/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 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.
 */

#pragma once

#include <U2Core/ExternalToolRunTask.h>
#include <U2Core/GUrl.h>

#include <U2Lang/LocalDomain.h>
#include <U2Lang/WorkflowUtils.h>

namespace U2 {
namespace LocalWorkflow {

class FilterBamPrompter;
typedef PrompterBase<FilterBamPrompter> FilterBamBase;

class FilterBamPrompter : public FilterBamBase {
    Q_OBJECT
public:
    FilterBamPrompter(Actor* p = 0)
        : FilterBamBase(p) {
    }

protected:
    QString composeRichDoc();
};  // FilterBamPrompter

class FilterBamWorker : public BaseWorker {
    Q_OBJECT
public:
    FilterBamWorker(Actor* a);
    void init();
    Task* tick();
    void cleanup();

private:
    IntegralBus* inputUrlPort;
    IntegralBus* outputUrlPort;
    QStringList outUrls;
public slots:
    void sl_taskFinished(Task* task);

private:
    QString takeUrl();
    void sendResult(const QString& url);
    QString getTargetName(const QString& fileUrl, const QString& outDir);

};  // FilterBamWorker

class FilterBamWorkerFactory : public DomainFactory {
    static const QString ACTOR_ID;

public:
    static void init();
    FilterBamWorkerFactory()
        : DomainFactory(ACTOR_ID) {
    }
    Worker* createWorker(Actor* a) {
        return new FilterBamWorker(a);
    }
};  // FilterBamWorkerFactory

class BamFilterSetting {
public:
    BamFilterSetting()
        : outDir(""), outName(""), inputUrl(""), inputFormat(""), outputFormat(""), mapq(0), acceptFilter(""), skipFilter(""), regionFilter("") {
    }

    QString outDir;
    QString outName;
    QString inputUrl;
    QString inputFormat;
    QString outputFormat;
    int mapq;
    QString acceptFilter;
    QString skipFilter;
    QString regionFilter;

    QStringList getSamtoolsArguments() const;
};

class SamtoolsViewFilterTask : public ExternalToolSupportTask {
    Q_OBJECT
public:
    SamtoolsViewFilterTask(const BamFilterSetting& settings);

    void prepare();
    void run();

    QString getResult() {
        return resultUrl;
    }

private:
    void start(const ProcessRun& pRun, const QString& toolName);
    void checkExitCode(QProcess* process, const QString& toolName);

private:
    BamFilterSetting settings;
    QString resultUrl;

    static const QString SAMTOOLS_ID;
};

}  // namespace LocalWorkflow
}  // namespace U2
