SSLContext SSLObject::sslContext()
{
SSL_CTX* ctx = SSL_get_SSL_CTX(d_ssl.get());
return SSLContext(std::shared_ptr<SSL_CTX>(ctx, null_deleter()));
}
format(log_element &e)
: m_identifier("unnamed")
{
boost::shared_ptr<loglite::log_element> p(&e, null_deleter());
m_element_list.push_back(p);
}
format(log_element &e, const std::string &identifier)
: m_identifier(identifier)
{
boost::shared_ptr<loglite::log_element> p(&e, null_deleter());
m_element_list.push_back(p);
}
/** Remove the child node.
* @param el The child node to remove. This Node will be deleted and therefore unusable after calling this method.
*/
void remove_child(xml_node* el) {child_list.remove(xml_nodeRef(el, null_deleter()));}
exception_ptr result::make_no_result_error()
{
static remote_error e(remote_error::no_result, "no result for one way call");
return exception_ptr(&e, null_deleter());
}
ControlDevice GetStreamDevice(std::istream & in, const std::string& name)
{
boost::shared_ptr<std::istream> inp(&in, null_deleter());
return ControlDevice(boost::shared_ptr<control_device_impl>(new istream_control_device_impl(inp,name)));
}
QList<StreamerServicePtr> VideoImplService::getStreamerServices()
{
QList<StreamerServicePtr> retval;
QList<StreamerService *> services = mStreamerServiceListener->getServices();
foreach(StreamerService* service, services)
{
if(service)
{
StreamerServicePtr temp(new StreamerServiceProxy(mBackend->mContext, service->getName()), null_deleter());
retval.append(temp);
}
}
return retval;
}
// -------------------------------------------------------------
// NonlinearSolverImplementation::solve
// -------------------------------------------------------------
void
NonlinearSolverImplementation::solve(Vector &x)
{
p_X.reset(&x, null_deleter());
this->p_solve();
}
bool Image::load(QString path)
{
ImagePtr self = ImagePtr(this, null_deleter());
DataReaderWriter().readInto(self, path);
return this->getBaseVtkImageData()!=0;
}
void FiltersWidget::onServiceAdded(Filter* service)
{
this->appendFilterIfWanted(FilterPtr(service, null_deleter()));
}
void XML::getOpArgs(const node_ptr script, block_ptr curBlock) {
std::vector<std::string> args;
std::vector<block_ptr> blockArgs;
std::string opStr;
int i(0);
node_ptr tmpScript(script);
if (std::strcmp(tmpScript->name(), "block") == 0 ||
std::strcmp(tmpScript->name(), "list") == 0) {
if (tmpScript->first_attribute("s")) {
curBlock->setOpcode(tmpScript->first_attribute("s")->value());
} else if (tmpScript->first_attribute("var")) {
curBlock->setOpcode("readVariable");
opStr = tmpScript->first_attribute("var")->value();
} else if (tmpScript->first_attribute("point")) {
curBlock->setOpcode("readPoint");
opStr = tmpScript->first_attribute("point")->value();
} else if (tmpScript->first_attribute("schedule")) {
curBlock->setOpcode("reportGetSched");
opStr = tmpScript->first_attribute("schedule")->value();
}
if (!opStr.empty()) {
args.push_back(opStr);
}
const node_ptr first(tmpScript->first_node(), null_deleter());
for (node_ptr child(first);
child;
child.reset(child->next_sibling(), null_deleter())) {
if (std::strcmp(child->name(), "block") == 0 ||
std::strcmp(child->name(), "script") == 0 ||
std::strcmp(child->name(), "list") == 0) {
block_ptr b(new blocks::Block);
getOpArgs(child, b);
if (b->opcode() == "nested") {
curBlock->addNestedStart(b->nestedBlocks()[0]);
} else if (b->opcode().empty()) {
blockArgs = b->blockArgs();
} else {
opStr = "block:" + std::to_string(i++);
blockArgs.push_back(b);
}
} else if (std::strcmp(child->name(), "l") == 0) {
if (child->first_node() != 0) {
opStr = child->value();
} else {
opStr = child->first_node("option")->value();
}
}
if (!opStr.empty()) {
args.push_back(opStr);
}
}
} else if (std::strcmp(tmpScript->name(), "script") == 0) {
curBlock->setOpcode("nested");
node_ptr child(tmpScript->first_node(), null_deleter());
curBlock->addNestedStart(getChildren(child, true));
}
if (args.size() > 0) curBlock->setArgs(args);
if (blockArgs.size() > 0) curBlock->setBlockArgs(blockArgs);
}
Cell::Cell(boost::shared_ptr<AbstractCellProperty> pMutationState,
AbstractCellCycleModel* pCellCycleModel,
AbstractSrnModel* pSrnModel,
bool archiving,
CellPropertyCollection cellPropertyCollection)
: mCanDivide(false),
mCellPropertyCollection(cellPropertyCollection),
mpCellCycleModel(pCellCycleModel),
mpSrnModel(pSrnModel),
mDeathTime(DBL_MAX), // This has to be initialised for archiving
mStartOfApoptosisTime(DBL_MAX),
mApoptosisTime(0.25), // cell takes 15 min to fully undergo apoptosis
mUndergoingApoptosis(false),
mIsDead(false),
mIsLogged(false)
{
if (SimulationTime::Instance()->IsStartTimeSetUp()==false)
{
EXCEPTION("Cell is setting up a cell-cycle model but SimulationTime has not been set up");
}
if (pCellCycleModel == NULL)
{
EXCEPTION("Cell-cycle model is null");
}
mpCellCycleModel->SetCell(CellPtr(this, null_deleter()));
// Create a null srn model if none given
if (pSrnModel == NULL)
{
pSrnModel = new NullSrnModel;
mpSrnModel = pSrnModel;
}
mpSrnModel->SetCell(CellPtr(this, null_deleter()));
if (!mCellPropertyCollection.HasPropertyType<CellId>())
{
// Set cell identifier this will be called all the time unless the constructor is called through archiving
MAKE_PTR(CellId, p_cell_id);
p_cell_id->AssignCellId();
mCellPropertyCollection.AddProperty(p_cell_id);
}
if (!pMutationState->IsSubType<AbstractCellMutationState>())
{
EXCEPTION("Attempting to create cell with a cell mutation state that is not a subtype of AbstractCellMutationState");
}
if (!mCellPropertyCollection.HasProperty(pMutationState))
{
mCellPropertyCollection.AddProperty(pMutationState);
}
if (!mCellPropertyCollection.HasPropertyType<CellData>())
{
// Add empty cell data
MAKE_PTR(CellData, p_cell_data);
mCellPropertyCollection.AddProperty(p_cell_data);
}
/*
* If a cell proliferative type was not passed in via the input
* argument cellPropertyCollection (for example as in the case
* of a daughter cell being created following division) then add
* add a 'default' cell proliferative type to the cell property
* collection. This ensures that the method GetCellProliferativeType()
* always returns a valid proliferative type.
*/
if (!mCellPropertyCollection.HasPropertyType<AbstractCellProliferativeType>())
{
mCellPropertyCollection.AddProperty(CellPropertyRegistry::Instance()->Get<DefaultCellProliferativeType>());
}
if (!archiving)
{
// Increment cell count for each cell property in mCellPropertyCollection
for (CellPropertyCollection::Iterator property_iter = mCellPropertyCollection.Begin();
property_iter != mCellPropertyCollection.End();
++property_iter)
{
(*property_iter)->IncrementCellCount();
}
}
}
void NodeBasedCellPopulation<DIM>::NonBlockingSendCellsToNeighbourProcesses()
{
if (!PetscTools::AmTopMost())
{
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > p_cells_right(&mCellsToSendRight, null_deleter());
int tag = SmallPow(2u, 1+ PetscTools::GetMyRank() ) * SmallPow (3u, 1 + PetscTools::GetMyRank() + 1);
mRightCommunicator.ISendObject(p_cells_right, PetscTools::GetMyRank() + 1, tag);
}
if (!PetscTools::AmMaster())
{
int tag = SmallPow (2u, 1 + PetscTools::GetMyRank() ) * SmallPow (3u, 1 + PetscTools::GetMyRank() - 1);
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > p_cells_left(&mCellsToSendLeft, null_deleter());
mLeftCommunicator.ISendObject(p_cells_left, PetscTools::GetMyRank() - 1, tag);
}
// Now post receives to start receiving data before returning.
if (!PetscTools::AmTopMost())
{
int tag = SmallPow (3u, 1 + PetscTools::GetMyRank() ) * SmallPow (2u, 1+ PetscTools::GetMyRank() + 1);
mRightCommunicator.IRecvObject(PetscTools::GetMyRank() + 1, tag);
}
if (!PetscTools::AmMaster())
{
int tag = SmallPow (3u, 1 + PetscTools::GetMyRank() ) * SmallPow (2u, 1+ PetscTools::GetMyRank() - 1);
mLeftCommunicator.IRecvObject(PetscTools::GetMyRank() - 1, tag);
}
}
void NodeBasedCellPopulation<DIM>::SendCellsToNeighbourProcesses()
{
MPI_Status status;
if (!PetscTools::AmTopMost())
{
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > p_cells_right(&mCellsToSendRight, null_deleter());
mpCellsRecvRight = mRightCommunicator.SendRecvObject(p_cells_right, PetscTools::GetMyRank() + 1, mCellCommunicationTag, PetscTools::GetMyRank() + 1, mCellCommunicationTag, status);
}
if (!PetscTools::AmMaster())
{
boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > p_cells_left(&mCellsToSendLeft, null_deleter());
mpCellsRecvLeft = mLeftCommunicator.SendRecvObject(p_cells_left, PetscTools::GetMyRank() - 1, mCellCommunicationTag, PetscTools::GetMyRank() - 1, mCellCommunicationTag, status);
}
}
/**
* Sets the stream.
*/
void setStream(std::ostream& aStream) {
setStreamImpl(shared_ptr<std::ostream>(&aStream, null_deleter()));
};
///This function checks if a typeID is parent to this.
so_type::weak_pointer RK_CALL so_type_impl::findAncestor_impl(const unsigned int* aTypeID ) const {
if( compare_equal(aTypeID, this->TypeID_begin()) )
return rk_static_ptr_cast<so_type>(mThis);
if(mAncestors.empty())
return so_type::weak_pointer();
detail::dummy_so_type d(aTypeID);
std::set< so_type::weak_pointer, so_type_impl::compare_weak_t>::const_iterator it = mAncestors.lower_bound(so_type::shared_pointer(&d,null_deleter()));
if((it != mAncestors.end()) && (it->lock()) && (compare_equal(it->lock()->TypeID_begin(),aTypeID)))
return *it;
for(it = mAncestors.begin(); it != mAncestors.end(); ++it) {
if(it->lock()) {
so_type::weak_pointer p = it->lock()->findAncestor(aTypeID);
if(p.lock())
return p;
};
};
return so_type::weak_pointer();
};
/// Create compatible render context
RenderContext::RenderContext(QGLWidget * widget)
{
/// Dirty hack, but we'll use it with caution, I promise.
m_context = shared_ptr<QGLContext>(const_cast<QGLContext*>(widget->context()), null_deleter());
}
StreamerServicePtr VideoServiceNull::getStreamerService(QString uid)
{
return StreamerServicePtr(new StreamerServiceNull() , null_deleter());
}
ControlDevice GetDuplexControlDevice(std::istream& in1,
const char* filename, const std::string& name) {
boost::shared_ptr<std::istream> in1p(&in1, null_deleter());
boost::shared_ptr<std::istream> in2p(new std::ifstream(filename));
return ControlDevice(boost::shared_ptr<control_device_impl>(new multi_istream_control_device(in1p,in2p,name)));
}
void StreamerServiceProxy::onServiceAdded(StreamerService* service)
{
if(service && service->getName() == mServiceName)
mStreamerService.reset(service, null_deleter());
}