void DatasetsListWidget::sl_newDataset() {
GCOUNTER(cvar, tvar, "WD::Dataset::New Dataset");
QString error;
QString text = getTip();
do {
bool ok = false;
text = QInputDialog::getText(this,
tr("Enter Dataset Name"),
tr("New dataset name:"),
QLineEdit::Normal,
text, &ok);
if (!ok) {
return;
}
U2OpStatusImpl os;
ctrl->addDataset(text, os);
error = os.getError();
if (!error.isEmpty()) {
QMessageBox::critical(this, tr("Error"), error);
}
} while (!error.isEmpty());
// activate the tab after adding
tabs->setCurrentIndex(tabs->count() - 1);
}
Task* HMM3SearchWorker::tick() {
while (hmmPort->hasMessage()) {
hmms << hmmPort->get().getData().toMap().value(HMM3Lib::HMM3_SLOT.getId()).value<const P7_HMM*>();
}
if (!hmmPort->isEnded()) { // || hmms.isEmpty() || !seqPort->hasMessage()
return NULL;
}
if (seqPort->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(seqPort);
if (inputMessage.isEmpty() || hmms.isEmpty()) {
output->transit();
return NULL;
}
SharedDbiDataHandler seqId = inputMessage.getData().toMap().value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
if (seqObj.isNull()) {
return NULL;
}
U2OpStatusImpl os;
DNASequence dnaSequence = seqObj->getWholeSequence(os);
CHECK_OP(os, new FailTask(os.getError()));
if (dnaSequence.alphabet->getType() != DNAAlphabet_RAW) {
QList<Task*> subtasks;
UHMM3SearchTaskSettings settings;
settings.inner = cfg;
foreach(const P7_HMM* hmm, hmms) {
subtasks << new UHMM3SWSearchTask (hmm, dnaSequence, settings);
}
void DatasetsListWidget::sl_renameDataset() {
GCOUNTER(cvar, tvar, "WD::Dataset::Rename Dataset");
QAction *a = dynamic_cast<QAction*>(sender());
CHECK(NULL != a, );
int idx = a->property("idx").toInt();
CHECK(idx < tabs->count(), );
bool error = false;
QString text = tabs->tabText(idx);
do {
bool ok = false;
text = QInputDialog::getText(this,
tr("Rename Dataset"),
tr("New dataset name:"),
QLineEdit::Normal,
text, &ok);
if (!ok) {
return;
}
U2OpStatusImpl os;
ctrl->renameDataset(idx, text, os);
if (os.hasError()) {
QMessageBox::critical(this, tr("Error"), os.getError());
}
error = os.hasError();
} while (error);
tabs->setTabText(idx, text);
}
void WizardPageController::applyLayout() {
wc->clearControllers();
qDeleteAll(controllers);
controllers.clear();
QLayout *old = wPage->layout();
removeLayout(old);
U2OpStatusImpl os;
page->validate(wc->getCurrentActors(), os);
if (os.hasError()) {
coreLog.error(os.getError());
setError(wPage);
return;
}
PageContentCreator pcc(wc);
page->getContent()->accept(&pcc);
if (wc->isBroken()) {
setError(wPage);
return;
}
pcc.setPageTitle(page->getTitle());
wPage->setLayout(pcc.getResult());
controllers << pcc.getControllers();
wPage->setFinalPage(page->isFinal());
}
IMPLEMENT_TEST(TextObjectUnitTests, clone_NullDbi) {
TextObject object("object", TextObjectTestData::getObjRef());
U2OpStatusImpl os;
GObject *clonedGObj = object.clone(U2DbiRef(), os);
Q_UNUSED(clonedGObj);
CHECK_TRUE(os.hasError(), "no error");
}
Task * BaseThroughWorker::processNextInputMessage() {
const Message message = getMessageAndSetupScriptValues(input);
U2OpStatusImpl os;
Task *task = createTask(message, os);
if (os.hasError()) {
reportError(os.getError());
}
return task;
}
IMPLEMENT_TEST(TextObjectUnitTests, clone_NullObj) {
U2EntityRef objRef = TextObjectTestData::getObjRef();
objRef.entityId = "some id";
TextObject object("object", objRef);
U2OpStatusImpl os;
GObject *clonedGObj = object.clone(TextObjectTestData::getDbiRef(), os);
Q_UNUSED(clonedGObj);
CHECK_TRUE(os.hasError(), "no error");
}
bool AssemblyModel::hasCachedCoverageStat() {
if(!cachedCoverageStat.isEmpty()) {
return true;
}
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(NULL != attributeDbi) {
U2OpStatusImpl status;
U2ByteArrayAttribute attr = U2AttributeUtils::findByteArrayAttribute(attributeDbi, assembly.id, COVERAGE_STAT_ATTRIBUTE_NAME, status);
if(!status.isCoR() && attr.hasValidId()) {
// TODO: check version
return true;
}
}
return false;
}
Task* CDSearchWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
SharedDbiDataHandler seqId = inputMessage.getData().toMap().value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
if (seqObj.isNull()) {
return NULL;
}
U2OpStatusImpl os;
DNASequence seq = seqObj->getWholeSequence(os);
CHECK_OP(os, new FailTask(os.getError()));
settings.query = seq.seq;
settings.alp = seq.alphabet;
if (!settings.alp->isAmino()) {
QString err = "Required amino acid input sequence";
return new FailTask(err);
}
settings.ev = actor->getParameter(EVALUE_ATTR)->getAttributeValue<float>(context);
settings.dbName = actor->getParameter(DATABASE_ATTR)->getAttributeValue<QString>(context);
bool local = actor->getParameter(LOCAL_ATTR)->getAttributePureValue().toBool();
CDSearchFactory* factory = NULL;
if (local) {
factory = AppContext::getCDSFactoryRegistry()->getFactory(CDSearchFactoryRegistry::LocalSearch);
if (!factory) {
QString err = tr("'External tools' plugin has to be loaded.");
return new FailTask(err);
}
settings.localDbFolder = actor->getParameter(DB_PATH_ATTR)->getAttributeValue<QString>(context);
} else { // remote
factory = AppContext::getCDSFactoryRegistry()->getFactory(CDSearchFactoryRegistry::RemoteSearch);
if (!factory) {
QString err = tr("'Remote blast' plugin has to be loaded.");
return new FailTask(err);
}
}
cds = factory->createCDSearch(settings);
Task* t = cds->getTask();
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
return t;
} else if (input->isEnded()) {
void DNAFlexDialog::accept()
{
// Verifying and passing the settings
// TODO
// Preparing the annotations object and other annotations parameters
QString err = annotController->validate();
if (!err.isEmpty()) {
QMessageBox::warning(this, tr("Error"), err);
return;
}
bool objectPrepared = annotController->prepareAnnotationObject();
if (!objectPrepared){
QMessageBox::warning(this, tr("Error"), tr("Cannot create an annotation object. Please check settings"));
return;
}
const CreateAnnotationModel& annotModel = annotController->getModel();
QString annotName = annotModel.data->name;
QString annotGroup = annotModel.groupName;
if(ctx != NULL){
ctx->getAnnotatedDNAView()->tryAddObject(annotModel.getAnnotationObject());
}
// Creating the task
U2OpStatusImpl os;
QByteArray seqData = ctx->getSequenceObject()->getWholeSequenceData(os);
CHECK_OP_EXT(os, QMessageBox::critical(this, L10N::errorTitle(), os.getError()), );
DNAFlexTask* task = new DNAFlexTask(
settings,
annotModel.getAnnotationObject(),
annotName,
annotGroup,
annotModel.description,
seqData);
// Registering the task
AppContext::getTaskScheduler()->registerTopLevelTask(task);
// Accepting the dialog
QDialog::accept();
}
Task* PWMatrixSearchWorker::tick() {
while (modelPort->hasMessage()) {
models << modelPort->get().getData().toMap().value(PWMatrixWorkerFactory::WMATRIX_SLOT.getId()).value<PWMatrix>();
}
if (!modelPort->isEnded()) {
return NULL;
}
if (dataPort->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(dataPort);
if (inputMessage.isEmpty() || models.isEmpty()) {
output->transit();
return NULL;
}
QVariantMap map = inputMessage.getData().toMap();
SharedDbiDataHandler seqId = map.value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
if (seqObj.isNull()) {
return NULL;
}
U2OpStatusImpl os;
DNASequence seq = seqObj->getWholeSequence(os);
CHECK_OP(os, new FailTask(os.getError()));
if (!seq.isNull() && seq.alphabet->getType() == DNAAlphabet_NUCL) {
WeightMatrixSearchCfg config(cfg);
config.complOnly = (strand < 0);
if (strand <= 0) {
DNATranslation* compTT = AppContext::getDNATranslationRegistry()->
lookupComplementTranslation(seq.alphabet);
if (compTT != NULL) {
config.complTT = compTT ;
}
}
QList<Task*> subtasks;
foreach(PWMatrix model, models) {
subtasks << new WeightMatrixSingleSearchTask(model, seq.seq, config, 0);
}
void uHMMPlugin::sl_search() {
//to select a sequence
//1. check that annotated DNA view is active
//2. if not -> check that DNASequence object is selected in project view
U2SequenceObject* obj = NULL;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(ov);
if (av!=NULL) {
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
obj = seqCtx->getSequenceObject();
}
}
}
if (obj == NULL) {
ProjectView* pv = AppContext::getProjectView();
if (pv!=NULL) {
const GObjectSelection* sel = pv->getGObjectSelection();
GObject* o = sel->getSelectedObjects().size() == 1 ? sel->getSelectedObjects().first() : NULL;
obj = qobject_cast<U2SequenceObject*>(o);
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
if (obj == NULL) {
QMessageBox::critical(p, tr("Error"), tr("Error! Select sequence in Project view or open sequence view."));
return;
}
U2OpStatusImpl os;
DNASequence sequence = obj->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, obj, p);
d->exec();
}
void HMMADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
QWidget *p;
if (av->getWidget()){
p = av->getWidget();
}else{
p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
}
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
if(seqCtx == NULL) {
QMessageBox::critical(p, tr("Error"), tr("No sequences found"));
return;
}
U2OpStatusImpl os;
DNASequence sequence = seqCtx->getSequenceObject()->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, seqCtx->getSequenceObject(), p);
d->exec();
}
IMPLEMENT_TEST(TextObjectUnitTests, createInstance_WrongDbi) {
U2OpStatusImpl os;
QScopedPointer<TextObject> object(TextObject::createInstance("some text", "object", U2DbiRef(), os));
CHECK_TRUE(os.hasError(), "no error");
}
Task* DNAStatWorker::tick() {
while (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler seqId = qm.value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
if (NULL == seqObj.data()) {
return NULL;
}
U2OpStatusImpl os;
DNASequence dna = seqObj->getWholeSequence(os);
CHECK_OP(os, new FailTask(os.getError()));
if(!dna.alphabet->isNucleic()) {
return new FailTask(tr("Sequence must be nucleotide"));
}
QList<SharedAnnotationData> res;
SharedAnnotationData gcAnn(new AnnotationData);
gcAnn->name = "statistics";
gcAnn->location->regions << U2Region( 0, dna.seq.size());
if (actor->getParameter(GCCONTENT)->getAttributeValue<bool>(context)) {
float gcContent = calcGCContent(dna.seq);
gcAnn->qualifiers.push_back(U2Qualifier("gc-content", QString::number(gcContent*100) + "%"));
}
if (actor->getParameter(GC1CONTENT)->getAttributeValue<bool>(context)) {
float gc1Content = calcGC1Content(dna.seq);
gcAnn->qualifiers.push_back(U2Qualifier("gc1-content", QString::number(gc1Content*100) + "%"));
}
if (actor->getParameter(GC2CONTENT)->getAttributeValue<bool>(context)) {
float gc2Content = calcGC2Content(dna.seq);
gcAnn->qualifiers.push_back(U2Qualifier("gc2-content", QString::number(gc2Content*100) + "%"));
}
if (actor->getParameter(GC3CONTENT)->getAttributeValue<bool>(context)) {
float gc3Content = calcGC3Content(dna.seq);
gcAnn->qualifiers.push_back(U2Qualifier("gc3-content", QString::number(gc3Content*100) + "%"));
}
if (gcAnn->qualifiers.isEmpty()) {
return new FailTask(tr("No statistics was selected"));
}
res << gcAnn;
const SharedDbiDataHandler tableId = context->getDataStorage()->putAnnotationTable(res);
const QVariant v = qVariantFromValue<SharedDbiDataHandler>(tableId);
output->put(Message(BaseTypes::ANNOTATION_TABLE_TYPE(), v));
}
if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
Task* RepeatWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
cfg.algo = RFAlgorithm(actor->getParameter(ALGO_ATTR)->getAttributeValue<int>(context));
cfg.minLen = actor->getParameter(LEN_ATTR)->getAttributeValue<int>(context);
if(actor->getParameter(USE_MIN_DISTANCE_ATTR)->getAttributeValue<bool>(context)){
cfg.minDist = actor->getParameter(MIN_DIST_ATTR)->getAttributeValue<int>(context);
}else{
cfg.minDist = 0;
}
if(actor->getParameter(USE_MAX_DISTANCE_ATTR)->getAttributeValue<bool>(context)){
cfg.maxDist = actor->getParameter(MAX_DIST_ATTR)->getAttributeValue<int>(context);
}else{
cfg.maxDist = INT_MAX;
}
int identity = actor->getParameter(IDENTITY_ATTR)->getAttributeValue<int>(context);
cfg.setIdentity(identity);
cfg.nThreads = actor->getParameter(THREADS_ATTR)->getAttributeValue<int>(context);
cfg.inverted = actor->getParameter(INVERT_ATTR)->getAttributeValue<bool>(context);
cfg.filter = RepeatsFilterAlgorithm(actor->getParameter(NESTED_ATTR)->getAttributeValue<int>(context));
cfg.excludeTandems = actor->getParameter(TANMEDS_ATTR)->getAttributeValue<bool>(context);
resultName = actor->getParameter(NAME_ATTR)->getAttributeValue<QString>(context);
if(resultName.isEmpty()){
resultName = "repeat_unit";
algoLog.error(tr("result name is empty, default name used"));
}
if(identity > 100 || identity < 0){
algoLog.error(tr("Incorrect value: identity value must be between 0 and 100"));
return new FailTask(tr("Incorrect value: identity value must be between 0 and 100"));
}
QVariantMap map = inputMessage.getData().toMap();
SharedDbiDataHandler seqId = map.value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
if (seqObj.isNull()) {
return NULL;
}
U2OpStatusImpl os;
DNASequence seq = seqObj->getWholeSequence(os);
CHECK_OP(os, new FailTask(os.getError()));
if(cfg.minDist < 0){
algoLog.error(tr("Incorrect value: minimal distance must be greater then zero"));
return new FailTask(tr("Incorrect value: minimal distance must be greater then zero"));
}
if (!seq.alphabet->isNucleic()) {
QString err = tr("Sequence alphabet is not nucleic!");
return new FailTask(err);
}
Task* t = new FindRepeatsToAnnotationsTask(cfg, seq, resultName, QString(), "", GObjectReference());
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}