static double testInsertThorough(tree *tr, nodeptr r, nodeptr q, boolean useVector)
{
double
result,
qz[NUM_BRANCHES],
z[NUM_BRANCHES];
nodeptr
x = q->back,
s = r->back;
int
j;
for(j = 0; j < tr->numBranches; j++)
{
qz[j] = q->z[j];
z[j] = sqrt(qz[j]);
if(z[j] < zmin)
z[j] = zmin;
if(z[j] > zmax)
z[j] = zmax;
}
hookup(r->next, q, z, tr->numBranches);
hookup(r->next->next, x, z, tr->numBranches);
hookupDefault(r, s, tr->numBranches);
newviewGeneric(tr, r);
localSmooth(tr, r, smoothings);
if(useVector)
result = evaluateGenericVector(tr, r);
else
result = evaluateGeneric(tr, r);
hookup(q, x, qz, tr->numBranches);
r->next->next->back = r->next->back = (nodeptr) NULL;
return result;
}
static void doNNIs(tree *tr, nodeptr p, double *lhVectors[3], boolean shSupport, int *interchanges, int *innerBranches,
double *pqz_0, double *pz1_0, double *pz2_0, double *qz1_0, double *qz2_0, double *pqz_1, double *pz1_1, double *pz2_1,
double *qz1_1, double *qz2_1, double *pqz_2, double *pz1_2, double *pz2_2, double *qz1_2, double *qz2_2)
{
nodeptr
q = p->back,
pb1 = p->next->back,
pb2 = p->next->next->back;
assert(!isTip(p->number, tr->mxtips));
if(!isTip(q->number, tr->mxtips))
{
int
whichNNI = 0;
nodeptr
qb1 = q->next->back,
qb2 = q->next->next->back;
double
lh[3];
*innerBranches = *innerBranches + 1;
nniSmooth(tr, p, 16);
if(shSupport)
{
evaluateGenericVector(tr, p);
memcpy(lhVectors[0], tr->perSiteLL, sizeof(double) * tr->cdta->endsite);
}
else
evaluateGeneric(tr, p);
lh[0] = tr->likelihood;
storeBranches(tr, p, pqz_0, pz1_0, pz2_0, qz1_0, qz2_0);
/*******************************************/
hookup(p, q, pqz_0, tr->numBranches);
hookup(p->next, qb1, qz1_0, tr->numBranches);
hookup(p->next->next, pb2, pz2_0, tr->numBranches);
hookup(q->next, pb1, pz1_0, tr->numBranches);
hookup(q->next->next, qb2, qz2_0, tr->numBranches);
newviewGeneric(tr, p);
newviewGeneric(tr, p->back);
nniSmooth(tr, p, 16);
if(shSupport)
{
evaluateGenericVector(tr, p);
memcpy(lhVectors[1], tr->perSiteLL, sizeof(double) * tr->cdta->endsite);
}
else
evaluateGeneric(tr, p);
lh[1] = tr->likelihood;
storeBranches(tr, p, pqz_1, pz1_1, pz2_1, qz1_1, qz2_1);
if(lh[1] > lh[0])
whichNNI = 1;
/*******************************************/
hookup(p, q, pqz_0, tr->numBranches);
hookup(p->next, qb1, qz1_0, tr->numBranches);
hookup(p->next->next, pb1, pz1_0, tr->numBranches);
hookup(q->next, pb2, pz2_0, tr->numBranches);
hookup(q->next->next, qb2, qz2_0, tr->numBranches);
newviewGeneric(tr, p);
newviewGeneric(tr, p->back);
nniSmooth(tr, p, 16);
if(shSupport)
{
evaluateGenericVector(tr, p);
memcpy(lhVectors[2], tr->perSiteLL, sizeof(double) * tr->cdta->endsite);
}
else
evaluateGeneric(tr, p);
lh[2] = tr->likelihood;
storeBranches(tr, p, pqz_2, pz1_2, pz2_2, qz1_2, qz2_2);
if(lh[2] > lh[0] && lh[2] > lh[1])
whichNNI = 2;
/*******************************************/
if(shSupport)
whichNNI = 0;
switch(whichNNI)
{
case 0:
hookup(p, q, pqz_0, tr->numBranches);
hookup(p->next, pb1, pz1_0, tr->numBranches);
hookup(p->next->next, pb2, pz2_0, tr->numBranches);
hookup(q->next, qb1, qz1_0, tr->numBranches);
hookup(q->next->next, qb2, qz2_0, tr->numBranches);
break;
case 1:
hookup(p, q, pqz_1, tr->numBranches);
hookup(p->next, qb1, pz1_1, tr->numBranches);
hookup(p->next->next, pb2, pz2_1, tr->numBranches);
hookup(q->next, pb1, qz1_1, tr->numBranches);
hookup(q->next->next, qb2, qz2_1, tr->numBranches);
break;
case 2:
hookup(p, q, pqz_2, tr->numBranches);
hookup(p->next, qb1, pz1_2, tr->numBranches);
hookup(p->next->next, pb1, pz2_2, tr->numBranches);
hookup(q->next, pb2, qz1_2, tr->numBranches);
hookup(q->next->next, qb2, qz2_2, tr->numBranches);
break;
default:
assert(0);
}
newviewGeneric(tr, p);
newviewGeneric(tr, q);
if(whichNNI > 0)
*interchanges = *interchanges + 1;
if(shSupport)
p->bInf->support = SHSupport(tr->cdta->endsite, 1000, tr->resample, lh, lhVectors);
}
if(!isTip(pb1->number, tr->mxtips))
doNNIs(tr, pb1, lhVectors, shSupport, interchanges, innerBranches,
pqz_0, pz1_0, pz2_0, qz1_0, qz2_0, pqz_1, pz1_1, pz2_1,
qz1_1, qz2_1, pqz_2, pz1_2, pz2_2, qz1_2, qz2_2);
if(!isTip(pb2->number, tr->mxtips))
doNNIs(tr, pb2, lhVectors, shSupport, interchanges, innerBranches,
pqz_0, pz1_0, pz2_0, qz1_0, qz2_0, pqz_1, pz1_1, pz2_1,
qz1_1, qz2_1, pqz_2, pz1_2, pz2_2, qz1_2, qz2_2);
return;
}