/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 UniPro <ugene@unipro.ru>
 * 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 "BowtieSettingsWidget.h"

#include <QMessageBox>

#include <U2Core/AppContext.h>
#include <U2Core/AppResources.h>
#include <U2Core/AppSettings.h>
#include <U2Core/ExternalToolRegistry.h>

#include <U2Gui/AppSettingsGUI.h>

#include "BowtieSupport.h"
#include "BowtieTask.h"

namespace U2 {

// BowtieSettingsWidget

BowtieSettingsWidget::BowtieSettingsWidget(QWidget* parent)
    : DnaAssemblyAlgorithmMainWidget(parent) {
    setupUi(this);
    layout()->setContentsMargins(0, 0, 0, 0);

    threadsSpinBox->setMaximum(AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount());
    threadsSpinBox->setValue(AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount());
#ifdef Q_OS_WIN
    threadsSpinBox->setValue(1);
    threadsLabel->setVisible(false);
    threadsSpinBox->setVisible(false);
#endif

    indexSuffixes << BowtieTask::indexSuffixes;
    indexSuffixes << BowtieTask::largeIndexSuffixes;

    requiredExtToolIds << BowtieSupport::ET_BOWTIE_ID << BowtieSupport::ET_BOWTIE_BUILD_ID;
}

QMap<QString, QVariant> BowtieSettingsWidget::getDnaAssemblyCustomSettings() const {
    QMap<QString, QVariant> settings;

    switch (mismatchesComboBox->currentIndex()) {
        case 0:
            settings.insert(BowtieTask::OPTION_N_MISMATCHES, mismatchesSpinBox->value());
            break;
        case 1:
            settings.insert(BowtieTask::OPTION_V_MISMATCHES, mismatchesSpinBox->value());
            break;
    }

    if (maqerrCheckBox->isChecked()) {
        settings.insert(BowtieTask::OPTION_MAQERR, maqerrSpinBox->value());
    }
    if (maxbtsCheckBox->isChecked()) {
        settings.insert(BowtieTask::OPTION_MAXBTS, maxbtsSpinBox->value());
    }
    if (seedlenCheckBox->isChecked()) {
        settings.insert(BowtieTask::OPTION_SEED_LEN, seedlenSpinBox->value());
    }
    if (chunckmbsCheckBox->isChecked()) {
        settings.insert(BowtieTask::OPTION_CHUNKMBS, chunkmbsSpinBox->value());
    }
    if (seedCheckBox->isChecked()) {
        settings.insert(BowtieTask::OPTION_SEED, seedSpinBox->value());
    }

    settings.insert(BowtieTask::OPTION_THREADS, threadsSpinBox->value());

    settings.insert(BowtieTask::OPTION_NOFW, nofwCheckBox->isChecked());
    settings.insert(BowtieTask::OPTION_NORC, norcCheckBox->isChecked());
    settings.insert(BowtieTask::OPTION_TRYHARD, tryhardCheckBox->isChecked());
    settings.insert(BowtieTask::OPTION_BEST, bestCheckBox->isChecked());
    settings.insert(BowtieTask::OPTION_ALL, allCheckBox->isChecked());
    settings.insert(BowtieTask::OPTION_NOMAQROUND, nomaqroundCheckBox->isChecked());

    return settings;
}

bool BowtieSettingsWidget::isValidIndex(const QString& oneIndexFileUrl) const {
    QStringList suffixes;
    suffixes << BowtieTask::indexSuffixes;
    suffixes << BowtieTask::largeIndexSuffixes;

    QString baseUrl = DnaAssemblyToReferenceTask::getBaseUrl(oneIndexFileUrl, suffixes);
    bool index = DnaAssemblyToReferenceTask::isPrebuiltIndex(baseUrl, BowtieTask::indexSuffixes);
    bool largeIndex = DnaAssemblyToReferenceTask::isPrebuiltIndex(baseUrl, BowtieTask::largeIndexSuffixes);
    return index || largeIndex;
}

// BowtieBuildSettingsWidget

BowtieBuildSettingsWidget::BowtieBuildSettingsWidget(QWidget* parent)
    : DnaAssemblyAlgorithmBuildIndexWidget(parent) {
    setupUi(this);
    layout()->setContentsMargins(0, 0, 0, 0);
}

QMap<QString, QVariant> BowtieBuildSettingsWidget::getBuildIndexCustomSettings() {
    QMap<QString, QVariant> settings;
    return settings;
}

QString BowtieBuildSettingsWidget::getIndexFileExtension() {
    return QString();
}

GUrl BowtieBuildSettingsWidget::buildIndexUrl(const GUrl&) {
    return GUrl();
}

// BowtieGUIExtensionsFactory

DnaAssemblyAlgorithmMainWidget* BowtieGUIExtensionsFactory::createMainWidget(QWidget* parent) {
    return new BowtieSettingsWidget(parent);
}

DnaAssemblyAlgorithmBuildIndexWidget* BowtieGUIExtensionsFactory::createBuildIndexWidget(QWidget* parent) {
    return new BowtieBuildSettingsWidget(parent);
}

bool BowtieGUIExtensionsFactory::hasMainWidget() {
    return true;
}

bool BowtieGUIExtensionsFactory::hasBuildIndexWidget() {
    return true;
}

}  // namespace U2
