void determineFullTraversal(nodeptr p, tree *tr)
{
nodeptr q = p->back;
int k;
tr->td[0].ti[0].pNumber = p->number;
tr->td[0].ti[0].qNumber = q->number;
for(k = 0; k < tr->numBranches; k++)
tr->td[0].ti[0].qz[k] = q->z[k];
assert(isTip(p->number, tr->mxtips));
tr->td[0].count = 1;
computeFullTraversalInfo(q, &(tr->td[0].ti[0]), &(tr->td[0].count), tr->mxtips, tr->numBranches);
computeFullTraversalInfo(p, &(tr->td[0].ti[0]), &(tr->td[0].count), tr->mxtips, tr->numBranches);
}
void determineFullTraversal(nodeptr p, tree *tr)
{
nodeptr q = p->back;
int k;
tr->td[0].ti[0].pNumber = p->number;
tr->td[0].ti[0].qNumber = q->number;
for(k = 0; k < tr->numBranches; k++)
tr->td[0].ti[0].qz[k] = q->z[k];
#ifdef _BASTIEN
if(tr->doBastienStuff)
{
for(k = 0; k < tr->numBranches; k++)
{
assert(q->secondDerivative[k] == q->back->secondDerivative[k]);
assert(p->secondDerivative[k] == p->back->secondDerivative[k]);
assert(q->secondDerivativeValid[k] && q->back->secondDerivativeValid[k]);
assert(p->secondDerivativeValid[k] && p->back->secondDerivativeValid[k]);
}
for(k = 0; k < tr->numBranches; k++)
{
tr->td[0].ti[0].secondDerivativeQ[k] = q->secondDerivative[k];
tr->td[0].ti[0].secondDerivativeP[k] = p->secondDerivative[k];
}
//printf("Start %f %f\n", q->secondDerivative[0], p->secondDerivative[0]);
}
#endif
assert(isTip(p->number, tr->mxtips));
tr->td[0].count = 1;
computeFullTraversalInfo(tr, q, &(tr->td[0].ti[0]), &(tr->td[0].count), tr->mxtips, tr->numBranches);
computeFullTraversalInfo(tr, p, &(tr->td[0].ti[0]), &(tr->td[0].count), tr->mxtips, tr->numBranches);
}
void computeFullTraversalInfo(nodeptr p, traversalInfo *ti, int *counter, int maxTips, int numBranches)
{
if(isTip(p->number, maxTips))
return;
{
int i;
nodeptr q = p->next->back;
nodeptr r = p->next->next->back;
/* set xnode info at this point */
p->x = 1;
p->next->x = 0;
p->next->next->x = 0;
if(isTip(r->number, maxTips) && isTip(q->number, maxTips))
{
ti[*counter].tipCase = TIP_TIP;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
}
*counter = *counter + 1;
}
else
{
if(isTip(r->number, maxTips) || isTip(q->number, maxTips))
{
nodeptr tmp;
if(isTip(r->number, maxTips))
{
tmp = r;
r = q;
q = tmp;
}
computeFullTraversalInfo(r, ti, counter, maxTips, numBranches);
ti[*counter].tipCase = TIP_INNER;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
}
*counter = *counter + 1;
}
else
{
computeFullTraversalInfo(q, ti, counter, maxTips, numBranches);
computeFullTraversalInfo(r, ti, counter, maxTips, numBranches);
ti[*counter].tipCase = INNER_INNER;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
}
*counter = *counter + 1;
}
}
}
}
void computeFullTraversalInfo(tree *tr, nodeptr p, traversalInfo *ti, int *counter, int maxTips, int numBranches)
{
if(isTip(p->number, maxTips))
return;
{
int i;
nodeptr q = p->next->back;
nodeptr r = p->next->next->back;
#ifdef _HET
boolean
parentIsTip;
if(isTip(p->back->number, maxTips))
parentIsTip = TRUE;
else
parentIsTip = FALSE;
#endif
/* set xnode info at this point */
p->x = 1;
p->next->x = 0;
p->next->next->x = 0;
if(isTip(r->number, maxTips) && isTip(q->number, maxTips))
{
ti[*counter].tipCase = TIP_TIP;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
#ifdef _HET
ti[*counter].parentIsTip = parentIsTip;
#endif
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
#ifdef _BASTIEN
if(tr->doBastienStuff)
{
assert(q->secondDerivative[i] == q->back->secondDerivative[i]);
assert(r->secondDerivative[i] == r->back->secondDerivative[i]);
assert(q->secondDerivativeValid[i] && q->back->secondDerivativeValid[i]);
assert(r->secondDerivativeValid[i] && r->back->secondDerivativeValid[i]);
}
ti[*counter].secondDerivativeQ[i] = q->secondDerivative[i];
ti[*counter].secondDerivativeR[i] = r->secondDerivative[i];
#endif
}
*counter = *counter + 1;
}
else
{
if(isTip(r->number, maxTips) || isTip(q->number, maxTips))
{
nodeptr tmp;
if(isTip(r->number, maxTips))
{
tmp = r;
r = q;
q = tmp;
}
computeFullTraversalInfo(tr, r, ti, counter, maxTips, numBranches);
ti[*counter].tipCase = TIP_INNER;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
#ifdef _HET
ti[*counter].parentIsTip = parentIsTip;
#endif
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
#ifdef _BASTIEN
if(tr->doBastienStuff)
{
assert(q->secondDerivative[i] == q->back->secondDerivative[i]);
assert(r->secondDerivative[i] == r->back->secondDerivative[i]);
assert(q->secondDerivativeValid[i] && q->back->secondDerivativeValid[i]);
assert(r->secondDerivativeValid[i] && r->back->secondDerivativeValid[i]);
}
ti[*counter].secondDerivativeQ[i] = q->secondDerivative[i];
ti[*counter].secondDerivativeR[i] = r->secondDerivative[i];
#endif
}
*counter = *counter + 1;
}
else
{
computeFullTraversalInfo(tr, q, ti, counter, maxTips, numBranches);
computeFullTraversalInfo(tr, r, ti, counter, maxTips, numBranches);
ti[*counter].tipCase = INNER_INNER;
ti[*counter].pNumber = p->number;
ti[*counter].qNumber = q->number;
ti[*counter].rNumber = r->number;
#ifdef _HET
ti[*counter].parentIsTip = parentIsTip;
#endif
for(i = 0; i < numBranches; i++)
{
double z;
z = q->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].qz[i] = z;
z = r->z[i];
z = (z > zmin) ? log(z) : log(zmin);
ti[*counter].rz[i] = z;
#ifdef _BASTIEN
if(tr->doBastienStuff)
{
assert(q->secondDerivative[i] == q->back->secondDerivative[i]);
assert(r->secondDerivative[i] == r->back->secondDerivative[i]);
assert(q->secondDerivativeValid[i] && q->back->secondDerivativeValid[i]);
assert(r->secondDerivativeValid[i] && r->back->secondDerivativeValid[i]);
}
ti[*counter].secondDerivativeQ[i] = q->secondDerivative[i];
ti[*counter].secondDerivativeR[i] = r->secondDerivative[i];
#endif
}
*counter = *counter + 1;
}
}
}
}
