/**
 * 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 <U2Core/Task.h>

#include "Header.h"
#include "Index.h"

namespace U2 {
namespace BAM {

class BAMInfo {
public:
    BAMInfo()
        : _hasIndex(false), unmappedSelected(false) {
    }
    BAMInfo(const BAMInfo& src) = default;

    inline QList<bool>& getSelected() {
        return selected;
    }
    inline bool hasNotEmptyIndex() const {
        return _hasIndex && !index.isEmpty();
    }
    inline bool isReferenceSelected(int id) {
        if (id == -1)
            return unmappedSelected;
        else
            return selected.at(id);
    }
    inline Index& getIndex() {
        return index;
    }
    inline const Header& getHeader() {
        return header;
    }
    inline bool isUnmappedSelected() const {
        return unmappedSelected;
    }
    void setIndex(Index& index) {
        this->index = index;
        _hasIndex = true;
    }
    void setHeader(const Header& header) {
        this->header = header;
        selected.clear();
        for (int i = 0; i < header.getReferences().count(); i++) {
            selected.append(true);
        }
    }
    void setUnmappedSelected(bool unmappedSelected) {
        this->unmappedSelected = unmappedSelected;
    }

private:
    Header header;
    QList<bool> selected;
    Index index;
    bool _hasIndex;
    bool unmappedSelected;
};

class LoadInfoTask : public Task {
    Q_OBJECT
public:
    LoadInfoTask(const GUrl& sourceUrl, bool sam);
    void run();
    inline BAMInfo& getInfo() {
        return bamInfo;
    }
    const GUrl& getSourceUrl() const;
    bool isSam() const {
        return sam;
    }

private:
    const GUrl sourceUrl;
    BAMInfo bamInfo;
    bool sam;
};

}  // namespace BAM
}  // namespace U2
