/**
 * 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 <QFile>

#include <U2Core/global.h>

typedef quint64 BMType;
typedef quint32 SAType;
#define MAX_BIT_MASK_LENGTH 31

namespace U2 {
class GenomeAlignerIndexTask;

class IndexPart {
    friend class GenomeAlignerIndexTask;
    friend class GenomeAlignerIndex;

public:
    IndexPart();
    ~IndexPart();
    SAType* sArray;
    BMType* bitMask;
    char* seq;

    SAType getLoadedPartSize() const;
    SAType getMaxLength();
    SAType getLoadedSeqStart();
    int getCurrentPart() {
        return currentPart;
    }
    bool load(int part);
    void writePart(int part, quint32 arrLen);

private:
    int partCount;
    int currentPart;
    SAType* seqStarts;
    SAType* seqLengths;
    SAType* saLengths;

    QFile* refFile;
    QFile** partFiles;

    BMType getBitValue(uchar* seq, SAType idx);
};

bool isLittleEndian();

}  // namespace U2
