void NodeCore::kill(NodeCore &ref)
{
StLock<Mutex> _(*this);
assert(hasReference(ref));
ref.kill();
removeReference(ref);
}
PaintInfo * TreeFuncNode::getPaintInfo( void )
//--------------------------------------------
{
OptionManager * mgr = WBRWinBase::optManager();
return new PaintInfo( mgr->getFunctionOpts().repeated( hasReference() ) );
}
bool GTUtilsAssemblyBrowser::hasReference(HI::GUITestOpStatus& os, const QString &viewTitle) {
Q_UNUSED(os);
AssemblyBrowserUi* view = getView(os, viewTitle);
GT_CHECK_RESULT(NULL != view, "Assembly browser wasn't found", false);
return hasReference(os, view);
}
std::shared_ptr<IDataArray> BaseTagHDF5::getReference(const std::string &name_or_id) const {
std::shared_ptr<IDataArray> da;
boost::optional<H5Group> g = refs_group(false);
std::string id = block()->resolveEntityId({name_or_id, ObjectType::DataArray});
if (g && hasReference(id)) {
H5Group group = g->openGroup(id);
da = std::make_shared<DataArrayHDF5>(file(), block(), group);
}
return da;
}
bool GTUtilsAssemblyBrowser::hasReference(HI::GUITestOpStatus& os, QWidget* view) {
Q_UNUSED(os);
if (NULL == view) {
view = GTUtilsMdi::activeWindow(os);
}
GT_CHECK_RESULT(NULL != view, "View is NULL", false);
AssemblyBrowserUi* assemblyBrowser = view->findChild<AssemblyBrowserUi*>("assembly_browser_" + view->objectName());
GT_CHECK_RESULT(NULL != assemblyBrowser, "Assembly browser wasn't found", false);
return hasReference(os, assemblyBrowser);
}
bool BaseTagHDF5::removeReference(const std::string &name_or_id) {
boost::optional<Group> g = refs_group();
bool removed = false;
if (g && hasReference(name_or_id)) {
shared_ptr<IDataArray> reference = getReference(name_or_id);
g->removeGroup(reference->id());
removed = true;
}
return removed;
}
shared_ptr<IDataArray> BaseTagHDF5::getReference(const std::string &name_or_id) const {
shared_ptr<IDataArray> da;
boost::optional<Group> g = refs_group();
std::string id = name_or_id;
if (!util::looksLikeUUID(name_or_id) && block()->hasDataArray(name_or_id)) {
id = block()->getDataArray(name_or_id)->id();
}
if (g && hasReference(id)) {
Group group = g->openGroup(id);
da = make_shared<DataArrayHDF5>(file(), block(), group);
}
return da;
}
qint64 AssemblyModel::getModelLength(U2OpStatus & os) {
if(NO_VAL == cachedModelLength) {
// try to set length from attributes
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(attributeDbi != NULL) {
U2IntegerAttribute attr = U2AttributeUtils::findIntegerAttribute(attributeDbi, assembly.id, U2BaseAttributeName::reference_length, os);
LOG_OP(os);
if(attr.hasValidId()) {
cachedModelLength = attr.value;
}
// ignore incorrect attribute value and remove corrupted attribute (auto-fix incorrectly converted ugenedb)
if(cachedModelLength == 0) {
coreLog.details(QString("ignored incorrect value of attribute %1: should be > 0, got %2. Bad attribute removed!").arg(QString(U2BaseAttributeName::reference_length)).arg(cachedModelLength));
cachedModelLength = NO_VAL;
U2AttributeUtils::removeAttribute(attributeDbi, attr.id, os);
}
}
// if cannot from attributes -> set from reference or max end pos
if(cachedModelLength == NO_VAL) {
qint64 refLen = hasReference() ? refObj->getSequenceLength() : 0;
qint64 assLen = assemblyDbi->getMaxEndPos(assembly.id, os);
LOG_OP(os);
cachedModelLength = qMax(refLen, assLen);
// and save in attribute
U2IntegerAttribute attr;
U2AttributeUtils::init(attr, assembly, U2BaseAttributeName::reference_length);
attr.value = cachedModelLength;
attributeDbi->createIntegerAttribute(attr, os);
}
if(cachedModelLength == NO_VAL){
os.setError("Can't get model length, database is corrupted");
LOG_OP(os);
}
}
return cachedModelLength;
}
void TreeNode::debugInfo( TreeRoot * root )
//-----------------------------------------
{
WString boundLine;
WString descendLine;
char * enabled;
char * placed;
WString statLine;
WString refLine;
WString rootLine;
TreeCoord ox, oy;
TreeRect rootRect;
ox = _parent->getXOff();
oy = _parent->getYOff();
root->getBound( rootRect );
rootLine.printf( "_rootNode = %s, bounding(%ld,%ld,%ld,%ld) ",
root->node()->name(), rootRect.x(), rootRect.y(),
rootRect.w(), rootRect.h() );
boundLine.printf( "_bounding [%s] = (%ld,%ld,%ld,%ld), offset = (%ld,%ld) ",
(_flags.boundSet) ? "set" : "unset",
_bounding.x(), _bounding.y(),
_bounding.w(), _bounding.h(),
ox, oy );
descendLine.printf( "_sibWidth = %ld, _descend = (%ld,%ld,%ld,%ld) ",
_sibWidth, _descend.x(), _descend.y(),
_descend.w(), _descend.h() );
switch( _flags.enabled ) {
case Hidden:
enabled = "Hidden";
break;
default:
enabled = "Visible";
break;
}
switch( _flags.placed ) {
case NotPlaced:
placed = "NotPlaced";
break;
case PartiallyPlaced:
placed = "PartiallyPlaced";
break;
case Arranging:
placed = "Arranging";
break;
default:
placed = "Placed";
}
statLine.printf( " enabled = %s, placed = %s, selected = %s, _level = %d\n",
enabled, placed, (_flags.selected) ? "true" : "false",
getLevel() );
refLine.printf( "hasReference() = %s, isReference() = %s",
hasReference() ? "true" : "false",
isReference() ? "true" : "false" );
WMessageDialog::messagef( _parent, MsgPlain, MsgOk, name(), "%s%s%s%s%s",
(const char *)rootLine, (const char *)boundLine,
(const char *)descendLine, (const char *)statLine,
(const char *)refLine );
}
void NodeCore::removeReference(NodeCore &p)
{
StLock<Mutex> _(*this);
assert(hasReference(p));
mReferences.erase(&p);
}
