOP] are set by ReconfigLength5PrimeTrunc()
*/
gm->L = 0; /* force ReconfigLength to reconfig */
if ((status = p7_ReconfigLength3PrimeTrunc(gm, L)) != eslOK) return status;
return eslOK;
}
/* Function: p7_ProfileConfig5PrimeAnd3PrimeTrunc()
*/
int
p7_ProfileConfig5PrimeAnd3PrimeTrunc(P7_PROFILE *gm, int L)
{
assert(gm->mode == p7_LOCAL);
/* gm should already be set up as local with equiprobable begins and ends,
* we just need to make it unihit, and make N->N and C->C transitions impossible
*/
gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_E][p7P_MOVE] = 0.0f;
gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_E][p7P_LOOP] = -eslINFINITY;
gm->nj = 0.0f;
gm->L = L;
gm->mode = p7_UNILOCAL;
/* don't call ReconfigLength() */
return eslOK;
}
/* Function: p7_ReconfigLength5PrimeTrunc()
*/
int
p7_ReconfigLength5PrimeTrunc(P7_PROFILE *gm, int L)
{
float ploop, pmove;
/* mode should be set as p7_UNIGLOCAL for 5' trunc case, even though its
* actually in a hybrid local/glocal mode. It's impt it is p7_UNIGLOCAL
* so it is behaves appropriately in other HMMER functions.
*/
assert(gm->mode == p7_UNIGLOCAL);
/* Configure C transitions so it bears the total
* unannotated sequence length L.
*/
pmove = (1.0f + gm->nj) / ((float) L + 1.0f + gm->nj); /* 1/(L+1) */
ploop = 1.0f - pmove;
gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = log(ploop); /* J should be irrelevant, b/c we've set unihit */
gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = log(pmove);
gm->L = L;
return eslOK;
}
/* Function: p7_ReconfigLength3PrimeTrunc()
*/
int
p7_ReconfigLength3PrimeTrunc(P7_PROFILE *gm, int L)
{
float ploop, pmove;
/* mode should be set as p7_UNILOCAL for 5' trunc case, even though its
* actually in a hybrid local/glocal mode. It's impt it is p7_UNILOCAL
* so it is behaves appropriately in other HMMER functions.
*/
assert(gm->mode == p7_UNILOCAL);
/* Configure N transitions so it bears the total
* unannotated sequence length L.
*/
pmove = (1.0f + gm->nj) / ((float) L + 1.0f + gm->nj); /* 1/(L+1) */
ploop = 1.0f - pmove;
gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = log(ploop); /* J should be irrelevant, b/c we've set unihit */
gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = log(pmove);
gm->L = L;
return eslOK;
}
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