Task::ReportResult GTest_DNASequencePart::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * objSequence = qobject_cast<U2SequenceObject*>(obj);
if (objSequence==NULL) {
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if (objSequence->getSequenceLength() < startPos + subseq.length()) {
stateInfo.setError(QString("sequence size is less that region end: size=%1, region-end=%2, objectName=%3").arg(objSequence->getSequenceLength()).arg(startPos + subseq.length()).arg(obj->getGObjectName()));
return ReportResult_Finished;
}
QByteArray objSubSeq = objSequence->getSequenceData(U2Region(startPos, subseq.length()));
if (!objSequence->getAlphabet()->isCaseSensitive()) {
subseq = subseq.toUpper();
}
if (objSubSeq != subseq){
stateInfo.setError(QString("region not matched: %1, expected %2").arg(objSubSeq.constData()).arg(subseq.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
void DotPlotDialog::sl_minLenHeuristics() {
identityBox->setValue(100);
// formula used here: nVariations / lenVariations = wantedResCount (==1000)
// where nVariations == area size
// lenVariations = 4^len where len is result
// so we have len = ln(nVariations/wantedResCount)/ln(4)
int xIdx = xAxisCombo->currentIndex();
int yIdx = yAxisCombo->currentIndex();
U2SequenceObject *objX = sequences.at(xIdx);
U2SequenceObject *objY = sequences.at(yIdx);
qint64 xSeqLen = objX->getSequenceLength();
qint64 ySeqLen = objY->getSequenceLength();
double nVariations = xSeqLen*ySeqLen;
double resCount = 1000;
double len = log(nVariations / resCount) / log(double(4));
minLenBox->setValue((int)len);
}
Task::ReportResult GTest_DNASequenceSize::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
int tempLength=mySequence->getSequenceLength();
if (tempLength != seqSize){
stateInfo.setError(QString("sequence size not matched: %1, expected %2 ").arg(tempLength).arg(seqSize));
}
return ReportResult_Finished;
}
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 {
