void pllMakeParsimonyTreeFast(tree *tr)
{
nodeptr
p,
f;
int
i,
nextsp,
*perm = (int *)malloc((size_t)(tr->mxtips + 1) * sizeof(int));
unsigned int
randomMP,
startMP;
assert(!tr->constrained);
makePermutationFast(perm, tr->mxtips, tr);
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
buildSimpleTree(tr, perm[1], perm[2], perm[3]);
f = tr->start;
while(tr->ntips < tr->mxtips)
{
nodeptr q;
tr->bestParsimony = INT_MAX;
nextsp = ++(tr->ntips);
p = tr->nodep[perm[nextsp]];
q = tr->nodep[(tr->nextnode)++];
p->back = q;
q->back = p;
if(tr->grouped)
{
int
number = p->back->number;
tr->constraintVector[number] = -9;
}
stepwiseAddition(tr, q, f->back);
{
nodeptr
r = tr->insertNode->back;
int counter = 4;
hookupDefault(q->next, tr->insertNode, tr->numBranches);
hookupDefault(q->next->next, r, tr->numBranches);
computeTraversalInfoParsimony(q, tr->ti, &counter, tr->mxtips, FALSE);
tr->ti[0] = counter;
newviewParsimonyIterativeFast(tr);
}
}
printf("ADD: %d\n", tr->bestParsimony);
nodeRectifierPars(tr);
randomMP = tr->bestParsimony;
do
{
startMP = randomMP;
nodeRectifierPars(tr);
for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
rearrangeParsimony(tr, tr->nodep[i], 1, 20, FALSE);
if(tr->bestParsimony < randomMP)
{
restoreTreeRearrangeParsimony(tr);
randomMP = tr->bestParsimony;
}
}
}
while(randomMP < startMP);
printf("OPT: %d\n", tr->bestParsimony);
}
void TreeRandomizer::createStepwiseAdditionParsimonyTree(TreeAln &traln, ParallelSetup& pl )
{
auto *tr = &(traln.getTrHandle());
auto *pr = &(traln.getPartitionsHandle());
assert(tr->fastParsimony == PLL_FALSE);
nodeptr
p,
f;
int
nextsp;
auto perm = std::vector<int>(tr->mxtips+1, 0);
assert(!tr->constrained);
makePermutationFast(perm.data(), tr->mxtips, tr);
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
buildSimpleTree(tr, pr, perm[1], perm[2], perm[3]);
f = tr->start;
while(tr->ntips < tr->mxtips)
{
nodeptr q;
tr->bestParsimony = std::numeric_limits<nat>::max();
nextsp = ++(tr->ntips);
p = tr->nodep[perm[nextsp]];
q = tr->nodep[(tr->nextnode)++];
p->back = q;
q->back = p;
if(tr->grouped)
{
int
number = p->back->number;
tr->constraintVector[number] = -9;
}
stepwiseAddition(tr, pr, q, f->back, pl);
// std::cout << SyncOut() << "bestPars: "<< tr->bestParsimony << std::endl;
{
nodeptr
r = tr->insertNode->back;
int counter = 4;
hookupDefault(q->next, tr->insertNode);
hookupDefault(q->next->next, r);
computeTraversalInfoParsimony(q, tr->ti, &counter, tr->mxtips, PLL_FALSE);
tr->ti[0] = counter;
newviewParsimonyIterativeFast(tr, pr);
}
}
}
