bool Box<DATA>::encloses
(
const Box<DATA>& ar_Box
)
{
return (encloses(ar_Box.upperBound) && encloses(ar_Box.lowerBound));
}
void OctTree::handleObjectPlacement(OctTree::ObjType * obj) {
int whereIsObj;
BoundingBox objbox = boundingBox.boundingBoxForCollideable(obj);
/// Remove object and try the parent.
if (parent != NULL
&& boundingBox.numCornersContained(objbox) != kNumNodes) {
remove(obj);
parent->handleObjectPlacement(obj);
}
/// We need to rebase and then add the object.
else {
/// First, if the do not enclode the object, then
while (boundingBox.numCornersContained(objbox) != kNumNodes) {
whereIsObj = whichChildForPoint(obj->getPosition());
rebase((~whereIsObj) & (kNumNodes - 1));
}
UTIL_ASSERT(encloses(obj->getPosition()));
UTIL_ASSERT(boundingBox.numCornersContained(objbox) == kNumNodes);
BoundingBox childbox = boundingBoxForChild(whichChildForPoint(
obj->getPosition()));
/// We pass it onto the child
if (!objectLiesOnChildBoundaries(obj) && (activeChildren != 0
|| numDirectlyHeldObjects() > getMaxLeafObjects())
&& (GUtils::norm(getBoundingBox().getDimensions()) / 2.0) > kMinLeafDim
&& childbox.numCornersContained(objbox) == kNumNodes) {
remove(obj);
whereIsObj = whichChildForPoint(obj->getPosition());
UTIL_ASSERT(0 <= whereIsObj && whereIsObj < kNumNodes);
if (children[whereIsObj] == NULL) {
children[whereIsObj] = createChild(whereIsObj);
}
//setChildActive(whereIsObj, true);
children[whereIsObj]->insert(obj);
}
/// We keep it to ourselves
else {
UTIL_ASSERT(encloses(obj->getPosition()));
UTIL_ASSERT(boundingBox.numCornersContained(objbox) == kNumNodes);
add(obj);
updateActiveStates(this);
obj->setPositionChanged(false);
}
}
}
bool encloses(BasicVector<T, 2> v) const {
return encloses(v.x, v.y);
}
bool OctTree::encloses(OctTree::ObjType * obj) {
Vec pos = obj->getPosition();
return obj != NULL && encloses(pos);
}
static void removeEnclosedDoubleSofts(struct rbTree *vertexTree, struct rbTree *edgeTree,
int maxBleedOver, double singleExonMaxOverlap)
/* Move double-softs that overlap spliced things to a very great extent into
* the spliced things. Also remove tiny double-softs (no more than 2*maxBleedOver). */
{
/* Traverse graph and build up range tree covering spliced exons. For each
* range of overlapping exons, assemble a singly-linked list of all exons in
* the range */
struct rbTree *rangeTree = rangeTreeNew(0);
struct slRef *edgeRef, *edgeRefList = rbTreeItems(edgeTree);
int removedCount = 0;
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *start = edge->start;
struct vertex *end = edge->end;
if (start->type == ggHardStart || end->type == ggHardEnd)
{
rangeTreeAddValList(rangeTree, start->position, end->position, edge);
}
}
/* Traverse graph yet one more time looking for doubly-soft exons
* that are overlapping the spliced exons. */
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *start = edge->start;
struct vertex *end = edge->end;
if (start->type == ggSoftStart && end->type == ggSoftEnd)
{
int s = start->position;
int e = end->position;
int size = e - s;
if (size <= maxBleedOver+maxBleedOver)
{
/* Tiny case, just remove edge and forget it. */
verbose(3, "Removing tiny double-soft edge from %d to %d\n", s, e);
rbTreeRemove(edgeTree, edge);
++removedCount;
}
else
{
/* Normal case, look for exon list that encloses us, and
* if any single exon in that list encloses us, merge into it. */
int splicedOverlap = rangeTreeOverlapSize(rangeTree, s, e);
if (splicedOverlap > 0 && splicedOverlap > singleExonMaxOverlap*size)
{
if (!trustedEdge(edge))
{
/* Once we find a range that overlaps the doubly-soft edge, find
* (half-hard or better) edge from that range that encloses the
* doubly soft edge. */
struct range *r = rangeTreeMaxOverlapping(rangeTree, s, e);
struct edge *nextEdge, *edgeList = r->val;
struct edge *enclosingEdge = NULL;
for (nextEdge = edgeList; edgeList != NULL; edgeList = edgeList->next)
{
if (encloses(nextEdge, edge))
{
enclosingEdge = nextEdge;
}
}
if (enclosingEdge != NULL)
{
enclosingEdge->evList = slCat(enclosingEdge->evList, edge->evList);
edge->evList = NULL;
verbose(3, "Removing doubly-soft edge %d-%d, reassigning to %d-%d\n",
s, e, enclosingEdge->start->position,
enclosingEdge->end->position);
rbTreeRemove(edgeTree, edge);
++removedCount;
}
}
}
}
}
}
/* Clean up and go home. */
if (removedCount > 0)
removeUnusedVertices(vertexTree, edgeTree);
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *nextEdge, *edge = edgeRef->val;
while (edge != NULL)
{
nextEdge = edge->next;
edge->next = NULL;
edge = nextEdge;
}
}
slFreeList(&edgeRefList);
rbTreeFree(&rangeTree);
}