static double evaluatePartialGTRCATPROT(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[20];
double *x1, *x2;
int scale = 0, k, l;
double *lVector = (double *)rax_malloc_aligned(sizeof(double) * 20 * mxtips);
traversalInfo *trav = &ti[0];
assert(isTip(trav->pNumber, mxtips));
x1 = &(tipVector[20 * yVector[trav->pNumber][i]]);
for(k = 1; k < counter; k++)
computeVectorGTRCATPROT(lVector, &scale, ki, i, ti[k].qz[branchReference], ti[k].rz[branchReference],
&ti[k], EIGN, EI, EV,
tipVector, yVector, mxtips);
x2 = &lVector[20 * (trav->qNumber - mxtips)];
assert(0 <= (trav->qNumber - mxtips) && (trav->qNumber - mxtips) < mxtips);
if(qz < zmin)
lz = zmin;
lz = log(qz);
lz *= ki;
d[0] = 1.0;
for(l = 1; l < 20; l++)
d[l] = EXP (EIGN[l-1] * lz);
term = 0.0;
for(l = 0; l < 20; l++)
term += x1[l] * x2[l] * d[l];
term = LOG(FABS(term)) + (scale * LOG(minlikelihood));
term = term * w;
rax_free(lVector);
return term;
}
static double evaluatePartialGTRCATPROT(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[20];
double *x1, *x2;
int scale = 0, k, l;
double
*lVector = (double *)malloc_aligned(sizeof(double) * 20 * mxtips),
myEI[400] __attribute__ ((aligned (BYTE_ALIGNMENT)));
traversalInfo *trav = &ti[0];
for(k = 0; k < 20; k++)
{
for(l = 0; l < 20; l++)
myEI[k * 20 + l] = EI[k * 20 + l];
}
assert(isTip(trav->pNumber, mxtips));
x1 = &(tipVector[20 * 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);
computeVectorGTRCATPROT(lVector, &scale, ki, i, qz, rz,
&ti[k], EIGN, myEI, EV,
tipVector, yVector, mxtips);
}
x2 = &lVector[20 * (trav->qNumber - mxtips)];
assert(0 <= (trav->qNumber - mxtips) && (trav->qNumber - mxtips) < mxtips);
if(qz < zmin)
lz = zmin;
lz = log(qz);
lz *= ki;
d[0] = 1.0;
for(l = 1; l < 20; l++)
d[l] = EXP (EIGN[l] * lz);
term = 0.0;
for(l = 0; l < 20; l++)
term += x1[l] * x2[l] * d[l];
term = LOG(FABS(term)) + (scale * LOG(minlikelihood));
term = term * w;
free(lVector);
return term;
}