/**
 * 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/GUrl.h>

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

namespace U2 {
namespace LocalWorkflow {

class SortBamPrompter;
typedef PrompterBase<SortBamPrompter> SortBamBase;

class SortBamPrompter : public SortBamBase {
    Q_OBJECT
public:
    SortBamPrompter(Actor* p = 0)
        : SortBamBase(p) {
    }

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

class SortBamWorker : public BaseWorker {
    Q_OBJECT
public:
    SortBamWorker(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();
    QString getTargetName(const QString& fileUrl, const QString& outDir);
    void sendResult(const QString& url);
};  // SortBamWorker

class SortBamWorkerFactory : public DomainFactory {
    static const QString ACTOR_ID;

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

class BamSortSetting {
public:
    BamSortSetting()
        : outDir(""), outName(""), inputUrl(""), index(true) {
    }

    QString outDir;
    QString outName;
    QString inputUrl;
    bool index;
};

class SamtoolsSortTask : public Task {
    Q_OBJECT
public:
    SamtoolsSortTask(const BamSortSetting& settings);

    void prepare();
    void run();

    QString getResult() {
        return resultUrl;
    }

private:
    BamSortSetting settings;
    QString resultUrl;
};

}  // namespace LocalWorkflow
}  // namespace U2
