void
free_updategenealogy (void)
{
free_genealogy_weights (&holdallgweight_updategenealogy);
free_genealogy_weights (&holdgweight_updategenealogy);
free_probcalc (&holdallpcalc_updategenealogy);
} //free_updategenealogy
void
free_t_RY (void)
{
int li;
free_genealogy_weights (&holdallgweight_t_RY);
for (li = 0; li < nloci; li++)
{
free_genealogy_weights (&holdgweight_t_RY[li]);
}
free_probcalc (&holdallpcalc_t_RY);
orig2d_free2D ((void **) skipflag, nloci);
} // free_changet_RY
void
freeanymemory ()
{
int ci;
int i;
int j;
int li;
int npnodes;
int nperiods;
unsetseeds ();
if (assignmentoptions[POPULATIONASSIGNMENTINFINITE] == 1)
{
npnodes = npops + 1;
nperiods = 2;
}
else if (modeloptions[SINGLEPOPULATION] == 1)
{
npnodes = 1;
nperiods = 1;
}
else
{
npnodes = 2 * npops - 1;
nperiods = npops;
for (i = 0; i < lastperiodnumber; i++)
{
free_value_record (T[i].v);
}
}
if (assignmentoptions[POPULATIONASSIGNMENT] == 1)
{
free_a_rec_multichain ();
}
for (ci = 0; ci < numchains; ci++)
{
for (i = 0; i < npnodes; i++)
{
free (C[ci]->poptree[i].up);
C[ci]->poptree[i].up = NULL;
}
XFREE (C[ci]->tvals);
XFREE (C[ci]->poptree);
free_genealogy_weights (&(C[ci]->allgweight));
free_probcalc (&(C[ci]->allpcalc));
if (C[ci]->plist != NULL)
{
for (j = 0; j < nperiods; j++)
{
XFREE (C[ci]->plist[j]);
}
XFREE (C[ci]->plist);
}
for (li = 0; li < nloci; li++)
{
free_genealogy_weights (&(C[ci]->G[li].gweight));
XFREE (C[ci]->G[li].uvals);
XFREE (C[ci]->G[li].pdg_a);
if (L[li].model == HKY)
{
XFREE (L[li].mult);
for (i = L[li].numgenes; i < 2 * L[li].numgenes - 1; i++)
{
XFREE (C[ci]->G[li].gtree[i].hkyi.scalefactor);
XFREE (C[ci]->G[li].gtree[i].hkyi.oldscalefactor);
for (j = 0; j < L[li].numsites; j++)
{
XFREE (C[ci]->G[li].gtree[i].hkyi.frac[j]);
XFREE (C[ci]->G[li].gtree[i].hkyi.newfrac[j]);
}
XFREE (C[ci]->G[li].gtree[i].hkyi.frac);
XFREE (C[ci]->G[li].gtree[i].hkyi.newfrac);
}
}
for (i = 0; i < L[li].numlines; i++)
{
XFREE (C[ci]->G[li].gtree[i].mig);
if (L[li].model == STEPWISE || L[li].model == JOINT_IS_SW)
{
XFREE (C[ci]->G[li].gtree[i].A);
XFREE (C[ci]->G[li].gtree[i].dlikeA);
}
if (L[li].model == INFINITESITES)
{
XFREE (C[ci]->G[li].gtree[i].seq);
}
}
XFREE (C[ci]->G[li].gtree);
XFREE (C[ci]->G[li].mut);
}
XFREE (C[ci]->G);
XFREE (C[ci]);
}
free_locus (); /* L is the global: global variable is too simple. */
/*JH 1/6/09 this will get deleted with these mig values are restored to a large array instead of pointers */
XFREE (oldedgemig.mtimeavail);
XFREE (oldedgemig.mp);
XFREE (oldsismig.mtimeavail);
XFREE (oldsismig.mp);
XFREE (newedgemig.mtimeavail);
XFREE (newedgemig.mp);
XFREE (newsismig.mtimeavail);
XFREE (newsismig.mp);
XFREE (C);
free_iparam (itheta, numpopsizeparams, 0);
free_iparam (imig, nummigrateparams, 1);
free_iparam (&isplit, 1, -1);
itheta = NULL;
if (npops > 2 && npops < 5 && outputoptions[PRINTJOINTTEST])
free_multi_t_arrays ();
if (assignmentoptions[POPULATIONASSIGNMENTINFINITE] == 0
&& modeloptions[SINGLEPOPULATION] == 0)
{
free_t_NW ();
free_t_RY ();
}
free_updategenealogy ();
free_updategenealogy_covar ();
free_treeweight ();
free_gtreecommon ();
free_sumlogk ();
for (i = 0; i < nomigrationchecklist.n; i++)
{
XFREE (nomigrationchecklist.p);
XFREE (nomigrationchecklist.r);
XFREE (nomigrationchecklist.c);
}
if (assignmentoptions[POPULATIONASSIGNMENTINFINITE] == 1
|| modeloptions[SINGLEPOPULATION] == 1)
{
/* no split time */
}
else
{
free_T ();
}
free_lpgpd_v (lpgpd_v);
if (outputoptions[MIGRATEHIST])
free_migration_counts_times (migration_counts_times);
free_autoc_pointers ();
XFREE (L);
return;
} //freeanymemory
