void DnaAssemblySupport::sl_showDnaAssemblyDialog()
{
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<DnaAssemblyDialog> dlg = new DnaAssemblyDialog(QApplication::activeWindow());
dlg->exec();
CHECK(!dlg.isNull(), );
if (QDialog::Accepted == dlg->result()) {
DnaAssemblyToRefTaskSettings s;
s.samOutput = dlg->isSamOutput();
s.refSeqUrl = dlg->getRefSeqUrl();
s.algName = dlg->getAlgorithmName();
s.resultFileName = dlg->getResultFileName();
s.setCustomSettings(dlg->getCustomSettings());
s.shortReadSets = dlg->getShortReadSets();
s.pairedReads = dlg->isPaired();
s.openView = true;
s.prebuiltIndex = dlg->isPrebuiltIndex();
Task* assemblyTask = new DnaAssemblyTaskWithConversions(s, true);
AppContext::getTaskScheduler()->registerTopLevelTask(assemblyTask);
}
}
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 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 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 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 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 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 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 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 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(), );
}
}
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 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 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 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);
}
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());
}
}
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 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 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 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);
}
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 SendSelectionDialog::sl_OK() {
QString error = ca_c->validate();
if (!error.isEmpty()) {
QMessageBox::critical(NULL, tr("Error"), error);
return;
}
retries = retrySpinBox->value();
db = dataBase->currentText();
if(db!="cdd") {
requestParameters = "CMD=Put";
addParametr(requestParameters,ReqParams::program,db);
double eValue = evalueSpinBox->value();
if(shortSequenceCheckBox->isChecked())
eValue = 1000;
addParametr(requestParameters,ReqParams::expect,eValue);
if(false == entrezQueryEdit->text().isEmpty())
addParametr(requestParameters, ReqParams::entrezQuery, entrezQueryEdit->text());
int maxHit = quantitySpinBox->value();
addParametr(requestParameters,ReqParams::hits,maxHit);
if(megablastCheckBox->isChecked()) {
addParametr(requestParameters,ReqParams::megablast,"true");
}
addParametr(requestParameters,ReqParams::database,dbComboBox->currentText().split(" ").last());
QString filter="";
if(lowComplexityFilterCheckBox->isChecked()&&!shortSequenceCheckBox->isChecked()) {
filter.append("L");
}
if(repeatsCheckBox->isChecked()) {
filter.append("R");
}
if(lookupMaskCheckBox->isChecked()) {
filter.append("m");
}
if(!filter.isEmpty()) {
addParametr(requestParameters,ReqParams::filter,filter);
}
addParametr(requestParameters,ReqParams::gapCost,costsComboBox->currentText());
if(db == "blastn"){
addParametr(requestParameters,ReqParams::matchScore,scoresComboBox->currentText().split(" ").first());
addParametr(requestParameters,ReqParams::mismatchScore,scoresComboBox->currentText().split(" ").last());
}
if(shortSequenceCheckBox->isChecked()) {
QString wordSize = wordSizeComboBox->currentText().toInt()>7 ? "7" : wordSizeComboBox->currentText();
addParametr(requestParameters,ReqParams::wordSize, wordSize);
}
else {
addParametr(requestParameters,ReqParams::wordSize,wordSizeComboBox->currentText());
}
if(lowerCaseCheckBox->isChecked()) {
addParametr(requestParameters,ReqParams::lowCaseMask,"yes");
}
if(db=="blastp") {
if(!isAminoSeq) {
translateToAmino = true;
}
addParametr(requestParameters,ReqParams::matrix,matrixComboBox->currentText());
addParametr(requestParameters,ReqParams::service,serviceComboBox->currentText());
if(serviceComboBox->currentText()=="phi") {
addParametr(requestParameters,ReqParams::phiPattern,phiPatternEdit->text());
}
}
}
else { //CDD
requestParameters = "CMD=Put";
db = "blastp";
addParametr(requestParameters,ReqParams::program, db);
addParametr(requestParameters,ReqParams::expect, evalueSpinBox->value());
addParametr(requestParameters,ReqParams::hits,quantitySpinBox->value());
QString dbName = dbComboBox->currentText().split(" ").last();
addParametr(requestParameters,ReqParams::database, dbName.toLower());
addParametr(requestParameters,ReqParams::service, "rpsblast");
}
if(translateToAmino) {
QObjectScopedPointer<QMessageBox> msg = new QMessageBox(this);
msg->setText(tr("You chose to search nucleotide sequence in protein database. This sequence will be converted into 6 sequences(3 translations for both strands)."
"Therefore this search may take some time. Continue?"));
msg->setWindowTitle(windowTitle());
msg->setStandardButtons(QMessageBox::Yes | QMessageBox::Cancel);
msg->setDefaultButton(QMessageBox::Yes);
msg->exec();
CHECK(!msg.isNull(), );
if (msg->result() == QMessageBox::Cancel) {
return;
}
}
int filterResults = 0;
filterResults |= (int)accessionCheckBox->isChecked();
filterResults |= (int)defCheckBox->isChecked() << 1;
filterResults |= (int)idCheckBox->isChecked() << 2;
cfg.filterResult = filterResults;
cfg.useEval = evalueRadioButton->isChecked();
cfg.retries = retrySpinBox->value();
cfg.params = requestParameters;
cfg.dbChoosen = db;
saveSettings();
accept();
}