/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 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.
 */

#include "U2Region.h"

#include <QDataStream>

#include <U2Core/FormatUtils.h>
#include <U2Core/U2SafePoints.h>

namespace U2 {

QString U2Region::toString(Format format) const {
    QString start = FormatUtils::splitThousands(startPos);
    QString end = FormatUtils::splitThousands(endPos());
    QString middle = FormatUtils::splitThousands(center());
    QString halfLength = FormatUtils::splitThousands(length / 2);

    switch (format) {
        case FormatDash:
            return QString("%1 - %2").arg(start, end);
        case FormatPlusMinus:
            return QString("%1 &plusmn; %2").arg(middle, halfLength);
        case FormatDots:
            return QString("%1..%2").arg(start, FormatUtils::splitThousands(endPos() - 1));
        case FormatBrackets:
        default:
            return QString("[%1, %2)").arg(start, end);
    }
}

QVector<U2Region> U2Region::circularContainingRegion(QVector<U2Region>& _regions, int seqLen) {
    CHECK(_regions.size() >= 2, _regions);

    QVector<U2Region> regions = join(_regions);
    CHECK(regions.size() >= 2, regions);
    U2Region maxInterval(regions[0].endPos(), regions[1].startPos - regions[0].endPos());
    for (int i = 1; i < regions.size() - 1; i++) {
        const U2Region& r0 = regions[i];
        const U2Region& r1 = regions[i + 1];
        if (maxInterval.length < r1.startPos - r0.endPos()) {
            maxInterval = U2Region(r0.endPos(), r1.startPos - r0.endPos());
        }
    }
    if (maxInterval.length > regions.first().startPos + seqLen - regions.last().endPos()) {
        return QVector<U2Region>() << U2Region(0, maxInterval.startPos)
                                   << U2Region(maxInterval.endPos(), seqLen - maxInterval.endPos());
    } else {
        return QVector<U2Region>() << U2Region(regions.first().startPos, regions.last().endPos() - regions.first().startPos);
    }
}

QVector<U2Region> U2Region::join(QVector<U2Region>& regions) {
    QVector<U2Region> result = regions;
    std::stable_sort(result.begin(), result.end());  // sort by region start pos first
    for (int i = 0; i < result.size() - 1;) {
        const U2Region& ri0 = result[i];
        const U2Region& ri1 = result[i + 1];
        if (!ri0.intersects(ri1)) {
            i++;
            continue;
        }
        U2Region newRi = containingRegion(ri0, ri1);
        result[i] = newRi;
        result.remove(i + 1);
    }
    return result;
}

void U2Region::bound(qint64 minPos, qint64 maxPos, QVector<U2Region>& regions) {
    for (int i = 0, n = regions.size(); i < n; i++) {
        U2Region& r = regions[i];
        int start = qBound(minPos, r.startPos, maxPos);
        int end = qBound(minPos, r.endPos(), maxPos);
        r.startPos = start;
        r.length = end - start;
    }
}

void U2Region::mirror(qint64 mirrorPos, QVector<U2Region>& regions) {
    for (int i = 0, n = regions.size(); i < n; i++) {
        U2Region& r = regions[i];
        assert(r.endPos() <= mirrorPos);
        r.startPos = mirrorPos - r.endPos();
    }
}

void U2Region::divide(qint64 div, QVector<U2Region>& regions) {
    for (int i = 0, n = regions.size(); i < n; i++) {
        U2Region& r = regions[i];
        r.startPos = r.startPos / div;
    }
}

void U2Region::multiply(qint64 mult, QVector<U2Region>& regions) {
    for (int i = 0, n = regions.size(); i < n; i++) {
        U2Region& r = regions[i];
        r.startPos = r.startPos * mult;
    }
}

void U2Region::reverse(QVector<U2Region>& regions) {
    QVector<U2Region> old = regions;
    regions.clear();
    foreach (const U2Region& r, old) {
        regions.prepend(r);
    }
}

void U2Region::shift(qint64 offset, QVector<U2Region>& regions) {
    QVector<U2Region> res;
    for (int i = 0, n = regions.size(); i < n; i++) {
        U2Region& r = regions[i];
        r.startPos += offset;
    }
}

QList<U2Region> U2Region::split(const U2Region& region, qint64 blockSize) {
    if (region.length <= blockSize) {
        return QList<U2Region>() << region;
    }
    QList<U2Region> result;
    for (qint64 pos = region.startPos; pos < region.endPos(); pos += blockSize) {
        qint64 size = qMin(region.endPos() - pos, blockSize);
        result << U2Region(pos, size);
    }
    return result;
}

qint64 U2Region::sumLength(const QVector<U2Region>& regions) {
    qint64 size = 0;
    foreach (const U2Region& region, regions) {
        size += region.length;
    }
    return size;
}

int U2Region::findIntersectedRegion(const QVector<U2Region>& rs) const {
    for (int i = 0, n = rs.size(); i < n; i++) {
        const U2Region& r = rs[i];
        if (intersects(r)) {
            return i;
        }
    }
    return -1;
}

int U2Region::findOverlappingRegion(const QVector<U2Region>& rs) const {
    for (int i = 0, n = rs.size(); i < n; i++) {
        const U2Region& r = rs[i];
        if (r.contains(*this)) {
            return i;
        }
    }
    return -1;
}

U2Region U2Region::fromXRange(const QRect& rect) {
    return U2Region(rect.x(), rect.width());
}

U2Region U2Region::fromYRange(const QRect& rect) {
    return U2Region(rect.y(), rect.height());
}

U2Region U2Region::fromStartAndEnd(qint64 startPos, qint64 endPos) {
    return U2Region(startPos, endPos - startPos);
}

static bool _registerMeta() {
    qRegisterMetaType<U2Region>("U2Region");
    qRegisterMetaTypeStreamOperators<U2Region>("U2::U2Region");

    qRegisterMetaType<QVector<U2Region>>("QVector<U2::U2Region>");
    qRegisterMetaTypeStreamOperators<QVector<U2Region>>("QVector<U2::U2Region>");
    return true;
}

bool U2Region::registerMeta = _registerMeta();

QDataStream& operator<<(QDataStream& out, const U2Region& myObj) {
    qint64 startPos = myObj.startPos;
    qint64 length = myObj.length;
    out << startPos << length;
    return out;
}

QDataStream& operator>>(QDataStream& in, U2Region& myObj) {
    in >> myObj.startPos;
    in >> myObj.length;
    return in;
}

QVector<U2Region> U2Region::headOf(const QVector<U2Region>& regions, qint64 headLength) {
    QVector<U2Region> result;
    qint64 currentLength = 0;
    for (const U2Region& region : qAsConst(regions)) {
        if (currentLength + region.length >= headLength) {
            qint64 trimmedRegionLength = headLength - currentLength;
            result << U2Region(region.startPos, trimmedRegionLength);
            break;
        }
        result << region;
        currentLength += region.length;
    }
    return result;
}

QVector<U2Region> U2Region::tailOf(const QVector<U2Region>& regions, qint64 tailLength) {
    QVector<U2Region> result;
    qint64 currentLength = 0;
    for (int i = regions.length(); --i >= 0;) {
        const U2Region& region = regions[i];
        if (currentLength + region.length >= tailLength) {
            qint64 trimmedRegionLength = tailLength - currentLength;
            result << U2Region(region.endPos() - trimmedRegionLength, trimmedRegionLength);
            break;
        }
        result << region;
        currentLength += region.length;
    }
    std::reverse(result.begin(), result.end());
    return result;
}

}  // namespace U2
