/* Function: cp9_Clone()
* Date: EPN, Thu Dec 1 10:30:18 2011
* Purpose: Clone a CP9 HMM CP9_t object
*/
CP9_t *
cp9_Clone(CP9_t *cp9)
{
CP9_t *cp9dup = NULL;
int status;
if ((cp9dup = AllocCPlan9(cp9->M, cp9->abc)) == NULL) return NULL;
if ((status = cp9_Copy(cp9, cp9dup)) != eslOK) goto ERROR;
return cp9dup;
ERROR:
FreeCPlan9(cp9dup);
return NULL;
}
/* Function: CP9_2sub_cp9()
* EPN 09.24.06
*
* Purpose: Given a template CM Plan 9 HMM, build a sub-model that
* models only a subset of the consensus columns of the
* original alignment. This requires a bit of care for
* the initial and final node of the sub CP9, and
* straightforward copying of parameters for the rest.
*
* The new CP9 is constructed in Global Needleman/Wunsch
* mode. The orig_hmm MUST be in global mode. THIS IS
* CHECKED FOR IN A VERY FRAGILE MANNER!
*
* The approach here is to allocate and fill the new
* sub CP9. There might be a better way - transforming
* the original CP9 into the new sub CP9 using a method
* involving pointer rearrangement, but I'm not sure
* how to do this.
*
* Args: orig_hmm - the CP9 model w/ data-dep prob's valid
* ret_sub_hmm - the new sub CP9 hmm, allocated here, must
* be freed by caller.
* spos - first consensus column modelled by original
* CP9 HMM the sub CP9 HMM models.
* epos - final consensus column modelled by original
* CP9 HMM the sub CP9 HMM models.
* orig_phi - the 2D phi array for the original CP9 HMM.
* Return: (void)
* HMM probabilities are modified.
*/
void
CP9_2sub_cp9(CP9_t *orig_hmm, CP9_t **ret_sub_hmm, int spos, int epos, double **orig_phi)
{
CP9_t *sub_hmm;
int i, x;
int orig_pos;
sub_hmm = AllocCPlan9((epos-spos+1), orig_hmm->abc);
for(x = 0; x < MAXABET; x++)
{
sub_hmm->null[x] = orig_hmm->null[x];
}
/* No special (*x* states in Plan 7) states in CM Plan 9 */
/* First we just copy the parameters for spos..epos from the template HMM.
* This is *slightly* wasteful, as we'll overwrite a few of these later.
*/
for(i = 0; i <= (epos-spos+1); i++)
{
orig_pos = i + spos - 1;
if(i > 0)
{
for(x = 0; x < MAXABET; x++)
{
sub_hmm->mat[i][x] = orig_hmm->mat[orig_pos][x];
sub_hmm->msc[x][i] = orig_hmm->msc[x][orig_pos];
}
sub_hmm->begin[i] = orig_hmm->begin[orig_pos];
sub_hmm->end[i] = orig_hmm->end[orig_pos];
sub_hmm->bsc[i] = orig_hmm->bsc[orig_pos];
sub_hmm->esc[i] = orig_hmm->esc[orig_pos];
if((i > 1) && ((0. - sub_hmm->begin[i] > 0.00000001) ||
(sub_hmm->begin[i] - 0. > 0.00000001)))
{
cm_Fail("ERROR in cp9_2sub_cp9() is original CP9 HMM not in global (NW) mode? i: %d\n", i);
}
}
for(x = 0; x < MAXABET; x++)
{
sub_hmm->ins[i][x] = orig_hmm->ins[orig_pos][x];
sub_hmm->isc[x][i] = orig_hmm->isc[x][orig_pos];
}
for(x = 0; x < cp9_NTRANS; x++)
{
sub_hmm->t[i][x] = orig_hmm->t[orig_pos][x];
sub_hmm->tsc[x][i] = orig_hmm->tsc[x][orig_pos];
}
}
/* Make the necessary modifications. */
CP9_reconfig2sub(sub_hmm, spos, epos, 1, sub_hmm->M, orig_phi);
sub_hmm->el_self = orig_hmm->el_self;
sub_hmm->el_selfsc = orig_hmm->el_selfsc;
sub_hmm->flags |= CPLAN9_HASBITS; /* raise the log-odds ready flag */
*ret_sub_hmm = sub_hmm;
return;
}
