static boolean isInformative(tree *tr, int dataType, int site)
{
int
informativeCounter = 0,
check[256],
j,
undetermined = getUndetermined(dataType);
const unsigned int
*bitVector = getBitVector(dataType);
unsigned char
nucleotide;
for(j = 0; j < 256; j++)
check[j] = 0;
for(j = 1; j <= tr->mxtips; j++)
{
nucleotide = tr->yVector[j][site];
check[nucleotide] = check[nucleotide] + 1;
assert(bitVector[nucleotide] > 0);
}
for(j = 0; j < undetermined; j++)
{
if(check[j] > 0)
informativeCounter++;
}
if(informativeCounter <= 1)
return FALSE;
else
{
for(j = 0; j < undetermined; j++)
{
if(check[j] > 1)
return TRUE;
}
}
return FALSE;
}
void fixModelIndices(tree *tr, int endsite, boolean fixRates)
{
int model, i;
assert(tr->NumberOfModels > 0);
tr->partitionData[0].lower = 0;
model = tr->model[0];
i = 1;
while(i < endsite)
{
if(tr->model[i] != model)
{
tr->partitionData[model].upper = i;
tr->partitionData[model + 1].lower = i;
model = tr->model[i];
}
i++;
}
tr->partitionData[tr->NumberOfModels - 1].upper = endsite;
for(model = 0; model < tr->NumberOfModels; model++)
tr->partitionData[model].width = tr->partitionData[model].upper - tr->partitionData[model].lower;
#ifndef _USE_PTHREADS
for(model = 0; model < tr->NumberOfModels; model++)
{
int
j,
lower = tr->partitionData[model].lower;
/* SOS what about sumBuffer? */
/* tr->partitionData[model].sumBuffer = &tr->sumBuffer[offset]; */
tr->partitionData[model].perSiteLL = &tr->perSiteLL[lower];
tr->partitionData[model].wgt = &tr->cdta->aliaswgt[lower];
tr->partitionData[model].invariant = &tr->invariant[lower];
tr->partitionData[model].rateCategory = &tr->cdta->rateCategory[lower];
for(j = 1; j <= tr->mxtips; j++)
tr->partitionData[model].yVector[j] = &(tr->yVector[j][tr->partitionData[model].lower]);
{
int
width = tr->partitionData[model].width,
undetermined = getUndetermined(tr->partitionData[model].dataType),
j;
tr->partitionData[model].gapVectorLength = ((int)width / 32) + 1;
memset(tr->partitionData[model].gapVector, 0, tr->partitionData[model].initialGapVectorSize);
for(j = 1; j <= tr->mxtips; j++)
for(i = 0; i < width; i++)
if(tr->partitionData[model].yVector[j][i] == undetermined)
tr->partitionData[model].gapVector[tr->partitionData[model].gapVectorLength * j + i / 32] |= mask32[i % 32];
}
}
#else
masterBarrier(THREAD_FIX_MODEL_INDICES, tr);
#endif
if(fixRates)
updatePerSiteRates(tr, TRUE);
}