int treeOptimizeThorough(tree *tr, int mintrav, int maxtrav)
{
int i;
bestlist *bestT;
nodeRectifier(tr);
bestT = (bestlist *) malloc(sizeof(bestlist));
bestT->ninit = 0;
initBestTree(bestT, 1, tr->mxtips);
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
tr->startLH = tr->endLH = tr->likelihood;
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
tr->bestOfNode = unlikely;
if(rearrangeBIG(tr, tr->nodep[i], mintrav, maxtrav))
{
if((tr->endLH > tr->startLH) && (tr->bestOfNode != unlikely))
{
restoreTreeFast(tr);
quickSmoothLocal(tr, 3);
tr->startLH = tr->endLH = tr->likelihood;
}
else
{
if(tr->bestOfNode != unlikely)
{
resetBestTree(bestT);
saveBestTree(bestT, tr);
restoreTreeFast(tr);
quickSmoothLocal(tr, 3);
if(tr->likelihood < tr->startLH)
{
int res;
res = recallBestTree(bestT, 1, tr);
assert(res > 0);
}
else
tr->startLH = tr->endLH = tr->likelihood;
}
}
}
}
freeBestTree(bestT);
free(bestT);
return 1;
}
double treeOptimizeRapid(tree *tr, int mintrav, int maxtrav, analdef *adef, bestlist *bt)
{
int i, index,
*perm = (int*)NULL;
nodeRectifier(tr);
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
resetInfoList();
resetBestTree(bt);
tr->startLH = tr->endLH = tr->likelihood;
if(tr->doCutoff)
{
if(tr->bigCutoff)
{
if(tr->itCount == 0)
tr->lhCutoff = 0.5 * (tr->likelihood / -1000.0);
else
tr->lhCutoff = 0.5 * ((tr->lhAVG) / ((double)(tr->lhDEC)));
}
else
{
if(tr->itCount == 0)
tr->lhCutoff = tr->likelihood / -1000.0;
else
tr->lhCutoff = (tr->lhAVG) / ((double)(tr->lhDEC));
}
tr->itCount = tr->itCount + 1;
tr->lhAVG = 0;
tr->lhDEC = 0;
}
if(adef->permuteTreeoptimize)
{
int n = tr->mxtips + tr->mxtips - 2;
perm = (int *)rax_malloc(sizeof(int) * (n + 1));
makePermutation(perm, n, adef);
}
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
tr->bestOfNode = unlikely;
if(adef->permuteTreeoptimize)
index = perm[i];
else
index = i;
if(rearrangeBIG(tr, tr->nodep[index], mintrav, maxtrav))
{
if(Thorough)
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
saveBestTree(bt, tr);
}
else
{
if(tr->bestOfNode != unlikely)
restoreTopologyOnly(tr, bt);
}
}
else
{
insertInfoList(tr->nodep[index], tr->bestOfNode);
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
}
}
}
}
if(!Thorough)
{
Thorough = 1;
for(i = 0; i < iList.valid; i++)
{
tr->bestOfNode = unlikely;
if(rearrangeBIG(tr, iList.list[i].node, mintrav, maxtrav))
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
saveBestTree(bt, tr);
}
else
{
if(tr->bestOfNode != unlikely)
{
restoreTopologyOnly(tr, bt);
}
}
}
}
Thorough = 0;
}
if(adef->permuteTreeoptimize)
rax_free(perm);
return tr->startLH;
}
int determineRearrangementSetting(tree *tr, analdef *adef, bestlist *bestT, bestlist *bt)
{
int i, mintrav, maxtrav, bestTrav, impr, index, MaxFast,
*perm = (int*)NULL;
double startLH;
boolean cutoff;
MaxFast = 26;
startLH = tr->likelihood;
cutoff = tr->doCutoff;
tr->doCutoff = FALSE;
mintrav = 1;
maxtrav = 5;
bestTrav = maxtrav = 5;
impr = 1;
resetBestTree(bt);
if(adef->permuteTreeoptimize)
{
int n = tr->mxtips + tr->mxtips - 2;
perm = (int *)rax_malloc(sizeof(int) * (n + 1));
makePermutation(perm, n, adef);
}
while(impr && maxtrav < MaxFast)
{
recallBestTree(bestT, 1, tr);
nodeRectifier(tr);
if (maxtrav > tr->ntips - 3)
maxtrav = tr->ntips - 3;
tr->startLH = tr->endLH = tr->likelihood;
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
if(adef->permuteTreeoptimize)
index = perm[i];
else
index = i;
tr->bestOfNode = unlikely;
if(rearrangeBIG(tr, tr->nodep[index], mintrav, maxtrav))
{
if(tr->endLH > tr->startLH)
{
restoreTreeFast(tr);
tr->startLH = tr->endLH = tr->likelihood;
}
}
}
treeEvaluate(tr, 0.25);
saveBestTree(bt, tr);
/*printf("DETERMINE_BEST: %d %f\n", maxtrav, tr->likelihood);*/
if(tr->likelihood > startLH)
{
startLH = tr->likelihood;
printLog(tr, adef, FALSE);
bestTrav = maxtrav;
impr = 1;
}
else
{
impr = 0;
}
maxtrav += 5;
if(tr->doCutoff)
{
tr->lhCutoff = (tr->lhAVG) / ((double)(tr->lhDEC));
tr->itCount = tr->itCount + 1;
tr->lhAVG = 0;
tr->lhDEC = 0;
}
}
recallBestTree(bt, 1, tr);
tr->doCutoff = cutoff;
if(adef->permuteTreeoptimize)
rax_free(perm);
return bestTrav;
}
