C++ U2SequenceObject::getGObjectName方法代码示例

Task::ReportResult GTest_DNAcompareSequencesNamesInTwoObjects::report() {
    Document* doc = getContext<Document>(this, docContextName);
    if (doc == NULL) {
        stateInfo.setError(QString("document not found %1").arg(docContextName));
        return ReportResult_Finished;
    }
    Document* doc2 = getContext<Document>(this, secondDocContextName);
    if (doc2 == NULL) {
        stateInfo.setError(QString("document not found %1").arg(secondDocContextName));
        return ReportResult_Finished;
    }

    const QList<GObject*>& objs = doc->getObjects();
    const QList<GObject*>& objs2 = doc2->getObjects();
    GObject*obj=NULL;
    GObject*obj2=NULL;
    U2SequenceObject * mySequence;
    U2SequenceObject * mySequence2;

    for(int i=0;(i!=objs.size())&&(i!=objs2.size());i++){
        obj = objs.at(i);
        obj2 = objs2.at(i);

        if((obj->getGObjectType()== GObjectTypes::SEQUENCE)&&(obj2->getGObjectType() == GObjectTypes::SEQUENCE)){
            mySequence = qobject_cast<U2SequenceObject*>(obj);
            if(mySequence==NULL){
                stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj->getGObjectName()).arg(i));
                return ReportResult_Finished;
            }
            mySequence2 = qobject_cast<U2SequenceObject*>(obj2);
            if(mySequence2==NULL){
                stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj2->getGObjectName()).arg(i));
                return ReportResult_Finished;
            }
            if(mySequence->getGObjectName()!=mySequence2->getGObjectName()){
                stateInfo.setError(QString("Name of object in position %1 not matched: '%2' vs '%3'").arg(i)
                    .arg(mySequence->getGObjectName()).arg(mySequence2->getGObjectName()));
                return ReportResult_Finished;
            }
        }

    }

    if (objs.size() != objs2.size()) {
        QString error("Number of objects in doc mismatches: [%1=%2] vs [%3=%4]");
        error = error.arg(docContextName).arg(objs.size())
            .arg(secondDocContextName).arg(objs2.size());
        if (obj) {
            error += QString("\nLast good object: %1").arg(obj->getGObjectName());
        }
        stateInfo.setError(error);
    }

    return ReportResult_Finished;
}

void DotPlotDialog::sl_loadTaskStateChanged(Task* t){
    DotPlotLoadDocumentsTask *loadTask = qobject_cast<DotPlotLoadDocumentsTask*>(t);
    if (!loadTask || !loadTask->isFinished()) {
            if(t->isFinished()){
                if(curURL == ""){
                    return;
                }
                GUrl URL(curURL);
                Project *project = AppContext::getProject();
                SAFE_POINT(project, "project is NULL", );
                Document *doc = project->findDocumentByURL(URL);
                if (!doc || !doc->isLoaded()) {
                    return;
                }
                QList<GObject*> docObjects  = doc->getObjects();
                foreach (GObject* obj, docObjects) {
                    U2SequenceObject* seqObj = qobject_cast<U2SequenceObject*>(obj);
                    if (seqObj != NULL){
                        QString name = seqObj->getGObjectName();
                        xAxisCombo->addItem(name);
                        yAxisCombo->addItem(name);
                        sequences << seqObj;
                    }
                }
                curURL = "";
            }
            return;
    }

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 {