/* HMM_initGlobals -
* Given a number of states and a sequence length, allocates or reallocates
* memory for internal variables.
*/
void HMM_initGlobals(int uu, int tt)
{ if (g_alpha==NULL||COLUMNS(g_alpha)<tt||ROWS(g_alpha)<uu)
{ if (g_alpha!=NULL)
{ freeRMat(g_alpha);
freeRMat(g_delta);
freeRMat(g_deltav); /* This could be int. */
freeRMat(g_beta);
freeRMat3d(g_psi);}
g_alpha = allocRMat(uu, tt);
g_delta = allocRMat(uu, tt);
g_deltav = allocRMat(uu, tt); /* This could be int. */
g_beta = allocRMat(uu, tt);
g_psi = allocRMat3d(uu, uu, tt);}}
/* allocHMM - Allocates space for an HMM and returns a pointer to it. */
Hmm *allocHMM(int uu)
{ Hmm *m = (Hmm *)safe_malloc(sizeof(Hmm));
assert(uu>0);
m->logA = allocRMat(uu, uu);
m->logB = allocRVec(uu);
m->uu = uu;
return m;}
xHmm *allocXHMM(int uu, int ii, int tt){
assert(uu > 0 && ii > 0 && tt > 0);
xHmm *xhmm = safe_malloc(sizeof *xhmm);
xhmm->m = allocHMM(uu);
xhmm->ii = ii;
xhmm->tt = tt;
if (tt > 1)
xhmm->bps = allocRMat3d(tt - 1, ii, ii);
else xhmm->bps = NULL;
xhmm->bss = allocRMat(tt, ii);
return xhmm;
}
