boolean update(tree *tr, nodeptr p)
{
nodeptr q;
boolean smoothedPartitions[NUM_BRANCHES];
int i;
double z[NUM_BRANCHES], z0[NUM_BRANCHES];
double _deltaz;
q = p->back;
for(i = 0; i < tr->numBranches; i++)
z0[i] = q->z[i];
if(tr->numBranches > 1)
makenewzGeneric(tr, p, q, z0, newzpercycle, z, TRUE);
else
makenewzGeneric(tr, p, q, z0, newzpercycle, z, FALSE);
for(i = 0; i < tr->numBranches; i++)
smoothedPartitions[i] = tr->partitionSmoothed[i];
for(i = 0; i < tr->numBranches; i++)
{
if(!tr->partitionConverged[i])
{
_deltaz = deltaz;
if(ABS(z[i] - z0[i]) > _deltaz)
{
smoothedPartitions[i] = FALSE;
}
p->z[i] = q->z[i] = z[i];
}
}
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = smoothedPartitions[i];
return TRUE;
}
static boolean qupdate (tree *tr, nodeptr p)
{
nodeptr q;
double z0[NUM_BRANCHES], z[NUM_BRANCHES];
int i;
q = p->back;
for(i = 0; i < tr->numBranches; i++)
z0[i] = q->z[i];
makenewzGeneric(tr, p, q, z0, 1, z, FALSE);
for(i = 0; i < tr->numBranches; i++)
p->z[i] = q->z[i] = z[i];
return TRUE;
}
nodeptr removeNodeBIG (tree *tr, nodeptr p, int numBranches)
{
double zqr[NUM_BRANCHES], result[NUM_BRANCHES];
nodeptr q, r;
int i;
q = p->next->back;
r = p->next->next->back;
for(i = 0; i < numBranches; i++)
zqr[i] = q->z[i] * r->z[i];
makenewzGeneric(tr, q, r, zqr, iterations, result, FALSE);
for(i = 0; i < numBranches; i++)
tr->zqr[i] = result[i];
hookup(q, r, result, numBranches);
p->next->next->back = p->next->back = (node *) NULL;
return q;
}
static void insertFast (tree *tr, nodeptr p, nodeptr q, int numBranches)
{
nodeptr r, s;
int i;
r = q->back;
s = p->back;
for(i = 0; i < numBranches; i++)
tr->lzi[i] = q->z[i];
if(Thorough)
{
double zqr[NUM_BRANCHES], zqs[NUM_BRANCHES], zrs[NUM_BRANCHES], lzqr, lzqs, lzrs, lzsum, lzq, lzr, lzs, lzmax;
double defaultArray[NUM_BRANCHES];
double e1[NUM_BRANCHES], e2[NUM_BRANCHES], e3[NUM_BRANCHES];
double *qz;
qz = q->z;
for(i = 0; i < numBranches; i++)
defaultArray[i] = defaultz;
makenewzGeneric(tr, q, r, qz, iterations, zqr, FALSE);
makenewzGeneric(tr, q, s, defaultArray, iterations, zqs, FALSE);
makenewzGeneric(tr, r, s, defaultArray, iterations, zrs, FALSE);
for(i = 0; i < numBranches; i++)
{
lzqr = (zqr[i] > zmin) ? log(zqr[i]) : log(zmin);
lzqs = (zqs[i] > zmin) ? log(zqs[i]) : log(zmin);
lzrs = (zrs[i] > zmin) ? log(zrs[i]) : log(zmin);
lzsum = 0.5 * (lzqr + lzqs + lzrs);
lzq = lzsum - lzrs;
lzr = lzsum - lzqs;
lzs = lzsum - lzqr;
lzmax = log(zmax);
if (lzq > lzmax) {lzq = lzmax; lzr = lzqr; lzs = lzqs;}
else if (lzr > lzmax) {lzr = lzmax; lzq = lzqr; lzs = lzrs;}
else if (lzs > lzmax) {lzs = lzmax; lzq = lzqs; lzr = lzrs;}
e1[i] = exp(lzq);
e2[i] = exp(lzr);
e3[i] = exp(lzs);
}
hookup(p->next, q, e1, numBranches);
hookup(p->next->next, r, e2, numBranches);
hookup(p, s, e3, numBranches);
}
else
{
double z[NUM_BRANCHES];
for(i = 0; i < numBranches; i++)
{
z[i] = sqrt(q->z[i]);
if(z[i] < zmin)
z[i] = zmin;
if(z[i] > zmax)
z[i] = zmax;
}
hookup(p->next, q, z, tr->numBranches);
hookup(p->next->next, r, z, tr->numBranches);
}
newviewGeneric(tr, p);
if(Thorough)
{
localSmooth(tr, p, smoothings);
for(i = 0; i < numBranches; i++)
{
tr->lzq[i] = p->next->z[i];
tr->lzr[i] = p->next->next->z[i];
tr->lzs[i] = p->z[i];
}
}
}
boolean update(tree *tr, nodeptr p)
{
nodeptr q;
boolean smoothedPartitions[NUM_BRANCHES];
int i;
double z[NUM_BRANCHES], z0[NUM_BRANCHES];
double _deltaz;
#ifdef _DEBUG_UPDATE
double
startLH;
evaluateGeneric(tr, p);
startLH = tr->likelihood;
#endif
q = p->back;
for(i = 0; i < tr->numBranches; i++)
z0[i] = q->z[i];
if(tr->numBranches > 1)
makenewzGeneric(tr, p, q, z0, newzpercycle, z, TRUE);
else
makenewzGeneric(tr, p, q, z0, newzpercycle, z, FALSE);
for(i = 0; i < tr->numBranches; i++)
smoothedPartitions[i] = tr->partitionSmoothed[i];
for(i = 0; i < tr->numBranches; i++)
{
if(!tr->partitionConverged[i])
{
_deltaz = deltaz;
if(ABS(z[i] - z0[i]) > _deltaz)
{
smoothedPartitions[i] = FALSE;
}
p->z[i] = q->z[i] = z[i];
}
}
#ifdef _DEBUG_UPDATE
evaluateGeneric(tr, p);
if(tr->likelihood <= startLH)
{
if(fabs(tr->likelihood - startLH) > 0.01)
{
printf("%f %f\n", startLH, tr->likelihood);
assert(0);
}
}
#endif
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = smoothedPartitions[i];
return TRUE;
}
