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);
}
void DownloadRemoteFileDialog::accept()
{
defaultDB = getDBId();
QString resourceId = getResourceId();
if( resourceId.isEmpty() ) {
QMessageBox::critical(this, L10N::errorTitle(), tr("Resource id is empty!"));
ui->idLineEdit->setFocus();
return;
}
QString fullPath = getFullpath();
if( ui->saveFilenameLineEdit->text().isEmpty() ) {
QMessageBox::critical(this, L10N::errorTitle(), tr("No folder selected for saving file!"));
ui->saveFilenameLineEdit->setFocus();
return;
}
U2OpStatus2Log os;
fullPath = GUrlUtils::prepareDirLocation(fullPath, os);
if (fullPath.isEmpty()) {
QMessageBox::critical(this, L10N::errorTitle(), os.getError());
ui->saveFilenameLineEdit->setFocus();
return;
}
QString dbId = getDBId();
QStringList resIds = resourceId.split(QRegExp("[\\s,;]+"));
QList<Task*> tasks;
QString fileFormat;
if (ui->formatBox->count() > 0) {
fileFormat = ui->formatBox->currentText();
}
QVariantMap hints;
hints.insert(FORCE_DOWNLOAD_SEQUENCE_HINT, ui->chbForceDownloadSequence->isVisible() && ui->chbForceDownloadSequence->isChecked());
int taskCount = 0;
bool addToProject = ui->chbAddToProjectCheck->isChecked();
if (addToProject && resIds.size() >= 100) {
QString message = tr("There are more than 100 files found for download.\nAre you sure you want to open all of them?");
int button = QMessageBox::question(QApplication::activeWindow(), tr("Warning"), message,
tr("Cancel"), tr("Open anyway"), tr("Don't open"));
if (button == 0) {
return; // return to dialog
} else if (button == 2) {
addToProject = false;
}
}
bool hasLoadOnlyDocuments = false;
foreach (const QString &resId, resIds) {
LoadRemoteDocumentMode mode = LoadRemoteDocumentMode_LoadOnly;
if (addToProject) {
mode = taskCount < OpenViewTask::MAX_DOC_NUMBER_TO_OPEN_VIEWS ? LoadRemoteDocumentMode_OpenView : LoadRemoteDocumentMode_AddToProject;
}
hasLoadOnlyDocuments = hasLoadOnlyDocuments || mode == LoadRemoteDocumentMode_LoadOnly;
tasks.append(new LoadRemoteDocumentAndAddToProjectTask(resId, dbId, fullPath, fileFormat, hints, mode));
taskCount++;
}
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;
}
void ExportProjectDialogController::accept(){
QString dirPath = exportFolderEdit->text();
projectFile = fixProjectFile(projectFileEdit->text());
U2OpStatus2Log os;
exportDir = GUrlUtils::prepareDirLocation(dirPath, os);
if (exportDir.isEmpty()) {
assert(os.hasError());
QMessageBox::critical(this, this->windowTitle(), os.getError());
return;
}
QDialog::accept();
}
Task* CAP3Worker::tick() {
U2OpStatus2Log os;
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
SAFE_POINT(!inputMessage.isEmpty(), "NULL message!", NULL);
QVariantMap data = inputMessage.getData().toMap();
if (!data.contains(IN_URL_SLOT_ID)) {
os.setError("CAP3 input slot is empty!");
return new FailTask(os.getError());
}
QString dataset = data[BaseSlots::DATASET_SLOT().getId()].toString();
bool runCapForPreviousDataset = false;
if (dataset != currentDatasetName) {
if (!currentDatasetName.isEmpty()) {
runCapForPreviousDataset = true;
}
settings.inputFiles = inputSeqUrls;
inputSeqUrls.clear();
currentDatasetName = dataset;
}
inputSeqUrls << data.value(IN_URL_SLOT_ID).value<QString>();
if (runCapForPreviousDataset) {
return runCap3();
}
settings.inputFiles = inputSeqUrls;
}
else if (input->isEnded()) {
if (!settings.inputFiles.isEmpty()) {
return runCap3();
}
else {
datasetNumber = 0;
setDone();
}
}
return NULL;
}
bool CreatePhyTreeDialogController::checkFileName() {
const QString fileName = saveController->getSaveFileName();
if (fileName.isEmpty()) {
QMessageBox::warning(this, tr("Warning"), tr("Please, input the file name."));
ui->fileNameEdit->setFocus();
return false;
}
settings.fileUrl = fileName;
U2OpStatus2Log os;
GUrlUtils::validateLocalFileUrl(GUrl(fileName), os);
if (os.hasError()) {
QMessageBox::warning(this, tr("Error"), tr("Please, change the output file.") + "\n" + os.getError());
ui->fileNameEdit->setFocus(Qt::MouseFocusReason);
return false;
}
return true;
}
void CreateDocumentFromTextDialogController::accept() {
QString validationError = w->validate();
if(!validationError.isEmpty()){
QMessageBox::critical(this, this->windowTitle(), validationError);
return;
}
const QString url = saveController->getSaveFileName();
QFileInfo fi(url);
if(fi.baseName().isEmpty()){
QMessageBox::critical(this, this->windowTitle(), tr("Filename is empty"));
return;
}
if(url.isEmpty()){
QMessageBox::critical(this, this->windowTitle(), tr("No path specified"));
return;
}
U2OpStatus2Log os;
QString fullPath = GUrlUtils::prepareFileLocation(url, os);
if (fullPath.isEmpty()) {
QMessageBox::critical(this, L10N::errorTitle(), os.getError());
return;
}
if(ui->nameEdit->text().isEmpty()) {
QMessageBox::critical(this, this->windowTitle(), tr("Sequence name is empty"));
return;
}
CHECK_OP(os, );
Task *task = new CreateSequenceFromTextAndOpenViewTask(prepareSequences(), saveController->getFormatIdToSave(), GUrl(fullPath), ui->saveImmediatelyBox->isChecked());
AppContext::getTaskScheduler()->registerTopLevelTask(task);
QDialog::accept();
}
void ADVClipboard::copySequenceSelection(bool complement, bool amino) {
ADVSequenceObjectContext* seqCtx = getSequenceContext();
if (seqCtx == NULL) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), "No sequence selected!");
return;
}
QString res;
QVector<U2Region> regions = seqCtx->getSequenceSelection()->getSelectedRegions();
#ifdef UGENE_X86
int totalLen = 0;
foreach (const U2Region& r, regions) {
totalLen += r.length;
}
if (totalLen > MAX_COPY_SIZE_FOR_X86) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), COPY_FAILED_MESSAGE);
return;
}
#endif
if (!regions.isEmpty()) {
U2SequenceObject* seqObj = seqCtx->getSequenceObject();
DNATranslation* complTT = complement ? seqCtx->getComplementTT() : NULL;
DNATranslation* aminoTT = amino ? seqCtx->getAminoTT() : NULL;
U2OpStatus2Log os;
QList<QByteArray> seqParts = U2SequenceUtils::extractRegions(seqObj->getSequenceRef(), regions, complTT, aminoTT, false, os);
if (os.hasError()) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), tr("An error occurred during getting sequence data: %1").arg(os.getError()));
return;
}
if (seqParts.size() == 1) {
putIntoClipboard(seqParts.first());
return;
}
res = U1SequenceUtils::joinRegions(seqParts);
}
putIntoClipboard(res);
}
Task *ConservationPlotWorker::tick() {
U2OpStatus2Log os;
while (inChannel->hasMessage()) {
Message m = getMessageAndSetupScriptValues(inChannel);
QVariantMap data = m.getData().toMap();
if (!data.contains(ANNOT_SLOT_ID)) {
os.setError("Annotations slot is empty");
return new FailTask(os.getError());
}
plotData = StorageUtils::getAnnotationTableHandlers(data[ANNOT_SLOT_ID]);
}
if (!inChannel->isEnded()) {
return NULL;
}
ConservationPlotSettings settings = createConservationPlotSettings(os);
if (os.hasError()) {
return new FailTask(os.getError());
}
ConservationPlotTask* t = new ConservationPlotTask(settings, context->getDataStorage(), plotData);
t->addListeners(createLogListeners());
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
if (inChannel->isEnded()) {
setDone();
}
return NULL;
}
bool StreamShortReadWriter::writeNextSequence(const U2SequenceObject *seq) {
U2OpStatus2Log os;
fastaFormat->storeSequence(seq, io, os);
return !os.hasError();
}
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 {
/**
* FASTQ format specification: http://maq.sourceforge.net/fastq.shtml
*/
static void load(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& hints, QList<GObject*>& objects, U2OpStatus& os,
int gapSize, int predictedSize, QString& writeLockReason, QMap<QString, QString>& skippedLines) {
DbiOperationsBlock opBlock(dbiRef, os);
CHECK_OP(os, );
Q_UNUSED(opBlock);
writeLockReason.clear();
bool merge = gapSize!=-1;
QByteArray sequence;
QByteArray qualityScores;
QStringList headers;
QSet<QString> uniqueNames;
QVector<U2Region> mergedMapping;
QByteArray gapSequence((merge ? gapSize : 0), 0);
sequence.reserve(predictedSize);
qualityScores.reserve(predictedSize);
// for lower case annotations
GObjectReference sequenceRef;
qint64 sequenceStart = 0;
U2SequenceImporter seqImporter(hints, true);
const QString folder = hints.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();
int seqNumber = 0;
int progressUpNum = 0;
const int objectsCountLimit = hints.contains(DocumentReadingMode_MaxObjectsInDoc) ? hints[DocumentReadingMode_MaxObjectsInDoc].toInt() : -1;
const bool settingsMakeUniqueName = !hints.value(DocumentReadingMode_DontMakeUniqueNames, false).toBool();
while (!os.isCoR()) {
U2OpStatus2Log warningOs;
//read header
QString sequenceName = readSequenceName(warningOs, io, '@');
// check for eof while trying to read another FASTQ block
if (io->isEof()) {
if (io->hasError()) {
os.setError(io->errorString());
}
break;
}
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
continue;
}
if(sequenceName.isEmpty()){
sequenceName = "Sequence";
}
if ((merge == false) || (seqNumber == 0)) {
QString objName = sequenceName;
if (settingsMakeUniqueName) {
objName = (merge) ? "Sequence" : TextUtils::variate(sequenceName, "_", uniqueNames);
objName.squeeze();
uniqueNames.insert(objName);
}
seqImporter.startSequence(warningOs, dbiRef, folder, objName, false);
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
}
//read sequence
if (merge && sequence.length() > 0) {
seqImporter.addDefaultSymbolsBlock(gapSize, warningOs);
sequenceStart += sequence.length();
sequenceStart+=gapSize;
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
}
sequence.clear();
readSequence(warningOs, io, sequence);
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
MemoryLocker lSequence(os, qCeil(sequence.size()/(1000*1000)));
CHECK_OP_BREAK(os);
Q_UNUSED(lSequence);
seqImporter.addBlock(sequence.data(),sequence.length(), warningOs);
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
QString qualSequenceName = readSequenceName(warningOs, io, '+');
if (!qualSequenceName.isEmpty()) {
if (sequenceName != qualSequenceName){
warningOs.setError(U2::FastqFormat::tr("Sequence name differs from quality scores name: %1 and %2").arg(sequenceName).arg(qualSequenceName));
}
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
}
// read qualities
qualityScores.clear();
readQuality(warningOs, io, qualityScores, sequence.size());
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
if(sequence.length() != qualityScores.length()){
warningOs.setError(U2::FastqFormat::tr("Bad quality scores: inconsistent size."));
}
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
U2OpStatusImpl seqOs;
seqImporter.finalizeSequenceAndValidate(seqOs);
continue;
}
seqNumber++;
progressUpNum++;
if (merge) {
headers.append(sequenceName);
mergedMapping.append(U2Region(sequenceStart, sequence.length() ));
}
else {
if (objectsCountLimit > 0 && objects.size() >= objectsCountLimit) {
os.setError(FastqFormat::tr("File \"%1\" contains too many sequences to be displayed. "
"However, you can process these data using instruments from the menu <i>Tools -> NGS data analysis</i> "
"or pipelines built with Workflow Designer.")
.arg(io->getURL().getURLString()));
break;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(warningOs);
if(errorLoggingBreak(warningOs, skippedLines, sequenceName)){
continue;
}
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U2SequenceObject* seqObj = new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
CHECK_EXT_BREAK(seqObj != NULL, os.setError("U2SequenceObject is NULL"));
seqObj->setQuality(DNAQuality(qualityScores));
objects << seqObj;
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
}
if (PROGRESS_UPDATE_STEP == progressUpNum) {
progressUpNum = 0;
os.setProgress(io->getProgress());
}
}
CHECK_OP_EXT(os, qDeleteAll(objects); objects.clear(), );
bool emptyObjects = objects.isEmpty();
CHECK_EXT(!emptyObjects || merge, os.setError(Document::tr("Document is empty.")), );
SAFE_POINT(headers.size() == mergedMapping.size(), "headers <-> regions mapping failed!", );
if (!merge) {
return;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP(os,);
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
objects << new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
objects << DocumentFormatUtils::addAnnotationsForMergedU2Sequence(sequenceRef, dbiRef, headers, mergedMapping, hints);
if (headers.size() > 1) {
writeLockReason = QObject::tr("Document sequences were merged");
}
}
