static double evaluatePartialGTRCAT(int i, double ki, int counter, traversalInfo *ti, double qz,
int w, double *EIGN, double *EI, double *EV,
double *tipVector, unsigned char **yVector,
int branchReference, int mxtips)
{
double lz, term;
double d[3];
double *x1, *x2;
int scale = 0, k;
double *lVector = (double *)malloc_aligned(sizeof(double) * 4 * mxtips);
traversalInfo *trav = &ti[0];
assert(isTip(trav->pNumber, mxtips));
x1 = &(tipVector[4 * yVector[trav->pNumber][i]]);
for(k = 1; k < counter; k++)
{
double
qz = ti[k].qz[branchReference],
rz = ti[k].rz[branchReference];
qz = (qz > zmin) ? log(qz) : log(zmin);
rz = (rz > zmin) ? log(rz) : log(zmin);
computeVectorGTRCAT(lVector, &scale, ki, i, qz, rz, &ti[k],
EIGN, EI, EV,
tipVector, yVector, mxtips);
}
x2 = &lVector[4 * (trav->qNumber - mxtips)];
assert(0 <= (trav->qNumber - mxtips) && (trav->qNumber - mxtips) < mxtips);
if(qz < zmin)
lz = zmin;
lz = log(qz);
lz *= ki;
d[0] = EXP (EIGN[1] * lz);
d[1] = EXP (EIGN[2] * lz);
d[2] = EXP (EIGN[3] * lz);
term = x1[0] * x2[0];
term += x1[1] * x2[1] * d[0];
term += x1[2] * x2[2] * d[1];
term += x1[3] * x2[3] * d[2];
term = LOG(FABS(term)) + (scale * LOG(minlikelihood));
term = term * w;
free(lVector);
return term;
}
static double evaluatePartialGTRCAT(int i, double ki, int counter, traversalInfo *ti, double qz,
int w, double *EIGN, double *EI, double *EV,
double *tipVector, unsigned char **yVector,
int branchReference, int mxtips, double* expVector)
{
double lz, term;
double d[3];
double *x1, *x2;
int scale = 0, k;
double *lVector = (double *)rax_malloc(sizeof(double) * 4 * mxtips);
traversalInfo *trav = &ti[0];
assert(isTip(trav->pNumber, mxtips));
x1 = &(tipVector[4 * yVector[trav->pNumber][i]]);
if (!expVector)
{
for(k = 1; k < counter; k++)
computeVectorGTRCAT(lVector, &scale, ki, i, ti[k].qz[branchReference], ti[k].rz[branchReference], &ti[k],
EIGN, EI, EV,
tipVector, yVector, mxtips);
}
else
{
for(k = 1; k < counter; k++)
{
double
*ev1 = &expVector[k*6],
*ev2 = &expVector[k*6+3];
computeVectorGTRCAT_FAST(lVector, &scale, ki, i, &ti[k], EI, EV,
tipVector, yVector, mxtips, ev1, ev2);
}
}
x2 = &lVector[4 * (trav->qNumber - mxtips)];
assert(0 <= (trav->qNumber - mxtips) && (trav->qNumber - mxtips) < mxtips);
if(qz < zmin)
lz = zmin;
lz = log(qz);
lz *= ki;
d[0] = EXP (EIGN[0] * lz);
d[1] = EXP (EIGN[1] * lz);
d[2] = EXP (EIGN[2] * lz);
term = x1[0] * x2[0];
term += x1[1] * x2[1] * d[0];
term += x1[2] * x2[2] * d[1];
term += x1[3] * x2[3] * d[2];
term = LOG(FABS(term)) + (scale * LOG(minlikelihood));
term = term * w;
rax_free(lVector);
return term;
}
