double evaluatePartialGeneric (tree *tr, int i, double ki, int _model)
{
double result;
int
branchReference,
states = tr->partitionData[_model].states;
int
index;
if(tr->manyPartitions)
index = i - tr->partitionData[_model].lower;
else
index = i;
if(tr->numBranches > 1)
branchReference = _model;
else
branchReference = 0;
#ifndef _OPTIMIZED_FUNCTIONS
if(tr->rateHetModel == CAT)
result = evaluatePartialCAT_FLEX(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips, states);
else
/*
the per-site site likelihood function should only be called for the CAT model
under the GAMMA model this is required only for estimating per-site protein models
which has however been removed in this version of the code
*/
assert(0);
#else
switch(states)
{
case 4: /* DNA */
assert(tr->rateHetModel == CAT);
result = evaluatePartialGTRCAT(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case 20: /* proteins */
if(tr->rateHetModel == CAT)
result = evaluatePartialGTRCATPROT(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
else
result = evaluatePartialGTRGAMMAPROT(index, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector,
tr->partitionData[_model].gammaRates,
branchReference, tr->mxtips);
break;
default:
assert(0);
}
#endif
return result;
}
double evaluatePartialGeneric (tree *tr, int i, double ki, int _model)
{
double result;
int
branchReference,
states = tr->partitionData[_model].states;
#ifdef _USE_PTHREADS
int index = i;
#else
int index = i - tr->partitionData[_model].lower;
#endif
if(tr->multiBranch)
branchReference = _model;
else
branchReference = 0;
assert(tr->rateHetModel == CAT);
switch(tr->partitionData[_model].dataType)
{
case BINARY_DATA:
result = evaluatePartialGTRCAT_BINARY(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case DNA_DATA:
result = evaluatePartialGTRCAT(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case AA_DATA:
result = evaluatePartialGTRCATPROT(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case SECONDARY_DATA:
result = evaluatePartialGTRCATSECONDARY(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case SECONDARY_DATA_6:
result = evaluatePartialGTRCATSECONDARY_6(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
break;
case SECONDARY_DATA_7:
result = evaluatePartialGTRCATSECONDARY_7(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips);
case GENERIC_32:
result = evaluatePartialFlex(index, ki, tr->td[0].count, tr->td[0].ti, tr->td[0].ti[0].qz[branchReference],
tr->partitionData[_model].wgt[index],
tr->partitionData[_model].EIGN,
tr->partitionData[_model].EI,
tr->partitionData[_model].EV,
tr->partitionData[_model].tipVector,
tr->partitionData[_model].yVector, branchReference, tr->mxtips, states);
break;
default:
assert(0);
}
return result;
}
