/**
 * 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 "BlastRunCommonDialog.h"

#include <QMessageBox>
#include <QToolButton>

#include <U2Core/AppContext.h>
#include <U2Core/AppResources.h>
#include <U2Core/AppSettings.h>
#include <U2Core/DNAAlphabet.h>
#include <U2Core/IOAdapter.h>
#include <U2Core/ProjectModel.h>

#include <U2Gui/HelpButton.h>

#include "BlastSupport.h"
#include "BlastWorker.h"

namespace U2 {

using namespace LocalWorkflow;

/** Composition based statistics tools. */
static const QStringList COMP_TOOLS = {"blastp", "blastx", "tblastn"};

////////////////////////////////////////
// BlastAllSupportRunCommonDialog
BlastRunCommonDialog::BlastRunCommonDialog(QWidget* parent, const DNAAlphabet* alphabet)
    : QDialog(parent) {
    setupUi(this);
    new HelpButton(this, buttonBox, "65930723");

    updateAvailableProgramsList(alphabet);

    buttonBox->button(QDialogButtonBox::Yes)->setText(tr("Restore to default"));
    buttonBox->button(QDialogButtonBox::Ok)->setText(tr("Search"));
    buttonBox->button(QDialogButtonBox::Cancel)->setText(tr("Cancel"));

    hitsLabel->setText(BlastWorkerFactory::getHitsName() + ":");
    QString hitsToolTip = BlastWorkerFactory::getHitsDescription();

    dbSelector = new BlastDBSelectorWidgetController(this);
    dbSelectorWidget->layout()->addWidget(dbSelector);
    hitsLabel->setToolTip(hitsToolTip);
    numberOfHitsSpinBox->setToolTip(hitsToolTip);

    optionsTab->setCurrentIndex(0);

    // I don`t know what this in local BLAST
    phiPatternEdit->hide();
    phiPatternLabel->hide();
    // set available number of threads
    numberOfCPUSpinBox->setMaximum(AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount());
    numberOfCPUSpinBox->setValue(AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount());
    // Connecting people
    connect(programNameComboBox, SIGNAL(currentIndexChanged(int)), SLOT(sl_onProgramNameChange(int)));
    connect(matrixComboBox, SIGNAL(currentIndexChanged(int)), SLOT(sl_onMatrixChanged(int)));
    sl_onMatrixChanged(0);

    connect(scoresComboBox, SIGNAL(currentIndexChanged(int)), SLOT(sl_onMatchScoresChanged(int)));
    sl_onMatchScoresChanged(0);
    connect(megablastCheckBox, SIGNAL(toggled(bool)), SLOT(sl_megablastChecked()));

    okButton = buttonBox->button(QDialogButtonBox::Ok);
    restoreButton = buttonBox->button(QDialogButtonBox::Yes);
    cancelButton = buttonBox->button(QDialogButtonBox::Cancel);
    connect(okButton, SIGNAL(clicked()), SLOT(sl_runQuery()));
    connect(restoreButton, SIGNAL(clicked()), SLOT(sl_restoreDefault()));
    sl_onProgramNameChange(0);
    okButton->setEnabled(false);

    connect(compStatsComboBox, SIGNAL(currentIndexChanged(int)), SLOT(sl_onCompStatsChanged()));
    connect(dbSelector, SIGNAL(si_dbChanged()), SLOT(sl_lineEditChanged()));
    setupCompositionBasedStatistics();
    sl_onCompStatsChanged();
}

void BlastRunCommonDialog::setupCompositionBasedStatistics() {
    bool visible = COMP_TOOLS.contains(programNameComboBox->currentText());
    compStatsLabel->setVisible(visible);
    compStatsComboBox->setVisible(visible);
}

const BlastTaskSettings& BlastRunCommonDialog::getSettings() const {
    return settings;
}
void BlastRunCommonDialog::sl_onMatchScoresChanged(int) {
    if (programNameComboBox->currentText() != "blastn") {
        return;
    }
    settings.matchReward = scoresComboBox->currentText().split(" ").at(0).toInt();
    settings.mismatchPenalty = scoresComboBox->currentText().split(" ").at(1).toInt();
    // For help see http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node76.html
    // Last values is default
    if ((scoresComboBox->currentText() == "1 -4") ||
        (scoresComboBox->currentText() == "1 -3")) {  //-G 1 -E 2; -G 0 -E 2;-G 2 -E 1; -G 1 -E 1; -G 2 -E 2
        costsComboBox->clear();
        costsComboBox->addItem("2 2");
        costsComboBox->addItem("1 2");
        costsComboBox->addItem("0 2");
        costsComboBox->addItem("2 1");
        costsComboBox->addItem("1 1");
    } else if (scoresComboBox->currentText() == "1 -2") {  //-G 1 -E 2; -G 0 -E 2; -G 3 -E 1; -G 2 -E 1; -G 1 -E 1; -G 2 -E 2
        costsComboBox->clear();
        costsComboBox->addItem("2 2");
        costsComboBox->addItem("1 2");
        costsComboBox->addItem("0 2");
        costsComboBox->addItem("3 1");
        costsComboBox->addItem("2 1");
        costsComboBox->addItem("1 1");
    } else if (scoresComboBox->currentText() == "1 -1") {  //-G 3 -E 2; -G 2 -E 2; -G 1 -E 2; -G 0 -E 2; -G 4 -E 1; -G 3 -E 1; -G 2 -E 1; -G 4 -E 2  :Not supported megablast
        costsComboBox->clear();
        costsComboBox->addItem("4 2");
        costsComboBox->addItem("3 2");
        costsComboBox->addItem("2 2");
        costsComboBox->addItem("1 2");
        costsComboBox->addItem("0 2");
        costsComboBox->addItem("4 1");
        costsComboBox->addItem("3 1");
        costsComboBox->addItem("2 1");
    } else if ((scoresComboBox->currentText() == "2 -7") ||
               (scoresComboBox->currentText() == "2 -5")) {  //-G 2 -E 4; -G 0 -E 4; -G 4 -E 2; -G 2 -E 2; -G 4 -E 4
        costsComboBox->clear();
        costsComboBox->addItem("4 4");
        costsComboBox->addItem("2 4");
        costsComboBox->addItem("0 4");
        costsComboBox->addItem("4 2");
        costsComboBox->addItem("2 2");
    } else if (scoresComboBox->currentText() == "2 -3") {  //-G 4 -E 4; -G 2 -E 4; -G 0 -E 4; -G 3 -E 3; -G 6 -E 2; -G 5 -E 2; -G 4 -E 2; -G 2 -E 2, -G 6 -E 4
        costsComboBox->clear();
        costsComboBox->addItem("6 4");
        costsComboBox->addItem("4 4");
        costsComboBox->addItem("2 4");
        costsComboBox->addItem("0 4");
        costsComboBox->addItem("3 3");
        costsComboBox->addItem("6 2");
        costsComboBox->addItem("5 2");
        costsComboBox->addItem("4 2");
        costsComboBox->addItem("2 2");
    } else if ((scoresComboBox->currentText() == "4 -5") ||
               (scoresComboBox->currentText() == "5 -4")) {  //-G 6 -E 5; -G 5 -E 5; -G 4 -E 5; -G 3 -E 5; -G 12 -E 8
        costsComboBox->clear();
        costsComboBox->addItem("12 8");
        costsComboBox->addItem("6 5");
        costsComboBox->addItem("5 5");
        costsComboBox->addItem("4 5");
        costsComboBox->addItem("3 5");
    } else {
        assert(0);
    }
}

void BlastRunCommonDialog::sl_onMatrixChanged(int) {
    if (programNameComboBox->currentText() == "blastn") {
        return;
    }
    QString matrix = matrixComboBox->currentText();
    settings.matrix = matrix;
    // For help see http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node77.html
    // Last values is default
    if (matrix == "PAM30") {  //-G 5 -E 2; -G 6 -E 2; -G 7 -E 2; -G 8 -E 1; -G 10 -E 1; -G 9 -E 1
        costsComboBox->clear();
        costsComboBox->addItem("9 1");
        costsComboBox->addItem("5 2");
        costsComboBox->addItem("6 2");
        costsComboBox->addItem("7 2");
        costsComboBox->addItem("8 1");
        costsComboBox->addItem("10 1");
    } else if (matrix == "PAM70") {  //-G 6 -E 2; -G 7 -E 2; -G 8 -E 2; -G 9 -E 2; -G 11 -E 1; -G 10 -E 1
        costsComboBox->clear();
        costsComboBox->addItem("10 1");
        costsComboBox->addItem("6 2");
        costsComboBox->addItem("7 2");
        costsComboBox->addItem("8 2");
        costsComboBox->addItem("9 2");
        costsComboBox->addItem("11 1");
    } else if (matrix == "BLOSUM45") {  //-G 10 -E 3; -G 11 -E 3; -G 12 -E 3; -G 12 -E 2; -G 13 -E 2, -G 14 -E 2;
        //-G 16 -E 2; -G 15 -E 1; -G 16 -E 1; -G 17 -E 1; -G 18 -E 1; -G 19 -E 1; -G 15 -E 2
        costsComboBox->clear();
        costsComboBox->addItem("15 2");
        costsComboBox->addItem("10 3");
        costsComboBox->addItem("11 3");
        costsComboBox->addItem("12 3");
        costsComboBox->addItem("12 2");
        costsComboBox->addItem("13 2");
        costsComboBox->addItem("14 2");
        costsComboBox->addItem("16 2");
        costsComboBox->addItem("15 1");
        costsComboBox->addItem("16 1");
        costsComboBox->addItem("17 1");
        costsComboBox->addItem("18 1");
        costsComboBox->addItem("19 1");
    } else if (matrix == "BLOSUM62") {  //-G 7 -E 2; -G 8 -E 2; -G 9 -E 2; -G 10 -E 1; -G 12 -E 1; -G 11 -E 1
        costsComboBox->clear();
        costsComboBox->addItem("11 1");
        costsComboBox->addItem("7 2");
        costsComboBox->addItem("8 2");
        costsComboBox->addItem("9 2");
        costsComboBox->addItem("10 1");
        costsComboBox->addItem("12 1");
    } else if (matrix == "BLOSUM80") {  //-G 6 -E 2; -G 7 -E 2; -G 8 -E 2; -G 9 -E 1; -G 11 -E 1; -G 10 -E 1
        costsComboBox->clear();
        costsComboBox->addItem("10 1");
        costsComboBox->addItem("6 2");
        costsComboBox->addItem("7 2");
        costsComboBox->addItem("8 2");
        costsComboBox->addItem("9 1");
        costsComboBox->addItem("11 1");
    } else {
        FAIL("Unsupported matrix type: " + matrix, );
    }
}

void BlastRunCommonDialog::sl_restoreDefault() {
    needRestoreDefault = true;
    //    sl_onProgNameChange(0);
    megablastCheckBox->setChecked(false);
    sl_megablastChecked();
    sl_onMatchScoresChanged(0);
    sl_onMatrixChanged(0);
    evalueSpinBox->setValue(10);
    needRestoreDefault = false;
    bothStrandsButton->setChecked(true);
}

void BlastRunCommonDialog::sl_megablastChecked() {
    if (megablastCheckBox->isChecked()) {
        if (wordSizeSpinBox->value() < 12 || needRestoreDefault) {
            wordSizeSpinBox->setValue(28);
        }
        wordSizeSpinBox->setMaximum(100);
        wordSizeSpinBox->setMinimum(12);
        xDropoffGASpinBox->setValue(20);
        xDropoffUnGASpinBox->setValue(20);
    } else {
        if (wordSizeSpinBox->value() < 7 || needRestoreDefault) {
            wordSizeSpinBox->setValue(11);
        }
        wordSizeSpinBox->setMaximum(100);
        wordSizeSpinBox->setMinimum(7);
        xDropoffGASpinBox->setValue(30);
        xDropoffUnGASpinBox->setValue(10);
    }
}

void BlastRunCommonDialog::sl_onProgramNameChange(int) {
    setupCompositionBasedStatistics();
    QString programName = programNameComboBox->currentText();
    settings.programName = programName;
    if (programName == "blastn") {
        programNameComboBox->setToolTip(tr("Direct nucleotide alignment"));
        thresholdSpinBox->setValue(0);
    } else if (programName == "blastp") {
        programNameComboBox->setToolTip(tr("Direct protein alignment"));
        thresholdSpinBox->setValue(11);
    } else if (programName == "blastx") {
        programNameComboBox->setToolTip(tr("Protein alignment, input nucleotide is translated input protein before the search"));
        thresholdSpinBox->setValue(12);
    } else if (programName == "tblastn") {
        programNameComboBox->setToolTip(tr("Protein alignment, nucleotide database is translated input protein before the search"));
        thresholdSpinBox->setValue(13);
    } else if (programName == "tblastx") {
        programNameComboBox->setToolTip(tr("Protein alignment, both input query and database are translated before the search"));
        thresholdSpinBox->setValue(13);
    } else {
        FAIL("Unsupported blast program name: " + settings.programName, );
    }

    enableStrandBox(programName == "blastn" || programName.contains("blastx"));

    costsLabel->setVisible(programName != "tblastx");
    costsComboBox->setVisible(programName != "tblastx");
    gappedAlignmentCheckBox->setEnabled(programName != "tblastx");

    if (programName == "blastn") {
        megablastCheckBox->setEnabled(true);
        if (megablastCheckBox->isChecked()) {
            wordSizeSpinBox->setValue(28);
            wordSizeSpinBox->setMaximum(100);
            wordSizeSpinBox->setMinimum(12);
        } else {
            wordSizeSpinBox->setValue(11);
            wordSizeSpinBox->setMaximum(100);
            wordSizeSpinBox->setMinimum(7);
        }
        windowSizeSpinBox->setValue(0);

        matchScoreLabel->show();
        scoresComboBox->show();
        matrixLabel->hide();
        matrixComboBox->hide();
        serviceLabel->hide();
        serviceComboBox->hide();
        thresholdSpinBox->hide();
        thresholdLabel->hide();
        sl_onMatchScoresChanged(0);
    } else {
        megablastCheckBox->setEnabled(false);
        wordSizeSpinBox->setValue(3);
        wordSizeSpinBox->setMaximum(3);
        wordSizeSpinBox->setMinimum(2);
        windowSizeSpinBox->setValue(40);

        matchScoreLabel->hide();
        scoresComboBox->hide();
        matrixLabel->show();
        matrixComboBox->show();
        serviceLabel->show();
        serviceComboBox->show();
        thresholdSpinBox->show();
        thresholdLabel->show();
        sl_onMatrixChanged(0);
    }
    // Set X drop-off values.
    if (programName == "blastn") {
        megablastCheckBox->setEnabled(true);
        if (megablastCheckBox->isChecked()) {
            xDropoffGASpinBox->setValue(20);
            xDropoffUnGASpinBox->setValue(10);
        } else {
            xDropoffGASpinBox->setValue(30);
            xDropoffUnGASpinBox->setValue(20);
        }
        xDropoffFGASpinBox->setValue(100);
        xDropoffGASpinBox->setEnabled(true);
        xDropoffFGASpinBox->setEnabled(true);
    } else if (programName == "tblastx") {
        xDropoffGASpinBox->setValue(0);
        xDropoffGASpinBox->setEnabled(false);
        xDropoffUnGASpinBox->setValue(7);
        xDropoffFGASpinBox->setValue(0);
        xDropoffFGASpinBox->setEnabled(false);
    } else {
        xDropoffGASpinBox->setValue(15);
        xDropoffUnGASpinBox->setValue(7);
        xDropoffFGASpinBox->setValue(25);
        xDropoffGASpinBox->setEnabled(true);
        xDropoffFGASpinBox->setEnabled(true);
    }
}

void BlastRunCommonDialog::sl_onCompStatsChanged() {
    QString value = compStatsComboBox->currentText();
    settings.compStats = value.left(1);
}

void BlastRunCommonDialog::getSettings(BlastTaskSettings& settingsSnapshot) {
    settingsSnapshot.programName = programNameComboBox->currentText();
    settingsSnapshot.databaseNameAndPath = dbSelector->databasePathLineEdit->text() + "/" + dbSelector->baseNameLineEdit->text();
    settingsSnapshot.expectValue = evalueSpinBox->value();
    settingsSnapshot.wordSize = wordSizeSpinBox->value();
    settingsSnapshot.megablast = megablastCheckBox->isChecked();
    settingsSnapshot.numberOfHits = numberOfHitsSpinBox->value();
    settingsSnapshot.numberOfProcessors = numberOfCPUSpinBox->value();

    settingsSnapshot.directStrand = directStrandButton->isChecked() ? TriState_Yes : (complStrandButton->isChecked() ? TriState_No : TriState_Unknown);

    QString cost = costsComboBox->currentText();
    settingsSnapshot.gapOpenCost = cost.split(" ").at(0).toInt();
    settingsSnapshot.gapExtendCost = cost.split(" ").at(1).toInt();
    // setup filters
    if (lowComplexityFilterCheckBox->isChecked()) {
        settingsSnapshot.filter = "L";
    }
    if (repeatsCheckBox->isChecked()) {
        settingsSnapshot.filter = settingsSnapshot.filter.isEmpty() ? "R" : settingsSnapshot.filter + "; R";
    }
    //    if(lowerCaseCheckBox->isChecked()){
    //        settings.filter=settings.filter.isEmpty() ? "???" : settings.filter+"; ???";
    //    }
    if (lookupMaskCheckBox->isChecked()) {
        settingsSnapshot.filter = settingsSnapshot.filter.isEmpty() ? "m" : "m " + settingsSnapshot.filter;
    }

    if (settingsSnapshot.isNucleotideSeq) {
        QString score = scoresComboBox->currentText();
        settingsSnapshot.isDefaultCosts = (((score == "1 -4") || (score == "1 -3")) && cost == "2 2") ||  //-G 2 -E 2
                                          ((score == "1 -2") && cost == "2 2") ||  //-G 2 -E 2
                                          ((score == "1 -1") && cost == "4 2") ||  //-G 4 -E 2
                                          (((score == "2 -7") || (score == "2 -5")) && cost == "4 4") ||  //-G 4 -E 4
                                          ((score == "2 -3") && cost == "6 4") ||  //-G 6 -E 4
                                          (((score == "4 -5") || (score == "5 -4")) && cost == "12 8");
        settingsSnapshot.isDefaultScores = (score == "1 -3");
    } else {
        QString matrix = matrixComboBox->currentText();
        settingsSnapshot.isDefaultCosts = ((matrix == "PAM30") && cost == "9 1") ||  //-G 9 -E 1
                                          ((matrix == "PAM70") && cost == "10 1") ||  //-G 10 -E 1
                                          ((matrix == "BLOSUM45") && cost == "15 2") ||
                                          ((matrix == "BLOSUM62") && cost == "11 1") ||
                                          ((matrix == "BLOSUM80") && cost == "10 1");
        settingsSnapshot.isDefaultMatrix = matrix == "BLOSUM62";
    }
    settingsSnapshot.isGappedAlignment = gappedAlignmentCheckBox->isChecked();
    settingsSnapshot.windowSize = windowSizeSpinBox->value();
    settingsSnapshot.threshold = thresholdSpinBox->value();
    settingsSnapshot.xDropoffGA = xDropoffGASpinBox->value();
    settingsSnapshot.xDropoffUnGA = xDropoffUnGASpinBox->value();
    settingsSnapshot.xDropoffFGA = xDropoffFGASpinBox->value();
    if ((settingsSnapshot.programName == "blastn" && settingsSnapshot.threshold != 0) ||
        (settingsSnapshot.programName == "blastp" && settingsSnapshot.threshold != 11) ||
        (settingsSnapshot.programName == "blastx" && settingsSnapshot.threshold != 12) ||
        (settingsSnapshot.programName == "tblastn" && settingsSnapshot.threshold != 13) ||
        (settingsSnapshot.programName == "tblastx" && settingsSnapshot.threshold != 13)) {
        settingsSnapshot.isDefaultThreshold = false;
    }
    if (COMP_TOOLS.contains(settings.programName)) {
        settingsSnapshot.compStats = settings.compStats;
    }
}

void BlastRunCommonDialog::enableStrandBox(bool enable) {
    bothStrandsButton->setEnabled(enable);
    directStrandButton->setEnabled(enable);
    complStrandButton->setEnabled(enable);
}

bool BlastRunCommonDialog::checkSelectedToolPath() const {
    QString programName = programNameComboBox->currentText();
    QString toolId = BlastSupport::getToolIdByProgramName(programName);
    return BlastSupport::checkBlastTool(toolId);
}

void BlastRunCommonDialog::updateAvailableProgramsList(const DNAAlphabet* alphabet) {
    QStringList nucleicTools({"blastn", "blastx", "tblastx"});
    QStringList aminoTools({"blastp", "tblastn"});
    QStringList newToolList = alphabet == nullptr || alphabet->isRaw() ? nucleicTools + aminoTools
                              : alphabet->isNucleic()                  ? nucleicTools
                                                                       : aminoTools;
    newToolList.sort();
    CHECK(activeToolList != newToolList, );  // Ignore the alphabet change if nothing is changed.

    activeToolList = newToolList;
    {
        QSignalBlocker clearBlocker(programNameComboBox);
        programNameComboBox->clear();
    }
    programNameComboBox->addItems(newToolList);
}

}  // namespace U2
