void update(node *p)
{ /* update branch lengths around a node */
boolean negatives;
if (p->tip)
return;
makedists(p);
makebigv(p,&negatives);
if (negatives)
correctv(p);
littlev(p);
nuview(p);
} /* update */
void update(node *p)
{
/* update branch lengths around a node */
if (p->tip)
return;
makedists(p);
if (p->iter || p->next->iter || p->next->next->iter) {
makebigv(p);
correctv(p);
}
nuview(p);
} /* update */
double evaluate(node *p, boolean saveit)
{
#ifdef CALLCOUNT
printf("evaluate\n");
#endif
#ifdef TIMINGS
get_start_time(eval_tk);
#endif
contribarr tterm;
double sum, sum2, sumc, y, lz, y1, z1zz, z1yy, prod12, prod1, prod2, prod3,
sumterm, lterm;
long i, j, k, lai;
node *q;
sitelike x1, x2;
sum = 0.0;
q = p->back;
if ( p->initialized == false && p->tip == false) nuview(p);
if ( q->initialized == false && q->tip == false) nuview(q);
y = p->v;
lz = -y;
for (i = 0; i < rcategs; i++)
for (j = 0; j < categs; j++) {
tbl[i][j]->orig_zz = exp(tbl[i][j]->ratxi * lz);
tbl[i][j]->z1 = exp(tbl[i][j]->ratxv * lz);
tbl[i][j]->z1zz = tbl[i][j]->z1 * tbl[i][j]->orig_zz;
tbl[i][j]->z1yy = tbl[i][j]->z1 - tbl[i][j]->z1zz;
}
for (i = 0; i < endsite; i++) {
k = category[alias[i]-1] - 1;
for (j = 0; j < rcategs; j++) {
if (y > 0.0) {
y1 = 1.0 - tbl[j][k]->z1;
z1zz = tbl[j][k]->z1zz;
z1yy = tbl[j][k]->z1yy;
} else {
y1 = 0.0;
z1zz = 1.0;
z1yy = 0.0;
}
memcpy(x1, p->x[i][j], sizeof(sitelike));
prod1 = freqa * x1[0] + freqc * x1[(long)C - (long)A] +
freqg * x1[(long)G - (long)A] + freqt * x1[(long)T - (long)A];
memcpy(x2, q->x[i][j], sizeof(sitelike));
prod2 = freqa * x2[0] + freqc * x2[(long)C - (long)A] +
freqg * x2[(long)G - (long)A] + freqt * x2[(long)T - (long)A];
prod3 = (x1[0] * freqa + x1[(long)G - (long)A] * freqg) *
(x2[0] * freqar + x2[(long)G - (long)A] * freqgr) +
(x1[(long)C - (long)A] * freqc + x1[(long)T - (long)A] * freqt) *
(x2[(long)C - (long)A] * freqcy + x2[(long)T - (long)A] * freqty);
prod12 = freqa * x1[0] * x2[0] +
freqc * x1[(long)C - (long)A] * x2[(long)C - (long)A] +
freqg * x1[(long)G - (long)A] * x2[(long)G - (long)A] +
freqt * x1[(long)T - (long)A] * x2[(long)T - (long)A];
tterm[j] = z1zz * prod12 + z1yy * prod3 + y1 * prod1 * prod2;
}
sumterm = 0.0;
for (j = 0; j < rcategs; j++)
sumterm += probcat[j] * tterm[j];
lterm = log(sumterm) + p->underflows[i] + q->underflows[i];
for (j = 0; j < rcategs; j++)
clai[j] = tterm[j] / sumterm;
memcpy(contribution[i], clai, rcategs*sizeof(double));
if (saveit && !auto_ && usertree && (which <= shimotrees))
l0gf[which - 1][i] = lterm;
sum += aliasweight[i] * lterm;
}
for (j = 0; j < rcategs; j++)
like[j] = 1.0;
for (i = 0; i < sites; i++) {
sumc = 0.0;
for (k = 0; k < rcategs; k++)
sumc += probcat[k] * like[k];
sumc *= lambda;
if ((ally[i] > 0) && (location[ally[i]-1] > 0)) {
lai = location[ally[i] - 1];
memcpy(clai, contribution[lai - 1], rcategs*sizeof(double));
for (j = 0; j < rcategs; j++)
nulike[j] = ((1.0 - lambda) * like[j] + sumc) * clai[j];
} else {
for (j = 0; j < rcategs; j++)
nulike[j] = ((1.0 - lambda) * like[j] + sumc);
}
memcpy(like, nulike, rcategs*sizeof(double));
}
sum2 = 0.0;
for (i = 0; i < rcategs; i++)
sum2 += probcat[i] * like[i];
sum += log(sum2);
curtree.likelihood = sum;
if (!saveit || auto_ || !usertree) {
#ifdef TIMINGS
get_stop_time(eval_tk);
#endif
return sum;
}
if(which <= shimotrees)
l0gl[which - 1] = sum;
if (which == 1) {
maxwhich = 1;
maxlogl = sum;
#ifdef TIMINGS
get_stop_time(eval_tk);
#endif
return sum;
}
if (sum > maxlogl) {
maxwhich = which;
maxlogl = sum;
}
#ifdef TIMINGS
get_stop_time(eval_tk);
#endif
return sum;
} /* evaluate */
