/** * UGENE - Integrated Bioinformatics Tools. * Copyright (C) 2008-2017 UniPro * http://ugene.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, * MA 02110-1301, USA. */ #include #include #include #include #include #include #include #include #include #include #include #include "Primer3Dialog.h" namespace U2 { Primer3Dialog::Primer3Dialog(const Primer3TaskSettings &defaultSettings, ADVSequenceObjectContext *context): QDialog(context->getAnnotatedDNAView()->getWidget()), defaultSettings(defaultSettings), context(context) { ui.setupUi(this); new HelpButton(this, ui.helpButton, "20880463"); QPushButton* pbPick = ui.pickPrimersButton; QPushButton* pbReset = ui.resetButton; pbPick->setDefault(true); connect(pbPick, SIGNAL(clicked()), SLOT(sl_pbPick_clicked())); connect(pbReset, SIGNAL(clicked()), SLOT(sl_pbReset_clicked())); connect(ui.saveSettingsButton, SIGNAL(clicked()), SLOT(sl_saveSettings())); connect(ui.loadSettingsButton, SIGNAL(clicked()), SLOT(sl_loadSettings())); ui.tabWidget->setCurrentIndex(0); { CreateAnnotationModel createAnnotationModel; createAnnotationModel.data->name = "top_primers"; createAnnotationModel.sequenceObjectRef = GObjectReference(context->getSequenceGObject()); createAnnotationModel.hideAnnotationType = true; createAnnotationModel.hideAnnotationName = false; createAnnotationModel.hideLocation = true; createAnnotationWidgetController = new CreateAnnotationWidgetController(createAnnotationModel,this); ui.annotationWidgetLayout->addWidget(createAnnotationWidgetController->getWidget()); } if(!context->getSequenceSelection()->getSelectedRegions().isEmpty()) { selection = context->getSequenceSelection()->getSelectedRegions().first(); } sequenceLength = context->getSequenceLength(); rs=new RegionSelector(this, sequenceLength, false, context->getSequenceSelection(), true); ui.rangeSelectorLayout->addWidget(rs); repeatLibraries.append(QPair(tr("NONE"), "")); repeatLibraries.append(QPair(tr("HUMAN"), "primer3/humrep_and_simple.txt")); repeatLibraries.append(QPair(tr("RODENT_AND_SIMPLE"), "primer3/rodrep_and_simple.txt")); repeatLibraries.append(QPair(tr("RODENT"), "primer3/rodent_ref.txt")); repeatLibraries.append(QPair(tr("DROSOPHILA"), "primer3/drosophila.w.transposons.txt")); for(int i=0;i < repeatLibraries.size();i++) { if(!repeatLibraries[i].second.isEmpty()) repeatLibraries[i].second = QFileInfo(QString(PATH_PREFIX_DATA) + ":" + repeatLibraries[i].second).absoluteFilePath().toLatin1(); } { QPair library; foreach(library, repeatLibraries) { ui.combobox_PRIMER_MISPRIMING_LIBRARY->addItem(library.first); ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->addItem(library.first); } } int spanIntronExonIdx = -1; for (int i = 0; i < ui.tabWidget->count(); ++i) { if ( ui.tabWidget->tabText(i).contains("Intron") ) { spanIntronExonIdx = i; break; } } if (spanIntronExonIdx != -1) { SplicedAlignmentTaskRegistry* sr = AppContext::getSplicedAlignmentTaskRegistry(); ui.tabWidget->setTabEnabled(spanIntronExonIdx, sr->getAlgNameList().size() > 0); } reset(); } Primer3TaskSettings Primer3Dialog::getSettings()const { return settings; } const CreateAnnotationModel &Primer3Dialog::getCreateAnnotationModel()const { return createAnnotationWidgetController->getModel(); } U2Region Primer3Dialog::getRegion(bool *ok) const { return rs->getRegion(ok); } bool Primer3Dialog::prepareAnnotationObject() { return createAnnotationWidgetController->prepareAnnotationObject(); } QString Primer3Dialog::intervalListToString(const QList< U2Region >& intervalList, const QString& delimiter, IntervalDefinition definition) { QString result; bool first = true; U2Region interval; foreach(interval, intervalList) { if(!first) { result += " "; } result += QString::number(interval.startPos); result += delimiter; if (definition == Start_End) { result += QString::number(interval.endPos() - 1); } else { result += QString::number(interval.length); } first = false; } return result; } bool Primer3Dialog::parseIntervalList(const QString& inputString, const QString& delimiter, QList< U2Region > *outputList, IntervalDefinition definition) { QList< U2Region > result; QStringList intervalStringList = inputString.split(QRegExp("\\s+"),QString::SkipEmptyParts); foreach(QString intervalString, intervalStringList) { QStringList valueStringList = intervalString.split(delimiter); if(2 != valueStringList.size()) { return false; } int firstValue = 0; { bool ok = false; firstValue = valueStringList[0].toInt(&ok); if(!ok) { return false; } } int secondValue = 0; { bool ok = false; secondValue = valueStringList[1].toInt(&ok); if(!ok) { return false; } } if (definition == Start_End) { result.append(U2Region(firstValue, secondValue - firstValue + 1)); } else { result.append(U2Region(firstValue, secondValue)); } } *outputList = result; return true; } void Primer3Dialog::reset() { foreach(QString key, defaultSettings.getIntPropertyList()) { int value = 0; if(defaultSettings.getIntProperty(key,&value)) { QSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { spinBox->setValue(value); } } } foreach(QString key, defaultSettings.getDoublePropertyList()) { double value = 0; if(defaultSettings.getDoubleProperty(key,&value)) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { spinBox->setValue(value); } } } foreach(QString key, defaultSettings.getAlignPropertyList()) { short value = 0; if(defaultSettings.getAlignProperty(key,&value)) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { spinBox->setValue((double)value/100); } } } ui.edit_PRIMER_START_CODON_POSITION->clear(); ui.edit_PRIMER_PRODUCT_MIN_TM->clear(); ui.edit_PRIMER_PRODUCT_OPT_TM->clear(); ui.edit_PRIMER_PRODUCT_MAX_TM->clear(); ui.edit_PRIMER_OPT_GC_PERCENT->clear(); ui.edit_PRIMER_INSIDE_PENALTY->clear(); ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT->clear(); ui.edit_EXCLUDED_REGION->setText(intervalListToString(defaultSettings.getExcludedRegion(),",")); ui.edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION->setText(intervalListToString(defaultSettings.getInternalOligoExcludedRegion(),",")); ui.edit_TARGET->setText(intervalListToString(defaultSettings.getTarget(),",")); ui.edit_PRIMER_PRODUCT_SIZE_RANGE->setText(intervalListToString(defaultSettings.getProductSizeRange(),"-", Start_End)); ui.edit_PRIMER_LEFT_INPUT->setText(defaultSettings.getLeftInput()); ui.edit_PRIMER_RIGHT_INPUT->setText(defaultSettings.getRightInput()); ui.edit_PRIMER_INTERNAL_OLIGO_INPUT->setText(defaultSettings.getInternalInput()); { QString qualityString; bool first = true; foreach(int qualityValue, defaultSettings.getSequenceQuality()) { if(!first) { qualityString += " "; } qualityString += QString::number(qualityValue); first = false; } ui.edit_PRIMER_SEQUENCE_QUALITY->setPlainText(qualityString); } { int value = 0; defaultSettings.getIntProperty("PRIMER_TM_SANTALUCIA",&value); ui.combobox_PRIMER_TM_SANTALUCIA->setCurrentIndex(value); } { int value = 0; defaultSettings.getIntProperty("PRIMER_SALT_CORRECTIONS",&value); ui.combobox_PRIMER_SALT_CORRECTIONS->setCurrentIndex(value); } { int value = 0; defaultSettings.getIntProperty("PRIMER_LIBERAL_BASE",&value); ui.checkbox_PRIMER_LIBERAL_BASE->setChecked(value); } { int value = 0; defaultSettings.getIntProperty("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS",&value); ui.checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS->setChecked(value); } { int value = 0; defaultSettings.getIntProperty("PRIMER_LOWERCASE_MASKING",&value); ui.checkbox_PRIMER_LOWERCASE_MASKING->setChecked(value); } { switch(defaultSettings.getTask()) { case pick_pcr_primers: ui.checkbox_PICK_LEFT->setChecked(true); ui.checkbox_PICK_RIGHT->setChecked(true); ui.checkbox_PICK_HYBRO->setChecked(false); break; case pick_left_only: ui.checkbox_PICK_LEFT->setChecked(true); ui.checkbox_PICK_RIGHT->setChecked(false); ui.checkbox_PICK_HYBRO->setChecked(false); break; case pick_right_only: ui.checkbox_PICK_LEFT->setChecked(false); ui.checkbox_PICK_RIGHT->setChecked(true); ui.checkbox_PICK_HYBRO->setChecked(false); break; case pick_hyb_probe_only: ui.checkbox_PICK_LEFT->setChecked(false); ui.checkbox_PICK_RIGHT->setChecked(false); ui.checkbox_PICK_HYBRO->setChecked(true); break; case pick_pcr_primers_and_hyb_probe: ui.checkbox_PICK_LEFT->setChecked(true); ui.checkbox_PICK_RIGHT->setChecked(true); ui.checkbox_PICK_HYBRO->setChecked(true); break; } } ui.edit_PRIMER_LEFT_INPUT->setEnabled(ui.checkbox_PICK_LEFT->isChecked()); ui.edit_PRIMER_RIGHT_INPUT->setEnabled(ui.checkbox_PICK_RIGHT->isChecked()); ui.edit_PRIMER_INTERNAL_OLIGO_INPUT->setEnabled(ui.checkbox_PICK_HYBRO->isChecked()); ui.combobox_PRIMER_MISPRIMING_LIBRARY->setCurrentIndex(0); ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->setCurrentIndex(0); { for(int i=0;i < repeatLibraries.size();i++) { if(repeatLibraries[i].second == settings.getRepeatLibrary()) { ui.combobox_PRIMER_MISPRIMING_LIBRARY->setCurrentIndex(i); } if(repeatLibraries[i].second == settings.getMishybLibrary()) { ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->setCurrentIndex(i); } } } } static U2Range parseExonRange(const QString& text, bool& ok) { U2Range res; ok = true; if (text.size() > 0) { QStringList items = text.split("-"); if (items.size() != 2) { ok = false; return res; } int startExon = items[0].toInt(&ok); if (!ok) { return res; } int endExon = items[1].toInt(&ok); if (!ok ) { return res; } res.minValue = startExon; res.maxValue = endExon; ok = startExon <= endExon && startExon > 0; } return res; } bool Primer3Dialog::doDataExchange() { settings = defaultSettings; if (ui.spanIntronExonBox->isChecked()) { SpanIntronExonBoundarySettings s; s.enabled = true; s.exonAnnotationName = ui.exonNameEdit->text(); s.maxPairsToQuery = ui.maxPairsBox->value(); s.minLeftOverlap = ui.leftOverlapSizeSpinBox->value(); s.minRightOverlap = ui.rightOverlapSizeSpinBox->value(); s.spanIntron = ui.spanIntronCheckBox->isChecked(); s.overlapExonExonBoundary = ui.spanJunctionBox->isChecked(); bool ok = false; s.exonRange = parseExonRange(ui.exonRangeEdit->text().trimmed(), ok); if (!ok) { showInvalidInputMessage(ui.exonRangeEdit, "Exon range"); return false; } settings.setSpanIntronExonBoundarySettings(s); } foreach(QString key, settings.getIntPropertyList()) { QSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { settings.setIntProperty(key,spinBox->value()); } } foreach(QString key, settings.getDoublePropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { settings.setDoubleProperty(key,spinBox->value()); } } foreach(QString key, settings.getAlignPropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { settings.setAlignProperty(key,(short)(spinBox->value()*100)); } } if(!ui.edit_PRIMER_START_CODON_POSITION->text().isEmpty()) { bool ok = false; int value = ui.edit_PRIMER_START_CODON_POSITION->text().toInt(&ok); if(ok) { settings.setIntProperty("PRIMER_START_CODON_POSITION", value); } else { showInvalidInputMessage(ui.edit_PRIMER_START_CODON_POSITION, tr("Start Codon Position")); return false; } } if(!ui.edit_PRIMER_PRODUCT_MIN_TM->text().isEmpty()) { bool ok = false; double value = ui.edit_PRIMER_PRODUCT_MIN_TM->text().toDouble(&ok); if(ok) { settings.setDoubleProperty("PRIMER_PRODUCT_MIN_TM", value); } else { showInvalidInputMessage(ui.edit_PRIMER_PRODUCT_MIN_TM, tr("Product Min Tm")); return false; } } if(!ui.edit_PRIMER_PRODUCT_OPT_TM->text().isEmpty()) { bool ok = false; double value = ui.edit_PRIMER_PRODUCT_OPT_TM->text().toDouble(&ok); if(ok) { settings.setDoubleProperty("PRIMER_PRODUCT_OPT_TM", value); } else { showInvalidInputMessage(ui.edit_PRIMER_PRODUCT_OPT_TM, tr("Product Opt Tm")); return false; } } if(!ui.edit_PRIMER_PRODUCT_MAX_TM->text().isEmpty()) { bool ok = false; double value = ui.edit_PRIMER_PRODUCT_MAX_TM->text().toDouble(&ok); if(ok) { settings.setDoubleProperty("PRIMER_PRODUCT_MAX_TM", value); } else { showInvalidInputMessage(ui.edit_PRIMER_PRODUCT_MAX_TM, tr("Product Max Tm")); return false; } } if(!ui.edit_PRIMER_OPT_GC_PERCENT->text().isEmpty()) { bool ok = false; short value = (short)(ui.edit_PRIMER_OPT_GC_PERCENT->text().toDouble(&ok)*100); if(ok) { settings.setAlignProperty("PRIMER_OPT_GC_PERCENT", value); } else { showInvalidInputMessage(ui.edit_PRIMER_OPT_GC_PERCENT, tr("Opt GC%")); return false; } } if(!ui.edit_PRIMER_INSIDE_PENALTY->text().isEmpty()) { bool ok = false; double value = ui.edit_PRIMER_INSIDE_PENALTY->text().toDouble(&ok); if(ok) { settings.setDoubleProperty("PRIMER_INSIDE_PENALTY", value); } else { showInvalidInputMessage(ui.edit_PRIMER_INSIDE_PENALTY, tr("Inside Penalty")); return false; } } if(!ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT->text().isEmpty()) { bool ok = false; short value = (short)(ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT->text().toDouble(&ok)*100); if(ok) { settings.setAlignProperty("PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT", value); } else { showInvalidInputMessage(ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT, tr("Internal Oligo Opt Tm")); return false; } } { QList< U2Region > list; if(parseIntervalList(ui.edit_EXCLUDED_REGION->text(), ",", &list)) { settings.setExcludedRegion(list); } else { showInvalidInputMessage(ui.edit_EXCLUDED_REGION, tr("Excluded Regions")); return false; } } { QList< U2Region > list; if(parseIntervalList(ui.edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION->text(), ",", &list)) { settings.setInternalOligoExcludedRegion(list); } else { showInvalidInputMessage(ui.edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION, tr("Internal Oligo Excluded Regions")); return false; } } { QList< U2Region > list; if(parseIntervalList(ui.edit_TARGET->text(), ",", &list)) { settings.setTarget(list); } else { showInvalidInputMessage(ui.edit_TARGET, tr("Targets")); return false; } } if(ui.checkbox_PICK_LEFT->isChecked()) { settings.setLeftInput(ui.edit_PRIMER_LEFT_INPUT->text().toLatin1()); } else { settings.setLeftInput(""); } if(ui.checkbox_PICK_RIGHT->isChecked()) { settings.setRightInput(ui.edit_PRIMER_RIGHT_INPUT->text().toLatin1()); } else { settings.setRightInput(""); } if(ui.checkbox_PICK_HYBRO->isChecked()) { settings.setInternalInput(ui.edit_PRIMER_INTERNAL_OLIGO_INPUT->text().toLatin1()); } else { settings.setInternalInput(""); } { QVector qualityList; QStringList stringList = ui.edit_PRIMER_SEQUENCE_QUALITY->toPlainText().split(QRegExp("\\s+"),QString::SkipEmptyParts); foreach(QString string, stringList) { bool ok = false; int value = string.toInt(&ok); if(!ok) { showInvalidInputMessage(ui.edit_PRIMER_SEQUENCE_QUALITY, tr("Sequence Quality")); return false; } qualityList.append(value); } if(!qualityList.isEmpty() && (qualityList.size() != (rs->getRegion().length)))//todo add check on wrong region { QMessageBox::critical(this, windowTitle(), tr("Sequence quality list length must be equal to the sequence length")); return false; } settings.setSequenceQuality(qualityList); } settings.setIntProperty("PRIMER_TM_SANTALUCIA", ui.combobox_PRIMER_TM_SANTALUCIA->currentIndex()); settings.setIntProperty("PRIMER_SALT_CORRECTIONS", ui.combobox_PRIMER_SALT_CORRECTIONS->currentIndex()); settings.setIntProperty("PRIMER_LIBERAL_BASE", ui.checkbox_PRIMER_LIBERAL_BASE->isChecked()); settings.setIntProperty("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS", ui.checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS->isChecked()); settings.setIntProperty("PRIMER_LOWERCASE_MASKING", ui.checkbox_PRIMER_LOWERCASE_MASKING->isChecked()); if(ui.checkbox_PICK_HYBRO->isChecked()) { if(ui.checkbox_PICK_LEFT->isChecked() && ui.checkbox_PICK_RIGHT->isChecked()) { settings.setTask(pick_pcr_primers_and_hyb_probe); } else if(!ui.checkbox_PICK_LEFT->isChecked() && !ui.checkbox_PICK_RIGHT->isChecked()) { settings.setTask(pick_hyb_probe_only); } else { QMessageBox::critical(this, windowTitle(), tr("Can't pick hyb oligo and only one primer")); return false; } } else { if(ui.checkbox_PICK_LEFT->isChecked() && ui.checkbox_PICK_RIGHT->isChecked()) { settings.setTask(pick_pcr_primers); } else if(ui.checkbox_PICK_LEFT->isChecked()) { settings.setTask(pick_left_only); } else if(ui.checkbox_PICK_RIGHT->isChecked()) { settings.setTask(pick_right_only); } else { QMessageBox::critical(this, windowTitle(), tr("Nothing to pick")); return false; } } { int index = ui.combobox_PRIMER_MISPRIMING_LIBRARY->currentIndex(); settings.setRepeatLibrary(repeatLibraries[index].second); } { int index = ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->currentIndex(); settings.setMishybLibrary(repeatLibraries[index].second); } { QList< U2Region > list; if(parseIntervalList(ui.edit_PRIMER_PRODUCT_SIZE_RANGE->text(), "-", &list, Start_End)) { settings.setProductSizeRange(list); bool isRegionOk = false; U2Region includedRegion = rs->getRegion(&isRegionOk); if (!settings.checkIncludedRegion(includedRegion)) { QMessageBox::critical(this, windowTitle(), tr("Included region is too small for current product size ranges")); return false; } settings.setIncludedRegion( includedRegion.startPos + settings.getFirstBaseIndex(), includedRegion.length); } else { showInvalidInputMessage(ui.edit_PRIMER_PRODUCT_SIZE_RANGE, tr("Product Size Ranges")); return false; } } return true; } void Primer3Dialog::showInvalidInputMessage(QWidget *field, QString fieldLabel) { ui.tabWidget->setCurrentWidget(field->parentWidget()); field->setFocus(Qt::OtherFocusReason); QMessageBox::critical(this, windowTitle(), tr("The field '%1' has invalid value").arg(fieldLabel)); } void Primer3Dialog::sl_pbPick_clicked() { bool isRegionOk=false; rs->getRegion(&isRegionOk); if(!isRegionOk){ rs->showErrorMessage(); return; } if(doDataExchange()) { bool objectPrepared = createAnnotationWidgetController->prepareAnnotationObject(); if (!objectPrepared){ QMessageBox::critical(this, L10N::errorTitle(), tr("Cannot create an annotation object. Please check settings.")); return; } const CreateAnnotationModel& m = createAnnotationWidgetController->getModel(); AnnotationTableObject *obj = m.getAnnotationObject(); context->getAnnotatedDNAView()->tryAddObject(obj); accept(); } } void Primer3Dialog::sl_saveSettings() { LastUsedDirHelper lod; QString fileName = U2FileDialog::getSaveFileName(this, tr("Save primer settings"), lod.dir, "Text files (*.txt)"); if (!fileName.endsWith(".txt")) { fileName += ".txt"; } QSettings diagSettings(fileName, QSettings::IniFormat); diagSettings.beginGroup("IntProperties"); foreach(const QString& key, settings.getIntPropertyList()) { QSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { diagSettings.setValue( key, spinBox->value() ); } } diagSettings.endGroup(); diagSettings.beginGroup("DoubleProperties"); foreach(const QString& key, settings.getDoublePropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { diagSettings.setValue(key, spinBox->value()); } } diagSettings.endGroup(); diagSettings.beginGroup("AlignProperties"); foreach(const QString& key, settings.getAlignPropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox) { diagSettings.setValue(key, spinBox->value()); } } diagSettings.endGroup(); diagSettings.beginGroup("GeneralProperties"); diagSettings.setValue("PRIMER_START_CODON_POSITION", ui.edit_PRIMER_START_CODON_POSITION->text()); diagSettings.setValue("PRIMER_PRODUCT_MIN_TM", ui.edit_PRIMER_PRODUCT_MIN_TM->text()); diagSettings.setValue("PRIMER_PRODUCT_OPT_TM", ui.edit_PRIMER_PRODUCT_OPT_TM->text()); diagSettings.setValue("PRIMER_PRODUCT_MAX_TM", ui.edit_PRIMER_PRODUCT_MAX_TM->text()); diagSettings.setValue("PRIMER_OPT_GC_PERCENT", ui.edit_PRIMER_OPT_GC_PERCENT->text()); diagSettings.setValue("PRIMER_INSIDE_PENALTY", ui.edit_PRIMER_INSIDE_PENALTY->text()); diagSettings.setValue("PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT", ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT->text()); diagSettings.setValue("EXCLUDED_REGION", ui.edit_EXCLUDED_REGION->text()); diagSettings.setValue("PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION", ui.edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION->text()); diagSettings.setValue("TARGET", ui.edit_TARGET->text()); diagSettings.setValue("PRIMER_PRODUCT_SIZE_RANGE", ui.edit_PRIMER_PRODUCT_SIZE_RANGE->text()); diagSettings.setValue("PRIMER_LEFT_INPUT", ui.edit_PRIMER_LEFT_INPUT->text()); diagSettings.setValue("PRIMER_RIGHT_INPUT", ui.edit_PRIMER_RIGHT_INPUT->text()); diagSettings.setValue("PRIMER_INTERNAL_OLIGO_INPUT", ui.edit_PRIMER_INTERNAL_OLIGO_INPUT->text()); diagSettings.setValue("PRIMER_TM_SANTALUCIA", ui.combobox_PRIMER_TM_SANTALUCIA->currentIndex()); diagSettings.setValue("PRIMER_SALT_CORRECTIONS", ui.combobox_PRIMER_SALT_CORRECTIONS->currentIndex()); diagSettings.setValue("PRIMER_LIBERAL_BASE", ui.checkbox_PRIMER_LIBERAL_BASE->isChecked()); diagSettings.setValue("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS", ui.checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS->isChecked()); diagSettings.setValue("PRIMER_LOWERCASE_MASKING", ui.checkbox_PRIMER_LOWERCASE_MASKING->isChecked()); diagSettings.setValue("PICK_HYBRO", ui.checkbox_PICK_HYBRO->isChecked() ); diagSettings.setValue("PICK_LEFT", ui.checkbox_PICK_LEFT->isChecked() ); diagSettings.setValue("PICK_RIGHT", ui.checkbox_PICK_RIGHT->isChecked() ); diagSettings.setValue("PRIMER_MISPRIMING_LIBRARY", ui.combobox_PRIMER_MISPRIMING_LIBRARY->currentIndex()); diagSettings.setValue("PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY", ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->currentIndex()); diagSettings.endGroup(); } void Primer3Dialog::sl_loadSettings() { LastUsedDirHelper lod; lod.url = U2FileDialog::getOpenFileName(this, tr("Load settings"), lod.dir, "Text files (*.txt)"); QSettings diagSettings(lod.url, QSettings::IniFormat); QStringList groups = diagSettings.childGroups(); bool validSettings = groups.contains("IntProperties") && groups.contains("DoubleProperties") && groups.contains("AlignProperties") && groups.contains("GeneralProperties"); if (!validSettings) { QMessageBox::warning(this, windowTitle(), tr("Can not load settings file: invalid format.") ); return; } diagSettings.beginGroup("IntProperties"); QStringList groupKeys = diagSettings.childKeys(); foreach(const QString& key, settings.getIntPropertyList()) { QSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox && groupKeys.contains(key)) { spinBox->setValue( diagSettings.value(key).toInt()); } } diagSettings.endGroup(); diagSettings.beginGroup("DoubleProperties"); groupKeys = diagSettings.childKeys(); foreach(const QString& key, settings.getDoublePropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox && groupKeys.contains(key)) { spinBox->setValue(diagSettings.value(key).toDouble()); } } diagSettings.endGroup(); diagSettings.beginGroup("AlignProperties"); groupKeys = diagSettings.childKeys(); foreach(const QString& key, settings.getAlignPropertyList()) { QDoubleSpinBox *spinBox = findChild("edit_" + key); if(NULL != spinBox && groupKeys.contains(key)) { spinBox->setValue(diagSettings.value(key).toDouble()); } } diagSettings.endGroup(); diagSettings.beginGroup("GeneralProperties"); groupKeys = diagSettings.childKeys(); ui.edit_PRIMER_START_CODON_POSITION->setText( diagSettings.value("PRIMER_START_CODON_POSITION").toString() ); ui.edit_PRIMER_PRODUCT_MIN_TM->setText( diagSettings.value("PRIMER_PRODUCT_MIN_TM").toString() ); ui.edit_PRIMER_PRODUCT_OPT_TM->setText( diagSettings.value("PRIMER_PRODUCT_OPT_TM").toString() ); ui.edit_PRIMER_PRODUCT_MAX_TM->setText( diagSettings.value("PRIMER_PRODUCT_MAX_TM").toString() ); ui.edit_PRIMER_OPT_GC_PERCENT->setText( diagSettings.value("PRIMER_OPT_GC_PERCENT").toString() ); ui.edit_PRIMER_INSIDE_PENALTY->setText( diagSettings.value("PRIMER_INSIDE_PENALTY").toString() ); ui.edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT->setText( diagSettings.value("PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT").toString()); ui.edit_EXCLUDED_REGION->setText( diagSettings.value("EXCLUDED_REGION").toString() ); ui.edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION->setText( diagSettings.value("PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION").toString() ); ui.edit_TARGET->setText( diagSettings.value("TARGET").toString() ); ui.edit_PRIMER_PRODUCT_SIZE_RANGE->setText( diagSettings.value("PRIMER_PRODUCT_SIZE_RANGE").toString() ); ui.edit_PRIMER_LEFT_INPUT->setText( diagSettings.value("PRIMER_LEFT_INPUT").toString() ); ui.edit_PRIMER_RIGHT_INPUT->setText( diagSettings.value("PRIMER_RIGHT_INPUT").toString() ); ui.edit_PRIMER_INTERNAL_OLIGO_INPUT->setText( diagSettings.value("PRIMER_INTERNAL_OLIGO_INPUT").toString() ); ui.combobox_PRIMER_TM_SANTALUCIA->setCurrentIndex( diagSettings.value("PRIMER_TM_SANTALUCIA").toInt() ); ui.combobox_PRIMER_SALT_CORRECTIONS->setCurrentIndex( diagSettings.value("PRIMER_SALT_CORRECTIONS").toInt() ); ui.checkbox_PRIMER_LIBERAL_BASE->setChecked( diagSettings.value("PRIMER_LIBERAL_BASE").toBool() ); ui.checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS->setChecked( diagSettings.value("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS").toBool() ); ui.checkbox_PRIMER_LOWERCASE_MASKING->setChecked( diagSettings.value("PRIMER_LOWERCASE_MASKING").toBool() ); ui.checkbox_PICK_HYBRO->setChecked( diagSettings.value("PICK_HYBRO").toBool() ); ui.checkbox_PICK_LEFT->setChecked( diagSettings.value("PICK_LEFT").toBool() ); ui.checkbox_PICK_RIGHT->setChecked( diagSettings.value("PICK_RIGHT").toBool() ); ui.combobox_PRIMER_MISPRIMING_LIBRARY->setCurrentIndex( diagSettings.value("PRIMER_MISPRIMING_LIBRARY").toInt() ); ui.combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY->setCurrentIndex( diagSettings.value("PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY").toInt() ); diagSettings.endGroup(); } void Primer3Dialog::sl_pbReset_clicked() { reset(); rs->reset(); } QString Primer3Dialog::checkModel() { return createAnnotationWidgetController->validate(); } } // namespace U2