void EditMarkerGroupDialog::sl_onEditButtonClicked() {
QItemSelectionModel *m = table->selectionModel();
QModelIndexList selected = m->selectedRows();
if (1 != selected.size()) {
return;
}
QMap<QString, QString>::iterator i = marker->getValues().begin();
i += selected.first().row();
QVariantList values;
MarkerUtils::stringToValue(MarkerTypes::getDataTypeById(marker->getType()),marker->getValues().key(*i), values);
QObjectScopedPointer<EditMarkerDialog> dlg = new EditMarkerDialog(false, marker->getType(), *i, values, this);
const int dialogResult = dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dialogResult) {
QString newValueString;
QString newName = dlg->getName();
MarkerUtils::valueToString(MarkerTypes::getDataTypeById(marker->getType()), dlg->getValues(), newValueString);
markerModel->removeRows(selected.first().row(), 1, selected.first());
markerModel->addMarker(newValueString, newName);
}
}
void EnzymesPlugin::sl_onOpenDigestSequenceDialog() {
GObjectViewWindow* w = GObjectViewUtils::getActiveObjectViewWindow();
if (w == NULL) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("There is no active sequence object.\nTo start partition open sequence document."));
return;
}
AnnotatedDNAView* view = qobject_cast<AnnotatedDNAView*>(w->getObjectView());
if (view == NULL) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("There is no active sequence object.\nTo start partition open sequence document."));
return;
}
if (!view->getSequenceInFocus()->getSequenceObject()->getAlphabet()->isNucleic()) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("Can not digest into fragments non-nucleic sequence."));
return;
}
QObjectScopedPointer<DigestSequenceDialog> dlg = new DigestSequenceDialog(view->getSequenceInFocus(), QApplication::activeWindow());
dlg->exec();
}
void CollocationsDialogController::sl_saveClicked() {
assert(resultsList->count() > 0);
CreateAnnotationModel m;
m.sequenceObjectRef = ctx->getSequenceGObject();
m.hideLocation = true;
m.useAminoAnnotationTypes = ctx->getAlphabet()->isAmino();
m.sequenceLen = ctx->getSequenceObject()->getSequenceLength();
QObjectScopedPointer<CreateAnnotationDialog> d = new CreateAnnotationDialog(this, m);
const int rc = d->exec();
CHECK(!d.isNull(), );
if (rc != QDialog::Accepted) {
return;
}
QList<SharedAnnotationData> list;
for (int i=0, n = resultsList->count(); i<n; ++i) {
CDCResultItem* item = static_cast<CDCResultItem*>(resultsList->item(i));
SharedAnnotationData data = m.data;
data->location->regions.append(item->r);
data->setStrand(U2Strand::Direct);
U1AnnotationUtils::addDescriptionQualifier(data, m.description);
list.append(data);
}
ADVCreateAnnotationsTask* t = new ADVCreateAnnotationsTask(ctx->getAnnotatedDNAView(), m.getAnnotationObject(), m.groupName, list);
AppContext::getTaskScheduler()->registerTopLevelTask(t);
}
void SecStructPredictViewAction::sl_execute() {
QAction *a = dynamic_cast<QAction*>(sender());
GObjectViewAction *viewAction = dynamic_cast<GObjectViewAction*>(a);
SAFE_POINT(NULL != viewAction, "NULL action",);
AnnotatedDNAView *av = qobject_cast<AnnotatedDNAView*>(viewAction->getObjectView());
SAFE_POINT(NULL != av, "NULL dna view",);
SecStructPredictAlgRegistry *sspar = AppContext::getSecStructPredictAlgRegistry();
SAFE_POINT(NULL != sspar, "NULL SecStructPredictAlgRegistry",);
if (sspar->getAlgNameList().isEmpty()) {
QMessageBox::information(av->getWidget(),
tr("Secondary Structure Prediction"),
tr("No algorithms for secondary structure prediction are available.\nPlease, load the corresponding plugins."));
return;
}
ADVSequenceObjectContext *seqCtx = av->getSequenceInFocus();
SAFE_POINT(NULL != seqCtx, "NULL sequence context",);
SAFE_POINT(NULL != seqCtx->getAlphabet(), "NULL alphabet",);
SAFE_POINT(seqCtx->getAlphabet()->isAmino(), "Wrong alphabet",);
QObjectScopedPointer<SecStructDialog> secStructDialog = new SecStructDialog(seqCtx, av->getWidget());
secStructDialog->exec();
}
void EnzymesPlugin::sl_onOpenCreateFragmentDialog() {
GObjectViewWindow* w = GObjectViewUtils::getActiveObjectViewWindow();
if (w == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
AnnotatedDNAView* view = qobject_cast<AnnotatedDNAView*>(w->getObjectView());
if (view == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
U2SequenceObject* dnaObj = view->getSequenceInFocus()->getSequenceObject();
assert(dnaObj != NULL);
if (!dnaObj->getAlphabet()->isNucleic()) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("The sequence doesn't have nucleic alphabet, it can not be used in cloning."));
return;
}
QObjectScopedPointer<CreateFragmentDialog> dlg = new CreateFragmentDialog(view->getSequenceInFocus(), QApplication::activeWindow());
dlg->exec();
}
void TrimmomaticPropertyWidget::sl_showDialog() {
QObjectScopedPointer<TrimmomaticPropertyDialog> dialog
(new TrimmomaticPropertyDialog(lineEdit->text(), this));
if (QDialog::Accepted == dialog->exec()) {
CHECK(!dialog.isNull(), );
lineEdit->setText(dialog->getValue());
emit si_valueChanged(value());
}
void PrimerGroupBox::sl_browse() {
QObjectScopedPointer<PrimerLibrarySelector> dlg = new PrimerLibrarySelector(AppContext::getMainWindow()->getQMainWindow());
dlg->exec();
CHECK(!dlg.isNull(), );
CHECK(QDialog::Accepted == dlg->result(), );
Primer result = dlg->getResult();
primerEdit->setInvalidatedText(result.sequence);
}
void DnaAssemblySupport::sl_showBuildIndexDialog()
{
DnaAssemblyAlgRegistry* registry = AppContext::getDnaAssemblyAlgRegistry();
if (registry->getRegisteredAlgorithmIds().isEmpty()) {
QMessageBox::information(QApplication::activeWindow(), tr("DNA Assembly"),
tr("There are no algorithms for DNA assembly available.\nPlease, check your plugin list.") );
return;
}
QObjectScopedPointer<BuildIndexDialog> dlg = new BuildIndexDialog(registry, QApplication::activeWindow());
dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dlg->result()) {
DnaAssemblyToRefTaskSettings s;
s.refSeqUrl = dlg->getRefSeqUrl();
s.algName = dlg->getAlgorithmName();
s.resultFileName = dlg->getIndexFileName();
s.indexFileName = dlg->getIndexFileName();
s.setCustomSettings(dlg->getCustomSettings());
s.openView = false;
s.prebuiltIndex = false;
s.pairedReads = false;
Task* assemblyTask = new DnaAssemblyTaskWithConversions(s, false, true);
AppContext::getTaskScheduler()->registerTopLevelTask(assemblyTask);
}
}
void EnzymesADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
assert(seqCtx->getAlphabet()->isNucleic());
QObjectScopedPointer<FindEnzymesDialog> d = new FindEnzymesDialog(seqCtx);
d->exec();
}
void DotPlotDialog::sl_invertedColorButton() {
QObjectScopedPointer<QColorDialog> d = new QColorDialog(invertedColor, this);
d->exec();
CHECK(!d.isNull(), );
if (QDialog::Accepted == d->result()) {
invertedColor = d->selectedColor();
invertedCheckBox->setChecked(true);
}
updateColors();
}
void ImportAnnotationsFromCSVDialog::configureColumn(int column) {
assert(column >= 0 && column < columnsConfig.size());
const ColumnConfig& config = columnsConfig.at(column);
QObjectScopedPointer<CSVColumnConfigurationDialog> d = new CSVColumnConfigurationDialog(this, config);
int rc = d->exec(); // TODO: set dialog position close to the header item
CHECK(!d.isNull(), );
if (rc == QDialog::Accepted) {
columnsConfig[column] = d->config;
}
previewTable->horizontalHeaderItem(column)->setText(getHeaderItemText(column));
}
void HMMMSAEditorContext::sl_build() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
MSAEditor* ed = qobject_cast<MSAEditor*>(action->getObjectView());
assert(ed!=NULL);
MAlignmentObject* obj = ed->getMSAObject();
if (obj) {
QString profileName = obj->getGObjectName() == MA_OBJECT_NAME ? obj->getDocument()->getName() : obj->getGObjectName();
QObjectScopedPointer<HMMBuildDialogController> d = new HMMBuildDialogController(profileName, obj->getMAlignment());
d->exec();
CHECK(!d.isNull(), );
}
}
void EnzymesPlugin::sl_onOpenConstructMoleculeDialog() {
Project* p = AppContext::getProject();
if (p == NULL) {
QMessageBox::information(QApplication::activeWindow(), openConstructMoleculeDialog->text(),
tr("There is no active project.\nTo start ligation create a project or open an existing."));
return;
}
QList<DNAFragment> fragments = DNAFragment::findAvailableFragments();
QObjectScopedPointer<ConstructMoleculeDialog> dlg = new ConstructMoleculeDialog(fragments, QApplication::activeWindow());
dlg->exec();
}
bool CreatePhyTreeDialogController::checkLicense() {
if (settings.algorithmId == "PHYLIP Neighbor Joining") { // This is a bad hack :(
QList<Plugin *> plugins = AppContext::getPluginSupport()->getPlugins();
foreach (Plugin *plugin, plugins) {
if (plugin->getName() == "PHYLIP") {
if (!plugin->isLicenseAccepted()) {
QObjectScopedPointer<LicenseDialog> licenseDialog = new LicenseDialog(plugin);
const int ret = licenseDialog->exec();
CHECK(!licenseDialog.isNull(), false);
return (ret == QDialog::Accepted);
}
}
}
}
void EditMarkerGroupDialog::sl_onAddButtonClicked() {
QObjectScopedPointer<EditMarkerDialog> dlg = new EditMarkerDialog(true, marker->getType(), "", QVariantList(), this);
const int dialogResult = dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dialogResult) {
QString valueString;
QString name = dlg->getName();
MarkerUtils::valueToString(MarkerTypes::getDataTypeById(marker->getType()), dlg->getValues(), valueString);
markerModel->addMarker(valueString, name);
}
}
void SharedConnectionsDialog::sl_editClicked() {
const QString dbiUrl = ui->lwConnections->currentItem()->data(UrlRole).toString();
const QString userName = ui->lwConnections->currentItem()->data(LoginRole).toString();
const QString connectionName = ui->lwConnections->currentItem()->text();
QObjectScopedPointer<EditConnectionDialog> editDialog = new EditConnectionDialog(this, dbiUrl, userName, connectionName);
editDialog->setReadOnly(U2DbiUtils::PUBLIC_DATABASE_URL == U2DbiUtils::createFullDbiUrl(userName, dbiUrl));
const int dialogResult = editDialog->exec();
CHECK(!editDialog.isNull(), );
if (QDialog::Accepted == dialogResult) {
QListWidgetItem* item = ui->lwConnections->currentItem();
const QString login = editDialog->getUserName();
const QString shortDbUrl = editDialog->getShortDbiUrl();
checkDbConnectionDuplicate(shortDbUrl, login, item->data(Qt::DisplayRole).toString());
if (connectionName != editDialog->getName()) {
removeRecentConnection(item);
}
item->setText(editDialog->getName());
item->setData(UrlRole, shortDbUrl);
item->setData(LoginRole, login);
connectionTasks.remove(item);
findUpgradeTasks();
saveRecentConnection(item);
updateState();
}
}
void AddNewDocumentDialogController::run(QWidget* p, AddNewDocumentDialogModel& m, const DocumentFormatConstraints& c) {
Project* proj = AppContext::getProject();
if (proj->isStateLocked()) {
QMessageBox::critical(NULL, L10N::errorTitle(), AddNewDocumentDialogImpl::tr("Project is locked"));
m.successful = false;
return;
}
QObjectScopedPointer<AddNewDocumentDialogImpl> d = new AddNewDocumentDialogImpl(p, m, c);
d->exec();
CHECK(!d.isNull(), );
m = d->model;
assert(proj->findDocumentByURL(m.url) == NULL);
}
bool CreatePhyTreeDialogController::checkMemory() {
SAFE_POINT(NULL != settingsWidget, "Settings widget is NULL", false);
QString msg;
const bool memCheckOk = settingsWidget->checkMemoryEstimation(msg, msa, settings);
if (!memCheckOk) {
QObjectScopedPointer<QMessageBox> mb = new QMessageBox(QMessageBox::Warning, tr("Warning"), msg, QMessageBox::Ok|QMessageBox::Cancel, this);
mb->exec();
CHECK(!mb.isNull(), false);
return (mb->result() == QMessageBox::Ok);
}
return true;
}
RemoteMachineSettingsPtr RemoteMachineMonitorDialogController::selectRemoteMachine(
RemoteMachineMonitor* monitor, bool runTaskMode /* = false */ )
{
QObjectScopedPointer<RemoteMachineMonitorDialogImpl> dlg = new RemoteMachineMonitorDialogImpl(QApplication::activeWindow(), monitor, runTaskMode);
const int ret = dlg->exec();
CHECK(!dlg.isNull(), RemoteMachineSettingsPtr());
if(ret == QDialog::Rejected) {
return RemoteMachineSettingsPtr();
}
assert(ret == QDialog::Accepted);
RemoteMachineSettingsPtr rms = dlg->getSelectedMachine();
if (runTaskMode && !rms) {
QMessageBox::critical(QApplication::activeWindow(),
RemoteMachineMonitorDialogImpl::tr("Selecting machines error!"),
RemoteMachineMonitorDialogImpl::tr("You didn't select a machine to run remote task!"));
}
return rms;
}
void RemoteMachineMonitorDialogImpl::sl_modifyPushButtonClicked() {
assert( 1 == topLevelItemsSelectedNum() );
int row = getSelectedTopLevelRow();
assert( 0 <= row && row < machinesItemsByOrder.size() );
QObjectScopedPointer<RemoteMachineSettingsDialog> settingsDlg = new RemoteMachineSettingsDialog(this, machinesItemsByOrder.at(row).settings);
const int rc = settingsDlg->exec();
CHECK(!settingsDlg.isNull(), );
if( QDialog::Rejected == rc ) {
return;
}
RemoteMachineSettingsPtr newMachine = settingsDlg->getMachineSettings();
if( NULL == newMachine ) {
return;
}
removeDialogItemAt( row );
addMachineSettings( newMachine, true );
}
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();
}
void uHMMPlugin::sl_build() {
MAlignment ma;
//try to find alignment check that MSA Editor is active
QString profileName;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
MSAEditor* av = qobject_cast<MSAEditor*>(ov);
if (av!=NULL) {
MAlignmentObject* maObj = av->getMSAObject();
if (maObj!=NULL) {
ma = maObj->getMAlignment();
profileName = maObj->getGObjectName() == MA_OBJECT_NAME ? maObj->getDocument()->getName() : maObj->getGObjectName();
}
}
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
QObjectScopedPointer<HMMBuildDialogController> d = new HMMBuildDialogController(profileName, ma, p);
d->exec();
}
void RemoteMachineMonitorDialogImpl::sl_addPushButtonClicked() {
QList< ProtocolInfo* > protoInfos = AppContext::getProtocolInfoRegistry()->getProtocolInfos();
if (protoInfos.size() < 1) {
QMessageBox::information(this, tr("Add remote macnine"), tr("No protocols for distributed computing are found.\nPlease check your plugin list."));
return;
}
QObjectScopedPointer<RemoteMachineSettingsDialog> settingsDlg = new RemoteMachineSettingsDialog(this);
const int rc = settingsDlg->exec();
CHECK(!settingsDlg.isNull(), );
if( QDialog::Rejected == rc ) {
return;
}
assert( QDialog::Accepted == rc );
RemoteMachineSettingsPtr newMachine = settingsDlg->getMachineSettings();
if( NULL == newMachine ) {
return;
}
addMachineSettings( newMachine, true );
}
void DnaAssemblySupport::sl_showConvertToSamDialog() {
QObjectScopedPointer<ConvertAssemblyToSamDialog> dlg = new ConvertAssemblyToSamDialog(QApplication::activeWindow());
dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dlg->result()) {
Task *convertTask = new ConvertAssemblyToSamTask(dlg->getDbFileUrl(), dlg->getSamFileUrl());
AppContext::getTaskScheduler()->registerTopLevelTask(convertTask);
}
}
void SharedConnectionsDialog::sl_addClicked() {
QObjectScopedPointer<EditConnectionDialog> editDialog = new EditConnectionDialog(this);
const int dialogResult = editDialog->exec();
CHECK(!editDialog.isNull(), );
if (QDialog::Accepted == dialogResult) {
checkDbConnectionDuplicate(editDialog->getShortDbiUrl(), editDialog->getUserName());
QListWidgetItem* item = insertConnection(editDialog->getName(), editDialog->getShortDbiUrl(), editDialog->getUserName());
CHECK(NULL != item, );
ui->lwConnections->setCurrentItem(item);
saveRecentConnection(item);
findUpgradeTasks();
updateState();
}
void MSAOverviewContextMenu::sl_colorActionTriggered() {
QObjectScopedPointer<QColorDialog> colorDialog = new QColorDialog(graphOverview->getCurrentColor(), this);
#ifdef Q_OS_MAC
if (qgetenv("UGENE_GUI_TEST").toInt() == 1 && qgetenv("UGENE_USE_NATIVE_DIALOGS").toInt() == 0) {
colorDialog->setOption(QColorDialog::DontUseNativeDialog);
}
#endif
colorDialog->exec();
CHECK(!colorDialog.isNull(), );
if (QDialog::Accepted == colorDialog->result()) {
emit si_colorSelected(colorDialog->selectedColor());
}
}
void DnaAssemblySupport::sl_showGenomeAssemblyDialog() {
GenomeAssemblyAlgRegistry* registry = AppContext::getGenomeAssemblyAlgRegistry();
if (registry->getRegisteredAlgorithmIds().isEmpty()) {
QMessageBox::information(QApplication::activeWindow(), tr("Genome Assembly"),
tr("There are no algorithms for genome assembly available.\nPlease, check external tools in the settings.") );
return;
}
QObjectScopedPointer<GenomeAssemblyDialog> dlg = new GenomeAssemblyDialog(QApplication::activeWindow());
dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dlg->result()) {
GenomeAssemblyTaskSettings s;
s.algName = dlg->getAlgorithmName();
s.outDir = dlg->getOutDir();
s.setCustomSettings(dlg->getCustomSettings());
s.reads = dlg->getReads();
s.openView = true;
Task* assemblyTask = new GenomeAssemblyMultiTask(s);
AppContext::getTaskScheduler()->registerTopLevelTask(assemblyTask);
}
}
void BAMImporterTask::initPrepareToImportTask() {
GUrl srcUrl = loadInfoTask->getSourceUrl();
isSqliteDbTransit = hintedDbiRef.isValid() && SQLITE_DBI_ID != hintedDbiRef.dbiFactoryId;
if (!isSqliteDbTransit) {
localDbiRef = U2DbiRef(SQLITE_DBI_ID, srcUrl.dirPath() + QDir::separator() + srcUrl.fileName() + ".ugenedb");
} else {
const QString tmpDir = AppContext::getAppSettings()->getUserAppsSettings()->getCurrentProcessTemporaryDirPath("assembly_conversion") + QDir::separator();
QDir().mkpath(tmpDir);
const QString pattern = tmpDir + "XXXXXX.ugenedb";
QTemporaryFile *tempLocalDb = new QTemporaryFile(pattern, this);
tempLocalDb->open();
const QString filePath = tempLocalDb->fileName();
tempLocalDb->close();
SAFE_POINT_EXT(QFile::exists(filePath), setError(tr("Can't create a temporary database")), );
localDbiRef = U2DbiRef(SQLITE_DBI_ID, filePath);
}
QString refUrl;
bool convert = true;
if (useGui) {
QObjectScopedPointer<ConvertToSQLiteDialog> convertDialog = new ConvertToSQLiteDialog(loadInfoTask->getSourceUrl(), loadInfoTask->getInfo(), loadInfoTask->isSam());
convertDialog->hideAddToProjectOption();
const int rc = convertDialog->exec();
CHECK_EXT(!convertDialog.isNull(), setError("NULL dialog"), );
if (rc == QDialog::Accepted) {
localDbiRef = U2DbiRef(SQLITE_DBI_ID, convertDialog->getDestinationUrl().getURLString());
refUrl = convertDialog->getReferenceUrl();
} else {
convert = false;
stateInfo.setCanceled(true);
}
} else if (loadInfoTask->isSam() && loadInfoTask->getInfo().getHeader().getReferences().isEmpty()) {
void ImportAnnotationsFromCSVDialog::sl_scriptSeparatorClicked() {
if (parsingScript.isEmpty()) {
lastUsedSeparator = separatorEdit->text();
}
QObjectScopedPointer<ScriptEditorDialog> d = new ScriptEditorDialog(this, scriptHeader);
if (!parsingScript.isEmpty()) {
d->setScriptText(parsingScript);
} else { //set sample script
QString l1 = "var firstColumn = ["+ReadCSVAsAnnotationsTask::LINE_NUM_VAR+"];\n";
QString l2 = "var otherColumns = "+ReadCSVAsAnnotationsTask::LINE_VAR+".split(\" \");\n";
QString l3 = "result =firstColumn.concat(otherColumns);";
d->setScriptText(l1 + l2 + l3);
}
const int rc = d->exec();
CHECK(!d.isNull(), );
if (rc != QDialog::Accepted) {
return;
}
parsingScript = d->getScriptText();
separatorEdit->setText(lastUsedSeparator);
}
