void addChainT(struct chrom *chrom, struct chrom *otherChrom, struct chain *chain)
/* Add T side of chain to fill/gap tree of chromosome.
* This is the easier case since there are no strand
* issues to worry about. */
{
struct slRef *spaceList;
struct slRef *ref;
struct cBlock *startBlock, *block, *nextBlock;
struct gap *gap;
spaceList = findSpaces(chrom->spaces,chain->tStart,chain->tEnd);
startBlock = chain->blockList;
for (ref = spaceList; ref != NULL; ref = ref->next)
{
struct space *space = ref->val;
struct fill *fill;
int gapStart, gapEnd;
for (;;)
{
nextBlock = startBlock->next;
if (nextBlock == NULL)
break;
gapEnd = nextBlock->tStart;
if (gapEnd > space->start)
break;
startBlock = nextBlock;
}
if ((fill = fillSpace(chrom, space, chain, startBlock, FALSE)) != NULL)
{
for (block = startBlock; ; block = nextBlock)
{
nextBlock = block->next;
if (nextBlock == NULL)
break;
gapStart = block->tEnd;
gapEnd = nextBlock->tStart;
if (strictlyInside(space->start, space->end, gapStart, gapEnd))
{
int qs = block->qEnd;
int qe = nextBlock->qStart;
if (chain->qStrand == '-')
reverseIntRange(&qs, &qe, chain->qSize);
gap = gapNew(gapStart, gapEnd, qs, qe);
addSpaceForGap(chrom, gap);
slAddHead(&fill->gapList, gap);
}
}
freez(&ref->val); /* aka space */
}
}
slFreeList(&spaceList);
}
void addChainQ(struct chrom *chrom, struct chrom *otherChrom, struct chain *chain)
/* Add Q side of chain to fill/gap tree of chromosome.
* For this side we have to cope with reverse strand
* issues. */
{
struct slRef *spaceList;
struct slRef *ref;
struct cBlock *startBlock, *block, *nextBlock;
int gapStart, gapEnd;
struct gap *gap;
boolean isRev = (chain->qStrand == '-');
int qStart = chain->qStart, qEnd = chain->qEnd;
if (isRev)
{
reverseIntRange(&qStart, &qEnd, chain->qSize);
reverseBlocksQ(&chain->blockList, chain->qSize);
}
spaceList = findSpaces(chrom->spaces,qStart,qEnd);
startBlock = chain->blockList;
for (ref = spaceList; ref != NULL; ref = ref->next)
{
struct space *space = ref->val;
struct fill *fill;
for (;;)
{
nextBlock = startBlock->next;
if (nextBlock == NULL)
break;
gapEnd = nextBlock->qStart;
if (gapEnd > space->start)
break;
startBlock = nextBlock;
}
if ((fill = fillSpace(chrom, space, chain, startBlock, TRUE))
!= NULL)
{
for (block = startBlock; ; block = nextBlock)
{
nextBlock = block->next;
if (nextBlock == NULL)
break;
gapStart = block->qEnd;
gapEnd = nextBlock->qStart;
if (strictlyInside(space->start, space->end, gapStart, gapEnd))
{
int ts, te;
if (chain->qStrand == '+')
{
ts = block->tEnd;
te = nextBlock->tStart;
}
else
{
ts = nextBlock->tStart;
te = block->tEnd;
}
gap = gapNew(gapStart, gapEnd, ts, te);
addSpaceForGap(chrom, gap);
slAddHead(&fill->gapList, gap);
}
}
freez(&ref->val); /* aka space */
}
}
slFreeList(&spaceList);
if (isRev)
reverseBlocksQ(&chain->blockList, chain->qSize);
}
std::shared_ptr<INodeSystem> NodeSystemBuilder::create() {
for (auto& link: me->links) {
if (!me->useExtraNodes) {
me->linkBuildNodes(link.first, link.second);
me->putSpring(link.first, link.second);
continue;
}
// both linked nodes
auto nodeFrom = me->model->getNode(link.first);
auto nodeTo = me->model->getNode(link.second);
size_t subNodeCount = 1;
if (me->useConstantNumberOfExtraNodes) {
subNodeCount = me->defaultExtraNodesPerEdge;
}
else {
double length = glm::length(nodeTo->getPosition() - nodeFrom->getPosition());
subNodeCount = (size_t) glm::round(length / me->defaultUnitsPerExtraNode);
}
if(subNodeCount == 0)
std::cout << "subnodes cannot be placed" << "\n";
// fill space between two nodes by adding a number of extra nodes
auto points = fillSpace(nodeFrom->getPosition(), nodeTo->getPosition(), subNodeCount);
std::vector<size_t> subNodeIds;
for (glm::dvec3& point: points) {
std::cout << "sn:" << point.x << " " << point.y << "\n";
subNodeIds.push_back(addNode(me->defaultSubNodeMass, point));
}
if(subNodeCount == 0)
{
std::cout << "subnodesCount = 0 after fillSpace" << "\n";
continue;
}
// link all nodes to make a chain
for (size_t i = 0; i < subNodeIds.size() - 1; ++i) {
me->linkBuildNodes(subNodeIds[i], subNodeIds[i + 1]);
me->putSpring(subNodeIds[i], subNodeIds[i + 1]);
}
// link main nodes with head and tail of list of sub-nodes
me->linkBuildNodes(link.first, subNodeIds.front());
me->linkBuildNodes(subNodeIds.back(), link.second);
std::cout << "connect subnodes to link edges" << "\n";
me->putSpring(link.first, subNodeIds.front());
me->putSpring(subNodeIds.back(), link.second);
}
std::cout << "Torsion springs mounting" << "\n";
for (auto& center: me->buildNodes) {
for (auto& left: center->prev) {
for (auto& right: center->next) {
me->putTorsionSpring(left, center->id, right);
}
}
}
// mount contstraints
for (auto& constraint: me->model->constraints)
constraint->assignToSystem(me->model);
me->model->grip->assignToSystem(me->model);
return me->model;
}
