/**
* UGENE - Integrated Bioinformatics Tools.
* Copyright (C) 2008-2021 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.
*/

#ifndef _U2_BAM_LOAD_BAM_INFO_TASK_H_
#define _U2_BAM_LOAD_BAM_INFO_TASK_H_

#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)
        : header(src.header), selected(src.selected), index(src.index), _hasIndex(src._hasIndex), unmappedSelected(src.unmappedSelected) {
    }

    inline QList<bool> &getSelected() {
        return selected;
    }
    inline bool hasIndex() const {
        return _hasIndex;
    }
    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() {
        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

#endif    // _U2_BAM_LOAD_BAM_INFO_TASK_H_
