void MoleculeURLListProperty::loadMolecules(bool selectedOnly /*= false*/, bool removeOnFailure /*= false*/) {
std::vector<std::string> failedURLs;
for (size_t i=0; i<value_.size(); i++) {
std::string url = value_[i];
if (selectedOnly && !isSelected(url))
continue;
if (getMolecule(url))
continue;
try {
loadMolecule(url);
}
catch (tgt::FileException& e) {
LERROR(e.what());
failedURLs.push_back(url);
}
catch (std::bad_alloc&) {
LERROR("bad allocation while loading molecule: " << url);
failedURLs.push_back(url);
}
catch (tgt::Exception& e) {
LERROR("unknown exception while loading molecule '" << url << "':" << e.what());
failedURLs.push_back(url);
}
}
if (removeOnFailure) {
for (size_t i=0; i<failedURLs.size(); i++)
removeURL(failedURLs.at(i));
}
}
void MoleculeURLListProperty::loadMolecule(const std::string& url)
throw (tgt::FileException, std::bad_alloc) {
if (!containsURL(url)) {
LWARNING("loadMolecule(): passed URL not contained by this property: " << url);
return;
}
// delete molecule, if already loaded and owned by the property
if (getMolecule(url) && isOwner(url))
delete getMolecule(url);
handleMap_.erase(url);
ownerMap_.erase(url);
ProgressBar* progressBar = getProgressBar();
if (progressBar) {
progressBar->setTitle("Loading molecule");
progressBar->setMessage("Loading molecule ...");
}
Molecule* handle = MoleculeIO::read(MoleculeURL(url));
if (handle) {
// url may have been altered by loading routine
if (url != handle->getOrigin().getURL()) {
bool selected = isSelected(url);
selectionMap_.erase(url);
selectionMap_[handle->getOrigin().getURL()] = selected;
for (size_t i=0; i<value_.size(); i++) {
if (value_[i] == url) {
value_[i] = handle->getOrigin().getURL();
break;
}
}
}
handleMap_[handle->getOrigin().getURL()] = handle;
ownerMap_[handle->getOrigin().getURL()] = true;
}
invalidate();
}
void MoleculeURLListProperty::removeMolecule(Molecule* handle) {
tgtAssert(handle, "null pointer passed");
std::string url = handle->getOrigin().getURL();
if (!containsURL(url)) {
LWARNING("removeMolecule(): passed handle's URL not contained by this property: " << url);
return;
}
if ((getMolecule(url) == handle) && isOwner(url)) {
delete handle;
}
handleMap_.erase(url);
ownerMap_[url] = false;
invalidate();
}
void MoleculeURLListProperty::removeURL(const std::string& url) {
if (!containsURL(url)) {
LWARNING("removeURL(): passed URL not contained by this property: " << url);
return;
}
// free corresponding molecule, if owned by the property
Molecule* handle = getMolecule(url);
if (handle)
removeMolecule(handle);
// remove url from url list
std::vector<std::string>::iterator it = std::find(value_.begin(), value_.end(), url);
tgtAssert(it != value_.end(), "url not found");
value_.erase(it);
// remove url from maps
handleMap_.erase(url);
selectionMap_.erase(url);
ownerMap_.erase(url);
invalidate();
}
const char * IndigoCdxMolecule::getName ()
{
return getMolecule().name.ptr();
}
BaseMolecule & IndigoCdxMolecule::getBaseMolecule ()
{
return getMolecule();
}
const char * IndigoSmilesMolecule::getName ()
{
if (getMolecule().name.ptr() == 0)
return "";
return getMolecule().name.ptr();
}
BaseMolecule & IndigoSmilesMolecule::getBaseMolecule ()
{
return getMolecule();
}
BaseMolecule & IndigoRdfMolecule::getBaseMolecule ()
{
return getMolecule();
}