TEST_F(QueueTest, UpdateParentDescendant) {
buildSimpleTree();
updatePriority(1, {5, false, 8});
dump();
EXPECT_EQ(nodes_, IDList({{5, 100}, {9, 50}, {1, 50}, {3, 33}, {7, 66}}));
}
TEST_F(QueueTest, UpdateParentAncestorExcl) {
buildSimpleTree();
updatePriority(9, {0, true, 16});
dump();
EXPECT_EQ(nodes_, IDList({{9, 100}, {1, 100}, {3, 25}, {5, 25}, {7, 50}}));
}
TEST_F(QueueTest, UpdateParentDescendantExcl) {
buildSimpleTree();
updatePriority(1, {5, true, 8});
dump();
EXPECT_EQ(nodes_, IDList({{5, 100}, {1, 100}, {3, 20}, {7, 40}, {9, 40}}));
}
TEST_F(QueueTest, RemoveLeaf) {
buildSimpleTree();
removeTransaction(3);
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {5, 33}, {9, 100}, {7, 66}}));
}
TEST_F(QueueTest, RemoveParent) {
buildSimpleTree();
removeTransaction(5);
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 20}, {7, 40}, {9, 40}}));
}
TEST_F(QueueTest, UpdateWeightExcl) {
buildSimpleTree();
updatePriority(5, {1, true, 8});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {5, 100}, {9, 40}, {3, 20}, {7, 40}}));
}
TEST_F(QueueTest, UpdateParentSiblingExcl) {
buildSimpleTree();
updatePriority(7, {5, true, 4});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 50}, {5, 50},
{7, 100}, {9, 100}}));
}
TEST_F(QueueTest, UpdateParentSibling) {
buildSimpleTree();
updatePriority(5, {3, false, 4});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 33}, {5, 100},
{9, 100}, {7, 66}}));
}
TEST_F(QueueTest, iterateBFS) {
buildSimpleTree();
auto stopFn = [this] {
return nodes_.size() > 2;
};
dumpBFS(stopFn);
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 25}, {5, 25}, {7, 50}}));
}
TEST_F(QueueTest, UpdateParentAncestor) {
buildSimpleTree();
updatePriority(9, {0, false, 15});
dump();
EXPECT_EQ(nodes_, IDList({{1, 50}, {3, 25}, {5, 25}, {7, 50}, {9, 50}}));
nextEgress();
EXPECT_EQ(nodes_, IDList({{1, 50}, {9, 50}}));
}
TEST_F(QueueTest, UpdateWeightExclDequeued) {
buildSimpleTree();
signalEgress(5, false);
updatePriority(5, {1, true, 7});
signalEgress(1, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{9, 40}, {7, 40}, {3, 20}}));
}
TEST_F(QueueTest, ExclusiveAdd) {
buildSimpleTree();
addTransaction(11, {1, true, 100});
dump();
EXPECT_EQ(nodes_, IDList({
{1, 100}, {11, 100}, {3, 25}, {5, 25}, {9, 100}, {7, 50}
}));
}
TEST_F(QueueTest, AddUnknown) {
buildSimpleTree();
addTransaction(11, {75, false, 16});
dump();
EXPECT_EQ(nodes_, IDList({
{1, 50}, {3, 25}, {5, 25}, {9, 100}, {7, 50}, {11, 50}
}));
}
TEST_F(QueueTest, Misc) {
buildSimpleTree();
EXPECT_FALSE(q_.empty());
EXPECT_EQ(q_.numPendingEgress(), 5);
signalEgress(1, false);
EXPECT_EQ(q_.numPendingEgress(), 4);
EXPECT_FALSE(q_.empty());
removeTransaction(9);
removeTransaction(1);
dump();
EXPECT_EQ(nodes_, IDList({{3, 25}, {5, 25}, {7, 50}}));
}
TEST_F(QueueTest, UpdateParentSiblingExcl) {
buildSimpleTree();
updatePriority(7, {5, true, 3});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 50}, {5, 50},
{7, 100}, {9, 100}}));
signalEgress(1, false);
signalEgress(3, false);
signalEgress(5, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 100}}));
}
TEST_F(QueueTest, UpdateParentDescendantExcl) {
buildSimpleTree();
updatePriority(1, {5, true, 7});
dump();
EXPECT_EQ(nodes_, IDList({{5, 100}, {1, 100}, {3, 20}, {7, 40}, {9, 40}}));
nextEgress();
EXPECT_EQ(nodes_, IDList({{5, 100}}));
signalEgress(5, false);
signalEgress(1, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 40}, {9, 40}, {3, 20}}));
}
TEST_F(QueueTest, nextEgressExclusiveAddWithEgress) {
buildSimpleTree();
// clear all egress, except 3
signalEgress(1, false);
signalEgress(5, false);
signalEgress(7, false);
signalEgress(9, false);
// Add a transaction with exclusive dependency, clear its egress
addTransaction(11, {1, true, 100});
signalEgress(11, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{3, 100}}));
}
TEST_F(QueueTest, nextEgressExclusiveAdd) {
buildSimpleTree();
// clear all egress
signalEgress(1, false);
signalEgress(3, false);
signalEgress(5, false);
signalEgress(7, false);
signalEgress(9, false);
// Add a transaction with exclusive dependency, clear its egress
addTransaction(11, {1, true, 100});
signalEgress(11, false);
// signal egress for a child that got moved via exclusive dep
signalEgress(3, true);
nextEgress();
EXPECT_EQ(nodes_, IDList({{3, 100}}));
}
TEST_F(QueueTest, nextEgressRemoveParent) {
buildSimpleTree();
// Clear egress for all except txn=9
signalEgress(1, false);
signalEgress(3, false);
signalEgress(5, false);
signalEgress(7, false);
// Remove parent of 9 (5)
removeTransaction(5);
nextEgress();
EXPECT_EQ(nodes_, IDList({{9, 100}}));
// signal egress for 9's new siblings to verify weights
signalEgress(3, true);
signalEgress(7, true);
nextEgress();
EXPECT_EQ(nodes_, IDList({{9, 40}, {7, 40}, {3, 20}}));
}
TEST_F(QueueTest, nextEgress) {
buildSimpleTree();
nextEgress();
EXPECT_EQ(nodes_, IDList({{1, 100}}));
addTransaction(11, {7, false, 15});
signalEgress(1, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 50}, {3, 25}, {5, 25}}));
signalEgress(5, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 50}, {3, 25}, {9, 25}}));
signalEgress(5, true);
signalEgress(3, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 66}, {5, 33}}));
signalEgress(5, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 66}, {9, 33}}));
signalEgress(7, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{11, 66}, {9, 33}}));
signalEgress(9, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{11, 100}}));
signalEgress(3, true);
signalEgress(7, true);
signalEgress(9, true);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 50}, {3, 25}, {9, 25}}));
}
TEST_F(QueueTest, UpdateParentSibling) {
buildSimpleTree();
updatePriority(5, {3, false, 3});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 33}, {5, 100},
{9, 100}, {7, 66}}));
signalEgress(1, false);
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 66}, {3, 33}}));
// Clear 5's egress (so it is only in the tree because 9 has egress) and move
// it back. Hit's a slightly different code path in reparent
signalEgress(5, false);
updatePriority(5, {1, false, 3});
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 25}, {7, 50}, {5, 25}, {9, 100}}));
nextEgress();
EXPECT_EQ(nodes_, IDList({{7, 50}, {3, 25}, {9, 25}}));
}
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);
}
TEST_F(QueueTest, Basic) {
buildSimpleTree();
dump();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 25}, {5, 25}, {9, 100}, {7, 50}}));
}
TEST_F(QueueTest, BreadthFirst) {
buildSimpleTree();
dumpBFS();
EXPECT_EQ(nodes_, IDList({{1, 100}, {3, 25}, {5, 25}, {7, 50}, {9, 100}}));
}
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);
}
}
}
