void CEditsSaver::ResetIds(const CBioseq_Handle& handle,
const TIds& ids,
ECallMode mode)
{
if (ids.empty())
return;
typedef CSeqEdit_Cmd_ResetIds::TRemove_ids TList;
CRef<CSeqEdit_Cmd> cmd;
TList& id_list =
SCmdCreator<CSeqEdit_Cmd::e_Reset_ids>::CreateCmd(handle,
CBioObjectId(*ids.begin()),
cmd)
.SetRemove_ids();
transform(ids.begin(), ids.end(), back_inserter(id_list), s_ConvertId);
GetDBEngine().SaveCommand(*cmd);
ITERATE(TIds, id, ids) {
GetDBEngine().NotifyIdChanged(*id,"");
;
}
/// not yet in SC-6.0...
void CAsnCache_DataLoader::GetGis(const TIds& ids, TLoaded& loaded, TIds& ret)
{
SCacheInfo& index = x_GetIndex();
CFastMutexGuard LOCK(index.cache_mtx);
ret.clear();
ret.resize(ids.size());
loaded.clear();
loaded.resize(ids.size());
for (size_t i = 0; i < ids.size(); ++i) {
CAsnIndex::TGi gi = 0;
time_t timestamp = 0;
if (index.cache->GetIdInfo(ids[i], gi, timestamp)) {
ret[i] = CSeq_id_Handle::GetHandle(GI_FROM(CAsnIndex::TGi, gi));
loaded[i] = true;
}
}
}
void CAsnCache_DataLoader::GetIds(const CSeq_id_Handle& idh,
TIds& ids)
{
///
/// okay, the contract is that we must return something if we know the
/// sequence. thus, if the sequence exists in the cache, we must return
/// something. If the SeqId index is available, the cache will use it to
/// get the ids quickly; otherwise it will use the expensive way, retrieving
/// the entire sequence.
///
SCacheInfo& index = x_GetIndex();
CFastMutexGuard LOCK(index.cache_mtx);
vector<CSeq_id_Handle> bioseq_ids;
bool res = index.cache->GetSeqIds(idh, bioseq_ids, false);
++index.requests;
if (res) {
ids.swap(bioseq_ids);
}
}
void ClusterNode::getClusters(osgUtil::CullVisitor* cv, ClusterList& out)
{
_nextLabel = 0;
osg::Camera* camera = cv->getCurrentCamera();
osg::Viewport* viewport = camera->getViewport();
if (!viewport)
{
return;
}
osg::Matrixd mvpw = camera->getViewMatrix() *
camera->getProjectionMatrix() *
camera->getViewport()->computeWindowMatrix();
std::vector<TPoint> points;
osg::NodeList validPlaces;
buildIndex();
for (osg::NodeList::iterator itr = _clusterIndex.begin(); itr != _clusterIndex.end(); ++itr)
{
osg::Group* index = static_cast<osg::Group*>(itr->get());
if (cv->isCulled(index->getBound()))
{
continue;
}
for (unsigned int i = 0; i < index->getNumChildren(); i++)
{
osg::Node* node = index->getChild(i);
osg::Vec3d world = node->getBound().center();
if (cv->isCulled(*node))
{
continue;
}
if (!_horizon->isVisible(world))
{
continue;
}
osg::Vec3d screen = world * mvpw;
if (screen.x() >= 0 && screen.x() <= viewport->width() &&
screen.y() >= 0 && screen.y() <= viewport->height())
{
validPlaces.push_back(node);
points.push_back(TPoint(screen.x(), screen.y()));
}
}
}
if (validPlaces.size() == 0) return;
kdbush::KDBush<TPoint> index(points);
std::set< unsigned int > clustered;
for (unsigned int i = 0; i < validPlaces.size(); i++)
{
TPoint &screen = points[i];
osg::Node* node = validPlaces[i].get();
// If this thing is already part of a cluster then just continue.
if (clustered.find(i) != clustered.end())
{
continue;
}
osg::Vec3d world = node->getBound().center();
// Get any matching indices that are part of this cluster.
TIds indices;
index.range(screen.first - _radius, screen.second - _radius, screen.first + _radius, screen.second + _radius, indices);
// Create a new cluster.
Cluster cluster;
unsigned int actualCount = 0;
// Add all of the points to the cluster.
for (unsigned int j = 0; j < indices.size(); j++)
{
if (clustered.find(indices[j]) == clustered.end())
{
if (_canClusterCallback.valid())
{
bool canCluster = (*_canClusterCallback)(node, validPlaces[indices[j]].get());
if (!canCluster) {
continue;
}
}
cluster.nodes.push_back(validPlaces[indices[j]]);
actualCount++;
clustered.insert(indices[j]);
}
}
std::stringstream buf;
buf << actualCount << std::endl;
PlaceNode* marker = getOrCreateLabel();
GeoPoint markerPos;
markerPos.fromWorld(_mapNode->getMapSRS(), world);
marker->setPosition(markerPos);
marker->setText(buf.str());
cluster.marker = marker;
out.push_back(cluster);
clustered.insert(i);
}
}
