QList<GObject *> DbiDocumentFormat::prepareObjects(DbiConnection &handle, const QList<U2DataId> &objectIds) {
QList<GObject *> objects;
U2EntityRef ref;
ref.dbiRef = handle.dbi->getDbiRef();
QMap<U2DataId, GObject*> match;
foreach(const U2DataId &id, objectIds) {
U2OpStatus2Log status;
ref.entityId = id;
U2Object object;
handle.dbi->getObjectDbi()->getObject(object, id, status);
CHECK_OPERATION(!status.isCoR(), continue);
if (object.visualName.isEmpty()) {
object.visualName = "Unnamed object";
}
GObject *gobject = GObjectUtils::createObject(ref.dbiRef, id, object.visualName);
CHECK_OPERATION(NULL != gobject, continue);
match[id] = gobject;
objects << gobject;
}
AssemblyNavigationWidget::AssemblyNavigationWidget(AssemblyBrowser *_browser, QWidget *p)
: QWidget(p), browser(_browser), savableTab(this, GObjectViewUtils::findViewByName(_browser->getName()))
{
QVBoxLayout* mainLayout = new QVBoxLayout;
mainLayout->setContentsMargins(0, 0, 0, 0);
mainLayout->setAlignment(Qt::AlignTop);
mainLayout->setSpacing(5);
setLayout(mainLayout);
U2OpStatus2Log os;
qint64 modelLen = browser->getModel()->getModelLength(os);
if(!os.isCoR()) {
posSelector = new PositionSelector(this, 1, modelLen, false);
connect(posSelector, SIGNAL(si_positionChanged(int)), browser, SLOT(sl_onPosChangeRequest(int)));
posSelector->setContentsMargins(0,0,10,0);
mainLayout->addWidget(new QLabel(tr("Enter position in assembly:"), this));
mainLayout->addWidget(posSelector);
connect(browser, SIGNAL( si_zoomOperationPerformed() ), SLOT( sl_updateZoomingState() ));
sl_updateZoomingState();
}
CoveredRegionsLabel * coveredLabel = new CoveredRegionsLabel(browser, this);
QWidget * coveredGroup = new ShowHideSubgroupWidget("COVERED", tr("Most Covered Regions"), coveredLabel, true);
mainLayout->addWidget(coveredGroup);
U2WidgetStateStorage::restoreWidgetState(savableTab);
}
QString AssemblyBrowser::tryAddObject(GObject * obj) {
Document * objDoc = obj->getDocument();
SAFE_POINT(NULL != objDoc, "", tr("Internal error: only object with document can be added to browser"));
if (GObjectTypes::SEQUENCE == obj->getGObjectType()) {
U2SequenceObject * seqObj = qobject_cast<U2SequenceObject*>(obj);
CHECK(NULL != seqObj, tr("Internal error: broken sequence object"));
SAFE_POINT(NULL != objDoc->getDocumentFormat(), "", tr("Internal error: empty document format"));
U2OpStatus2Log os;
qint64 seqLen = seqObj->getSequenceLength();
QStringList errs;
qint64 modelLen = model->getModelLength(os);
if (seqLen != modelLen) {
errs << tr("The lengths of the sequence and assembly are different.");
}
if (seqObj->getGObjectName() != gobject->getGObjectName()) {
errs << tr("The sequence and assembly names are different.");
}
// commented: waiting for fix
//QByteArray refMd5 = model->getReferenceMd5();
//if(!refMd5.isEmpty()) {
// //QByteArray data = QString(seqObj->getSequence()).remove("-").toUpper().toUtf8();
// QByteArray data = QString(seqObj->getSequence()).toUpper().toUtf8();
// QByteArray seqObjMd5 = QCryptographicHash::hash(data, QCryptographicHash::Md5).toHex();
// if(seqObjMd5 != refMd5) {
// errs << tr("- Reference MD5 not match with MD5 written in assembly");
// }
//}
bool setRef = !isAssemblyObjectLocked(true) && !model->isLoadingReference();
setRef &= model->checkPermissions(QFile::WriteUser, setRef);
if(!errs.isEmpty() && setRef) {
const NotificationStack *notificationStack = AppContext::getMainWindow()->getNotificationStack();
const QString message = tr("It seems that sequence \"%1\", set as reference to assembly \"%2\", does not match it.").arg(seqObj->getGObjectName()).arg(gobject->getGObjectName())
+ "\n- " + errs.join("\n- ");
notificationStack->addNotification(message, Warning_Not);
}
if(setRef) {
model->setReference(seqObj);
U2Assembly assembly = model->getAssembly();
U2DataId refId;
QString folder;
const QStringList folders = model->getDbiConnection().dbi->getObjectDbi()->getObjectFolders(assembly.id, os);
if (folders.isEmpty() || os.isCoR()) {
folder = U2ObjectDbi::ROOT_FOLDER;
} else {
folder = folders.first();
}
if (seqObj->getEntityRef().dbiRef == model->getDbiConnection().dbi->getDbiRef()) {
refId = seqObj->getEntityRef().entityId;
} else {
U2CrossDatabaseReferenceDbi * crossDbi = model->getDbiConnection().dbi->getCrossDatabaseReferenceDbi();
U2CrossDatabaseReference crossDbRef;
// Cannot simply use seqObj->getSequenceRef(), since it points to a temporary dbi
// TODO: make similar method seqObj->getPersistentSequenctRef()
crossDbRef.dataRef.dbiRef.dbiId = objDoc->getURLString();
crossDbRef.dataRef.dbiRef.dbiFactoryId = "document";
crossDbRef.dataRef.entityId = seqObj->getGObjectName().toUtf8();
crossDbRef.visualName = "cross_database_reference: " + seqObj->getGObjectName();
crossDbRef.dataRef.version = 1;
crossDbi->createCrossReference(crossDbRef, folder, os);
LOG_OP(os);
refId = crossDbRef.id;
addObjectToView(obj);
}
model->associateWithReference(refId);
}
} else if (GObjectTypes::VARIANT_TRACK == obj->getGObjectType()) {
VariantTrackObject *trackObj = qobject_cast<VariantTrackObject*>(obj);
CHECK(NULL != trackObj, tr("Internal error: broken variant track object"));
model->addTrackObject(trackObj);
addObjectToView(obj);
connect(model.data(), SIGNAL(si_trackRemoved(VariantTrackObject *)), SLOT(sl_trackRemoved(VariantTrackObject *)));
} else {
