void FinishDeferredSF (void)
{
if (deferSetFormula->lLength) {
SortLists (deferSetFormula, &deferIsConstant);
_SimpleList tcache;
long iv,
i = variableNames.Traverser (tcache,iv,variableNames.GetRoot());
for (; i >= 0; i = variableNames.Traverser (tcache,iv)) {
_Variable* theV = FetchVar(i);
if (theV->IsContainer()) {
((_VariableContainer*)theV)->SetMDependance (*deferSetFormula);
}
}
for (long j = 0; j<likeFuncList.lLength; j++)
if (((_String*)likeFuncNamesList(j))->sLength) {
_LikelihoodFunction * lf = (_LikelihoodFunction*)likeFuncList(j);
for (long k = 0; k < deferSetFormula->lLength; k++) {
lf->UpdateIndependent(deferSetFormula->lData[k],deferIsConstant.lData[k]);
}
}
}
DeleteObject (deferSetFormula);
deferSetFormula = nil;
deferIsConstant.Clear();
}
void InitializeQTExporters(void)
{
if (!graphicsFormats.lLength)
{
qtGrexComponents.Clear();
findGraphicsExporterComponents (graphicsFormats, qtGrexComponents);
}
}
void _LikelihoodFunction::ComputeSiteLikelihoodsForABlock (long index, _Parameter* results, _SimpleList& scalers, long branchIndex, _SimpleList* branchValues, char mpiRunMode)
// assumes that results is at least blockLength slots long
{
if (blockDependancies.lData[index])
PopulateConditionalProbabilities(index, mpiRunMode == _hyphyLFMPIModeREL ?_hyphyLFConditionMPIIterate:_hyphyLFConditionProbsWeightedSum, results, scalers, branchIndex, branchValues);
else
{
ComputeBlock (index, results, -1, branchIndex, branchValues);
scalers.Clear ();
scalers.Duplicate (siteCorrections(index));
}
}
//__________________________________________________________________
long ComputeHashMarkPlacement (_HYRect line, _Parameter min, _Parameter max, _Parameter& tickStep,
_Parameter&minLabel, _SimpleList& offsets, _List& labels,
int count, _HYFont& f)
{
if (max>min)
{
offsets.Clear();
labels.Clear();
long w = line.right-line.left,
h = line.bottom-line.top,
t = 0;
_Parameter scalingFactor = (w>h)?w/(max-min):h/(max-min);
tickStep = log(max-min)/log(10.);
tickStep = pow (10.,floor (tickStep))*2.;
minLabel = min;
t = count-1;
while (t<count)
{
tickStep/=2.;
if (tickStep>1.)
tickStep = floor (tickStep);
if (min)
minLabel = ceil(min/tickStep)*tickStep;
t = ceil((max-minLabel)/tickStep);
if (min)
minLabel = ceil(min/tickStep)*tickStep;
}
if (h>w)
{
_Parameter tracer = minLabel;
long res = 0,
last = -100000,
k,
sw;
w = h;
for (h=0; h<=t; h++,tracer+=tickStep)
{
_String buffer (tracer);
sw = GetVisibleStringWidth (buffer,f);
k = (tracer-min)*scalingFactor;
if (k>w)
break;
if (k-last>f.size)
{
offsets << k;
offsets << sw;
labels && & buffer;
last = k;
}
if (sw>res)
res = sw;
}
return res;
}
else
{
_Parameter tracer = minLabel;
long res = 0,
last = -100000,
k,
sw;
for (h=0; h<=t; h++,tracer+=tickStep)
{
_String buffer (tracer);
sw = GetVisibleStringWidth (buffer,f);
k = (tracer-min)*scalingFactor;
if (k>w)
break;
if (k-last>sw)
{
offsets << k;
offsets << sw;
labels && & buffer;
last = k;
}
}
}
return f.size;
}
return 0;
}
